Wellcome Trust Sanger Institute

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This DAC controls 713 datasets

Dataset ID	Description	Technology	Samples
EGAD00000000001	WTCCC1 project samples from 1958 British Birth Cohort	Affymetrix 500K	1504
EGAD00000000002	WTCCC1 project samples from UK National Blood Service	Affymetrix 500K	1500
EGAD00000000003	WTCCC1 project Bipolar Disorder (BD) samples		1
EGAD00000000004	WTCCC1 project Coronary Artery Disease (CAD) samples		1
EGAD00000000005	WTCCC1 project Inflammatory Bowel Disease (IBD) samples		1
EGAD00000000006	WTCCC1 project Hypertension (HT) samples		1
EGAD00000000007	WTCCC1 project Rheumatooid arthritis (RA) samples		1
EGAD00000000008	WTCCC1 project Type 1 Diabetes (T1D) samples		1
EGAD00000000009	WTCCC1 project Type 2 Diabetes (T2D) samples		1
EGAD00000000010	WTCCC1 project Ankylosing Spondylitis (AS) samples	Illumina 15K	957
EGAD00000000011	WTCCC1 project Autoimmune Thyroid Disease (ATD) samples	Illumina 15K	900
EGAD00000000012	WTCCC1 project Multiple Sclerosis (MS) samples		975
EGAD00000000013	WTCCC1 project Breast cancer (BC) samples	Illumina 15K	1004
EGAD00000000014	WTCCC1 project samples from 1958 British Birth Cohort		1504
EGAD00000000015	WTCCC project African control samples	Affymetrix 500K	1496
EGAD00000000016	WTCCC project Tuberculosis (TB) samples	Affymetrix 500K	1498
EGAD00000000021	WTCCC2 project samples from 1958 British Birth Cohort		3000
EGAD00000000022	WTCCC2 project samples from 1958 British Birth Cohort		3000
EGAD00000000023	WTCCC2 project samples from National Blood Donors (NBS) Cohort		1
EGAD00000000024	WTCCC2 project samples from National Blood Donors (NBS) Cohort		1
EGAD00000000025	WTCCC2 project Ulcerative Colitis (UC) samples	Affymetrix 6.0	2869
EGAD00000000030	T1DGC project 1958 British Birth Cohort samples		2604
EGAD00000000031	HLA genotyping of 1958 British Birth Cohort samples		1
EGAD00000000056	WTCCC project samples from the primary biliary cirrhosis cohort	Illumina 610K Quad	1705
EGAD00000000057	WTCCC project samples from the Parkinson's disase cohort	Illumina 610K Quad	1705
EGAD00000000120	WTCCC2 project Multiple Sclerosis (MS) samples	Human670-QuadCustom v1	11375
EGAD00001000016	Familial Melanoma Sequencing	Illumina Genome Analyzer II Illumina HiSeq 2000	89
EGAD00001000019	Lethal malformation syndrome	Illumina Genome Analyzer II	6
EGAD00001000021	Paroxysmal neurological disorders	Illumina Genome Analyzer II Illumina HiSeq 2000	97
EGAD00001000024	Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.	Illumina Genome Analyzer II	4
EGAD00001000031	Human Colorectal Cancer Exome Sequencing	Illumina Genome Analyzer II	16
EGAD00001000052	UK10K_NEURO_MUIR REL-2011-01-28	Illumina Genome Analyzer II	104
EGAD00001000053	Exome sequencing in patients with Calcific Aortic Valve Stenosis	Illumina HiSeq 2000	20
EGAD00001000054	Mutational Screening of Human Acute Myleloid Leukaemia Samples	Illumina HiSeq 2000	10
EGAD00001000105	MuTHER adipose tissue small RNA expression	Illumina Genome Analyzer II	130
EGAD00001000108	Paroxysmal neurological disorders	Illumina Genome Analyzer II Illumina HiSeq 2000	327
EGAD00001000151	UK10K OBESITY REL-2011-07-14	Illumina HiSeq 2000	88
EGAD00001000152	UK10K_RARE_THYROID REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	27
EGAD00001000153	UK10K_RARE_SIR REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	38
EGAD00001000167	UK10K_RARE_HYPERCHOL REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	48
EGAD00001000168	UK10K_RARE_CILIOPATHIES REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	50
EGAD00001000170	UK10K_NEURO_MUIR REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	167
EGAD00001000171	UK10K_RARE_FIND REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	44
EGAD00001000173	UK10K_NEURO_ASD_FI REL-2012-01-13	Illumina HiSeq 2000	85
EGAD00001000178	UK10K_RARE_CHD REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	46
EGAD00001000179	UK10K_RARE_COLOBOMA REL-2012-01-13	Illumina Genome Analyzer II Illumina HiSeq 2000	75
EGAD00001000180	UK10K_RARE_NEUROMUSCULAR REL-2012-01-13	Illumina HiSeq 2000	47
EGAD00001000182	UK10K_NEURO_UKSCZ REL-2012-01-13	Illumina HiSeq 2000	95
EGAD00001000183	UK10K_NEURO_FSZNK REL-2012-01-13	Illumina HiSeq 2000	273
EGAD00001000184	UK10K_NEURO_FSZ_REL_2012_01_13	Illumina HiSeq 2000	120
EGAD00001000185	UK10K_RARE_COLOBOMA REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	98
EGAD00001000186	UK10K_RARE_HYPERCHOL REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	71
EGAD00001000187	UK10K_RARE_THYROID REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	65
EGAD00001000188	UK10K_RARE_SIR REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	63
EGAD00001000189	UK10K_RARE_NEUROMUSCULAR REL-2012-02-22	Illumina HiSeq 2000	86
EGAD00001000190	UK10K_RARE_FIND REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	90
EGAD00001000191	UK10K_RARE_CILIOPATHIES REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	128
EGAD00001000192	UK10K_RARE_CHD REL-2012-02-22	Illumina Genome Analyzer II Illumina HiSeq 2000	46
EGAD00001000193	UK10K_OBESITY_SCOOP REL-2012-02-22	Illumina HiSeq 2000	573
EGAD00001000194	UK10K_COHORT_TWINS REL-2011-12-01	Illumina Genome Analyzer II Illumina HiSeq 2000	1713
EGAD00001000195	For information about this sample set, please contact the sample custodian Nic Timpson: N.J.Timpson@bristol.ac.uk	Illumina HiSeq 2000	740
EGAD00001000206	UK10K_RARE_COLOBOMA REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	123
EGAD00001000207	UK10K_RARE_HYPERCHOL REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	88
EGAD00001000208	UK10K_RARE_THYROID REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	65
EGAD00001000209	UK10K_RARE_FIND REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	121
EGAD00001000210	UK10K_RARE_CHD REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	124
EGAD00001000217	UK10K_RARE_CILIOPATHIES REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	150
EGAD00001000218	UK10K_RARE_SIR REL-2012-07-05	Illumina Genome Analyzer II Illumina HiSeq 2000	81
EGAD00001000219	UK10K_RARE_NEUROMUSCULAR REL-2012-07-05	Illumina HiSeq 2000	117
EGAD00001000227	EGAD00001000227_UK10K_NEURO_ABERDEEN_REL_2012_07_05	Illumina HiSeq 2000	347
EGAD00001000228	EGAD00001000228_UK10K_NEURO_ASD_BIONED_REL_2012_07_05	Illumina HiSeq 2000	59
EGAD00001000229	EGAD00001000229_UK10K_NEURO_ASD_FI_REL_2012_07_05	Illumina HiSeq 2000	85
EGAD00001000230	EGAD00001000230_UK10K_NEURO_ASD_GALLAGHER_REL_2012_07_05	Illumina HiSeq 2000	72
EGAD00001000231	EGAD00001000231_UK10K_NEURO_ASD_SKUSE_REL_2012_07_05	Illumina HiSeq 2000	320
EGAD00001000232	EGAD00001000232_UK10K_NEURO_ASD_TAMPERE_REL_2012_07_05	Illumina HiSeq 2000	54
EGAD00001000233	EGAD00001000233_UK10K_NEURO_EDINBURGH_REL_2012_07_05	Illumina HiSeq 2000	219
EGAD00001000234	EGAD00001000234_UK10K_NEURO_FSZNK_REL_2012_07_05	Illumina HiSeq 2000	281
EGAD00001000235	EGAD00001000235_UK10K_NEURO_IOP_COLLIER_REL_2012_07_05	Illumina HiSeq 2000	170
EGAD00001000236	EGAD00001000236_UK10K_NEURO_MUIR_REL_2012_07_05	Illumina Genome Analyzer II Illumina HiSeq 2000	167
EGAD00001000237	EGAD00001000237_UK10K_NEURO_GURLING_REL_2012_07_05	Illumina HiSeq 2000	43
EGAD00001000239	EGAD00001000239_UK10K_NEURO_IMGSAC_REL_2012_07_05	Illumina HiSeq 2000	114
EGAD00001000240	UK10K_NEURO_FSZ_REL_2012_07_05	Illumina HiSeq 2000	120
EGAD00001000241	EGAD00001000241_UK10K_OBESITY_SCOOP_REL_2012_07_05	Illumina HiSeq 2000	674
EGAD00001000242	EGAD00001000242_UK10K_NEURO_ASD_MGAS_REL_2012_07_05	Illumina HiSeq 2000	60
EGAD00001000251	De novo mutations in schizophrenia	Illumina HiSeq 2000	611
EGAD00001000256	UK10K_NEURO_UKSCZ REL-2012-07-05	Illumina HiSeq 2000	595
EGAD00001000294	UK10K_RARE_CHD REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	124
EGAD00001000295	UK10K_RARE_HYPERCHOL REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	120
EGAD00001000296	UK10K_RARE_CILIOPATHIES REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	108
EGAD00001000297	UK10K_RARE_FIND REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	124
EGAD00001000298	UK10K_RARE_NEUROMUSCULAR REL-2012-11-27	Illumina HiSeq 2000	130
EGAD00001000300	UK10K_OBESITY_GS_REL_2012_07_05	Illumina HiSeq 2000	430
EGAD00001000307	UK10K_RARE_COLOBOMA REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	117
EGAD00001000309	UK10K_OBESITY_GS REL-2012-11-27	Illumina HiSeq 2000	424
EGAD00001000310	UK10K_NEURO_ASD_BIONED REL-2012-11-27	Illumina HiSeq 2000	76
EGAD00001000311	UK10K_NEURO_ASD_FI REL-2012-11-27	Illumina HiSeq 2000	84
EGAD00001000312	UK10K_NEURO_ASD_MGAS REL-2012-11-27	Illumina HiSeq 2000	96
EGAD00001000313	UK10K_NEURO_ASD_SKUSE REL-2012-11-27	Illumina HiSeq 2000	305
EGAD00001000314	UK10K_NEURO_ASD_TAMPERE REL-2012-11-27	Illumina HiSeq 2000	48
EGAD00001000315	UK10K_NEURO_ABERDEEN REL-2012-11-27	Illumina HiSeq 2000	313
EGAD00001000316	UK10K_NEURO_ASD_GALLAGHER REL-2012-11-27	Illumina HiSeq 2000	75
EGAD00001000317	UK10K_NEURO_EDINBURGH REL-2012-11-27	Illumina HiSeq 2000	214
EGAD00001000319	UK10K_NEURO_GURLING REL-2012-11-27	Illumina HiSeq 2000	48
EGAD00001000320	UK10K_NEURO_IMGSAC REL-2012-11-27	Illumina HiSeq 2000	111
EGAD00001000321	UK10K_NEURO_IOP_COLLIER REL-2012-11-27	Illumina HiSeq 2000	158
EGAD00001000322	UK10K_NEURO_MUIR REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	166
EGAD00001000329	UK10K_RARE_THYROID REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	113
EGAD00001000332	UK10K_NEURO_FSZNK REL-2012-11-27	Illumina HiSeq 2000	258
EGAD00001000334	UK10K_RARE_SIR REL-2012-11-27	Illumina Genome Analyzer II Illumina HiSeq 2000	111
EGAD00001000335	UK10K_NEURO_UKSCZ REL-2012-11-27	Illumina HiSeq 2000	527
EGAD00001000336	UK10K_OBESITY_SCOOP REL-2012-11-27	Illumina HiSeq 2000	784
EGAD00001000340	The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations	Illumina Genome Analyzer II	3
EGAD00001000341	This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified.	Illumina HiSeq 2000	6
EGAD00001000342	This project aims to find causal variants in 50 patients diagnosed with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD), of presumed recessive inheritance performing whole exome sequencing to ~50x mean depth.This is a collaboration with Prof A. Jackson, MRC Human Genetics Unit, Edinburgh	Illumina Genome Analyzer II Illumina HiSeq 2000	66
EGAD00001000343	This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina)	Illumina HiSeq 2000	24
EGAD00001000344	Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.	Illumina HiSeq 2000	90
EGAD00001000345	Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations.	Illumina HiSeq 2000	9
EGAD00001000346	Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies.	Illumina HiSeq 2000	30
EGAD00001000347	These samples include exome sequences of family members with dyslipidemias from Finnish origin.	Illumina HiSeq 2000	95
EGAD00001000348	This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Bilateral Anophthalmia.	Illumina Genome Analyzer II	16
EGAD00001000351	This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Congenital Heart Disease (CHD).	Illumina Genome Analyzer II	16
EGAD00001000362	Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine.	Illumina HiSeq 2000	7
EGAD00001000363	Common variable immunodeficiency (CVID) is the most common form of primary immunodeficiency with an estimated incidence of 1:10,000. It has been apparent for many years that CVID has a genetic component, occurs frequently in families and can have both a recessive or dominant mode of inheritance. In recent years, 4 genes underlying CVID have been identified; however, mutations within in them are estimated to account for no more than 10% of all cases of CVID. We have identified a multi-generational family with autosomal dominant CVID. Genome-wide linkage analysis has mapped the locus underlying CVID in this family to an approximately 9.2 Mb interval on chromosome 3q27.3-q29, between the markers D3S3570 and D3S1265. This locus is distinct from any of the previously mapped susceptibility loci suggesting a novel genetic variant is responsible for disease in this family. The aim of this study is to use exome sequencing of affected (n = 4) and unaffected (n = 4) individuals, in tandem with the available genetic mapping data, to identify the causal variant underlying CVID in this family.	Illumina HiSeq 2000	8
EGAD00001000380	Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.	Illumina Genome Analyzer II Illumina HiSeq 2000	64
EGAD00001000381	Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.	Illumina HiSeq 2000	3
EGAD00001000382	Whole Exome Sequencing of Permanent Neonatal Diabetes Patients	Illumina HiSeq 2000	25
EGAD00001000383	In collaboration with Dr Robert Semple we have identified a family harbouring an autosomal dominant variant, which leads to severe insulin resistance (SIR), short stature and facial dysmorphism. This family is unique within the SIR cohort in having normal lipid profiles, preserved adiponectin and normal INSR expression and phosphorylation. DNA is available for 7 affected and 7 unaffected family members across 3 generations. All 14 samples have been genotyped using microsatellites and the Affymetrix 6.0 SNP chip. Linkage analysis identified an 18.8Mb haplotype on chromosome 19 as a possible location of the causative variant. However, Exome sequencing of 3 affected and 1 unaffected family members has not identified the causative variant suggesting the possibility of an intronic or intergenic variant in this region or elsewhere in the genome. We propose to conduct whole genome sequencing of 5 members of the pedigree at a depth of 20X. The chosen samples are two sets of parents plus one member of an unaffected branch of the pedigree who shares the risk haplotype on chromosome 19. Sequencing of the two sets of parents will be used along with the genome-wide SNP data to impute 4 affected children giving an effect sample size of 6 affected individuals.	Illumina HiSeq 2000	7
EGAD00001000384	In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.	Illumina HiSeq 2000	35
EGAD00001000399	In 2009 we identified a four-generation family with over 700 members and 41 affected with Crohn's disease (CD). At the time we sequenced the exome of 6 affected individuals but did not identify any coding variants which appear to explain the high prevalence of disease. Since then we have collected DNA from a large number of additional family members, genotyped linkage arrays on the entire family to refine genomic regions shared by identity by descent and genotyped affected and unaffected members at known CD risk loci identified by Genome Wide Association Studies (GWAS). These analyses have confirmed that a significant unexplained excess of disease remains after accounting for all known genetic factors, and that several regions of the genome are shared by a large fraction of affected individuals. We therefore perform whole genomes sequencing from 8 individuals which will allow us to impute the complete sequence of nearly all the members of the two largest and most severely affected branches of the family.	Illumina HiSeq 2000	8
EGAD00001000401	Population based sequencing of whole genomes of Crohn's disease patients.	Illumina HiSeq 2000	2926
EGAD00001000404	Acute myeloid leukaemia (AML) is an aggressive and molecularly diverse disease with a poor overall survival of 20-25%. With an annual incidence of 2.9 per 100,000, AML is currently the commonest myeloid malignancy in Europe, yet the two main therapeutic options for this disease, anthracyclines and purine analogues, have remained unchanged for over 20 years. Currently patients are stratified at diagnosis according to a series of clinicopathological parameters (e.g. age, white cell count and presence/absence of previous clonal haematological disease) and molecular markers (e.g. chromosomal translocations/deletions, aneuploidy and mutations in genes such as FLT3 and NPM1). Patients with adverse prognostic features, whose prognosis is particularly poor (e.g. <15% long-term survival) are offered treatment with allogeneic bone marrow transplantation (allo-BMT) if a sibling or unrelated donor is available. This can significantly improve survival (e.g. up to 40% long-term survival in some contexts), albeit at the expense of significant toxicity and transplant-related mortality (TRM). Allo-BMT is thought to work in part by allowing the delivery of large doses of chemotherapy followed by haemopoietic "rescue" with donor haemopoietic stem cells (haemopoietic failure would otherwise ensue). However, potentially the most potent effect of allo-BMT is the cytotoxic effect of donor lymphocytes against AML blasts, a phenomenon known as graft-vs-leukaemia (GVL) effect. Increasingly, transplants using reduced chemotherapy intensity (mini-allografts) are being used that partially circumvent the toxicity from chemotherapy and rely on GVL to effect cure. Nevertheless, AML relapse after allo-BMT still occurs at a significant rate of up to 80% depending on the type of transplant. There is accumulating evidence that genetic events in residual leukaemic cells enable them to evade immunodetection and therefore survive the GVL effect and expand to cause relapse. The most striking example of this is the loss of HLA antigens after transplants in which donor and recipient are not fully HLA-matched. In these cases, the leukaemia "deletes" the genomic region containing the disparate HLA antigen which was preferentially targeted as "foreign" by the GVL effect. However, the genetic basis of immune evasion in the majority of transplants, which are fully HLA matched, is not known. One possibility is that loss of genes coding for antigens outside the HLA locus but which are also targets of GVL may operate, alternatively genetic events that affect processes downstream of immunological cytotoxicity may be responsible. The identification of genetic events that mediate immune evasion would not only facilitate the understanding of this process but can help plan therapeutic interventions that improve the outcomes of allogeneic transplantation for AML and other disorders. We intend to study this by conducting exome sequencing on 6 cases of AMLs from patients that attend my clinic at Addenbrooke's hospital and have relapsed after allogeneic transplantation. Samples from AML diagnosis, remission/normal and AML relapse (total n=18) will be studied to identify somatic mutations in the primary AML and those acquired by the relapsed clone. The 18 samples will also be studied by array CGH to detect regions of genomic amplification or deletion.	Illumina HiSeq 2000	25
EGAD00001000405	In this project we will sequence the exomes of 250 patients with Parkinson's disease	Illumina HiSeq 2000	247
EGAD00001000406	Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive haematological malignancy derived from precursors of plasmacytoid dendritic cells. Due to the rarity of BPDCNs our knowledge of their molecular pathogenesis was until recently confined to observations describing reccurent chromosomal deletions involving chromosomes 5q, 12p, 13q, 6q, 15q and 9. A recent publication went on to delineate the common deleted regions using aCGH and demonstrated that these centred around known tumour suppressor genes including CDKN2A/B (9p21.3), RB1 (12p13.2-14.3), CDKN1B (13q11-q12) and IKZF1 (7p12.2). These mutations are found recurrently in several different cancers and in most cases are thought to be involved in tumour progression rather than initiation. However, the well-defined nature and cellular ontogeny of these neoplasms suggests strongly that they share one or a few characteristic mutations as has been demonstrated for other uncommon but well-defined neoplasms such as Hairy Cell Leukemia (BRAF) and ovarian Granulosa Cell tumours (FOXL2).	Illumina HiSeq 2000	14
EGAD00001000407	We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.	Illumina HiSeq 2000	327
EGAD00001000408	We aim to whole-exome sequence DNA samples from 75 individuals with severe forms of Inflammatory Bowel Disease and related autoimmune diseases to identify the rare, highly penetrant, variants that we believe underlie these phenotypes. Case samples will be obtained from both new and existing (UK IBD Genetics Consortium) collaborators to ensure only the most extreme cases are sequenced.	Illumina HiSeq 2000	4
EGAD00001000409	2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD.	Illumina HiSeq 2000	1992
EGAD00001000410	We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.	Illumina HiSeq 2000	78
EGAD00001000411	These samples include exome sequences of family members with dyslipidemias from northern Finnish origin.	Illumina HiSeq 2000	68
EGAD00001000412	We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.	Illumina HiSeq 2000	477
EGAD00001000413	UK10K_RARE_CHD REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	125
EGAD00001000414	UK10K_RARE_CILIOPATHIES REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	122
EGAD00001000415	UK10K_RARE_COLOBOMA REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	123
EGAD00001000416	UK10K_RARE_FIND REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	124
EGAD00001000417	UK10K_RARE_HYPERCHOL REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	125
EGAD00001000418	UK10K_RARE_NEUROMUSCULAR REL-2013-04-20	Illumina HiSeq 2000	140
EGAD00001000419	UK10K_RARE_SIR REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	121
EGAD00001000420	UK10K_RARE_THYROID REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	124
EGAD00001000422	We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.	Illumina HiSeq 2000	86
EGAD00001000423	The aim is to find rare variants of intermediate penetrance in those at risk of Crohn's disease	Illumina Genome Analyzer II	10
EGAD00001000429	UK10K_OBESITY_TWINSUK REL-2013-04-20	Illumina HiSeq 2000	68
EGAD00001000430	UK10K_NEURO_UKSCZ REL-2013-04-20	Illumina HiSeq 2000	554
EGAD00001000431	UK10K_OBESITY_GS REL-2013-04-20	Illumina HiSeq 2000	428
EGAD00001000432	UK10K_OBESITY_SCOOP REL-2013-04-20	Illumina HiSeq 2000	985
EGAD00001000433	UK10K_NEURO_ABERDEEN REL-2013-04-20	Illumina HiSeq 2000	392
EGAD00001000434	UK10K_NEURO_ASD_BIONED REL-2013-04-20	Illumina HiSeq 2000	77
EGAD00001000435	UK10K_NEURO_ASD_FI REL-2013-04-20	Illumina HiSeq 2000	84
EGAD00001000436	UK10K_NEURO_ASD_GALLAGHER REL-2013-04-20	Illumina HiSeq 2000	77
EGAD00001000437	UK10K_NEURO_ASD_TAMPERE REL-2013-04-20	Illumina HiSeq 2000	55
EGAD00001000438	UK10K_NEURO_EDINBURGH REL-2013-04-20	Illumina HiSeq 2000	234
EGAD00001000439	UK10K_NEURO_FSZNK REL-2013-04-20	Illumina HiSeq 2000	285
EGAD00001000440	UK10K_NEURO_GURLING REL-2013-04-20	Illumina HiSeq 2000	46
EGAD00001000441	UK10K_NEURO_IMGSAC REL-2013-04-20	Illumina HiSeq 2000	113
EGAD00001000442	UK10K_NEURO_IOP_COLLIER REL-2013-04-20	Illumina HiSeq 2000	172
EGAD00001000443	UK10K_NEURO_MUIR REL-2013-04-20	Illumina Genome Analyzer II Illumina HiSeq 2000	175
EGAD00001000445	We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.	Illumina MiSeq	9
EGAD00001000596	This project is to develop and validate a method to detect de novo mutations in a foetal genome through deep sequencing of cell-free DNA from the plasma of pregnant women. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	5
EGAD00001000598	The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.	Illumina HiSeq 2000	120
EGAD00001000599	We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.	Illumina HiSeq 2000	6
EGAD00001000603	We recently used the Agilent SureSelect platform to re-sequence a set of genes known to be mutated in human AML. The results from 10 AML DNA samples were very satisfactory, but the effort required was significant. Thus, we decided to re-sequence the same genes using the Haloplax system for target enrichment in 48 AML samples. We planned to do this using MiSeq and have data from a pilot of 3 samples. The data is promising but coverage appears pathcy so far. However, in order to get a better understanding of the data we will need deeper sequencing. We will need two lanes of HiSeq to get the same degree coverage as Sureselect. his data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000 Illumina MiSeq	54
EGAD00001000604	In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The transcriptomes of these iPS cells will be compared. Protocol: primary cultures of cells were reprogrammed to iPS cells. RNA was extracted using a standard column extraction kit.	Illumina HiSeq 2000	47
EGAD00001000605	CR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000 Illumina MiSeq	10
EGAD00001000607	PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	2
EGAD00001000608	PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	60
EGAD00001000613	UK10K_NEURO_ASD_MGAS REL-2013-04-20	Illumina HiSeq 2000	97
EGAD00001000614	UK10K_NEURO_ASD_SKUSE REL-2013-04-20	Illumina HiSeq 2000	341
EGAD00001000615	UK10K_NEURO_FSZ REL-2013-04-20	Illumina HiSeq 2000	128
EGAD00001000631	PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	4
EGAD00001000640	Transcriptome studies in patients with rare genetic diseases can potentially aid in the interpretation of likely causal genetic variation through identification of altered transcript abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating transcript structure and abundance The primary aim of this pilot project is to investigate to what degree integrating exome-Seq and RNA-Seq data on the same individual can accelerate the identification of causal alleles for rare genetic diseases. There are two main strands to this: (i) identifying which variants discovered in exome-seq appear to be having a functional impact on transcripts, and (ii) identifying transcript outliers, especially among known causal genes, that may not necessarily have a causal variant identified from exome sequencing. The latter may identify the presence of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites deep within introns, or loss of long range regulatory elements), which can be confirmed with further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g. nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs). This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with primordial dwarfism syndromes, for 10 of these samples we have previously generate exome data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining samples are positive controls where the causal mutation is known, and is known to affect transcript structure and/or abundance. Primordial dwarfism is a prime candidate for these RNA-seq studies because all known causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the products of the causal genes are typically ubiquitously expressed. Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads. Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	24
EGAD00001000647	We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.	Illumina HiSeq 2000	110
EGAD00001000694	This is an ongoing project and continuation to all the sequencing we have been doing over the last few years. We have some additional families and probands with syndromes of insulin resistance not previously sequenced within uk10k or other core funded projects. We would like to complete the sequencing in all of the good quality families and probands we have, this would require another ~50 samples to be WES sequenced. This cohort has already proven to be a rich source of interesting findings with papers in Science and Nature genetics.	Illumina HiSeq 2000	68
EGAD00001000696	The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity. This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum. The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.	Illumina HiSeq 2000	5
EGAD00001000728	Low coverage whole genome sequencing of samples from individuals from Friuli Venezia Giulia, an Italian genetic isolate population.	Illumina HiSeq 2000	199
EGAD00001000729	The Val Borbera is a region characterized by low iodine and high prevalence of thyroid disorders, the commonest endocrine disorders in the general population. About 30% of the participants of the Val Borbera Project were affected by such disorders and were characterized by several parameters, TSH level, anti TPO antibodies, echography, family origin. Individuals with extreme phenotypes were identified and could be clustered based on family origin and genotype. We propose to exome sequence 6 of them, affected with true goiter, at high dept (40-60x) to obtain information on exonic rare variants. Due to the family structure and to the availability of whole genome sequence information on 110 individuals from the isolated population we expect to be able to identify putative causative variants for thyroid disorders that may be studied in the remaining affected individuals.	Illumina HiSeq 2000	8
EGAD00001000730	The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.	Illumina HiSeq 2000	110
EGAD00001000731	This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.	Illumina HiSeq 2000	100
EGAD00001000740	UK10K_COHORT_ALSPAC REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing	Illumina HiSeq 2000	2307
EGAD00001000741	UK10K_COHORT_TWINSUK REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing	Illumina Genome Analyzer II Illumina HiSeq 2000	1854
EGAD00001000750	UK10K_RARE_FIND REL-2013-10-31 variant calling	Illumina HiSeq 2000	1151
EGAD00001000752	UK10K_RARE_CILWG REL-2013-09-09	Illumina HiSeq 2000	4
EGAD00001000753	UK10K_RARE_FINDWG REL-2013-09-09	Illumina HiSeq 2000	4
EGAD00001000754	UK10K_RARE_NMWG REL-2013-09-09	Illumina HiSeq 2000	5
EGAD00001000755	UK10K_OBESITY_GS UK10K_EXOME_EXTRAS	Illumina HiSeq 2000	5
EGAD00001000756	UK10K_OBESITY_SCOOP UK10K_EXOME_EXTRAS	Illumina HiSeq 2000	1
EGAD00001000757	UK10K_RARE_SIR UK10K_EXOME_EXTRAS	Illumina HiSeq 2000	2
EGAD00001000774	This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.	Illumina HiSeq 2000	106
EGAD00001000776	UK10K_COHORT_IMPUTATION REL-2012-06-02: imputation reference panel (20140306); Merged UK10K+1000Genomes Phase 3 imputation reference panel added (20160420)	Illumina Genome Analyzer II Illumina HiSeq 2000	3781
EGAD00001000789	UK10K_COHORT_ALSPAC REL-2012-06-02: Phenotype data		1927
EGAD00001000790	UK10K_COHORT_TWINSUK REL-2012-06-02: Phenotype data		1854
EGAD00001000796	This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).	Illumina HiSeq 2000	167
EGAD00001000797	This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected at the Royal, Brompton Hospital in collaboration with Stuart Cook and Piers Daubeney. Ethic approval has been sought for in the UK and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).	Illumina HiSeq 2000	48
EGAD00001000798	In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unclear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina MiSeq	28
EGAD00001000799	The exome sequencing is performed using Agilent SureSelect 50Mb exome v3 and Hiseq 75bp paired reads with an mean sequencing coverage target of 50X.	Illumina HiSeq 2000	95
EGAD00001000802	UK10K_RARE_CILWG REL-2013-03-06	Illumina HiSeq 2000	2
EGAD00001000803	UK10K_RARE_FINDWG REL-2013-03-06	Illumina HiSeq 2000	2
EGAD00001000804	UK10K_RARE_NMWG REL-2013-03-06	Illumina HiSeq 2000	1
EGAD00001000805	UK10K_RARE_THYWG REL-2013-03-06	Illumina HiSeq 2000	2
EGAD00001000827	n order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The methylation status of these iPS cells will be compared. Protocol: Primary cell cultures were generated and reprogrammed to iPS cells. DNA was extracted and immunoprecipitated using anti-methyl cytosine and anti-hydroxymethyl cytosine antibodies. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	4
EGAD00001000828	Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	6
EGAD00001000893	HipSci - Healthy Normals - Exome Sequencing - May 2014	Illumina HiSeq 2000	15
EGAD00001000897	HipSci - Healthy Normals - RNA Sequencing - May 2014	Illumina HiSeq 2000	22
EGAD00001000979	We are developing a protocol to differentiate mouse and human induced pluripotent stem (IPS) and embryonic stem (ES) cells towards the haematopoietic pathway to generate erythrocytes in vitro. This system has many applications such as the study of the role of specific genes and human polymorphisms in infectious diseases such as malaria, as well as haematological diseases such as myelodysplastic syndrome. The nature of the in vitro differentiation process means that a heterogeneous population of cells is generated. In order to understand the types of cells produced with our protocol, we have performed a single cell analysis, which has the power to reveal the different populations of cells and their characteristics. For this, a cDNA library has been made that needs to be sequenced to obtain the gene expression profiles of the different cells. With this information we will be able to assess the quality of the differentiation protocol and improve it in order to produce better cells for the downstream applications.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	192
EGAD00001001025	The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 50-80%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.	Illumina HiSeq 2000	1156
EGAD00001001026	The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.	Illumina HiSeq 2000	452
EGAD00001001027	The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.	Illumina HiSeq 2000	130
EGAD00001001079	The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group. This dataset contains all the data available for this study on 2014-11-20.	Illumina HiSeq 2000	2702
EGAD00001001092	Approximately 80% of clinically clearly diagnosed patients suffering from primary ciliary dyskinesia (PCD) cannot be assigned to a specific gene defect. Despite extensive research on PCD and despite the increasing number of PCD genes and knowledge about their sites of action as e.g structural component or cytoplasmic pre-assembly factor, the biology of motile cilia and the pathomechanism leading to PCD is largely unknown. The aim of this study is to identify novel PCD related genes and processes relevant for motile cilia function.We will perform exome sequencing, aiming on the analysis of family trios. In these families, the diagnosis of PCD is secured, but the underlying gene defects has so far not been identified.	Illumina HiSeq 2000	150
EGAD00001001106	In the first part of this project, we will differentiate IPS cells from 5 human donors into macrophages, and extract RNA from unstimulated and LPS stimulated macrophages to perform RNA sequencing. We will also extract RNA before and after stimulation in blood- derived macrophages from 5 additional, unrelated healthy samples. In the second part of the project, RNA-seq data will be analysed to compare LPS response of these two macrophage populations. In summary, we will perform 75bp PE RNA-seq on 20 samples (10 pre and post stimulus), on the HiSeq 2500 platform. Samples will be multiplexed at 5 samples / lane, so we will require 4 flow cells in total.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	18
EGAD00001001124	Our aim is to analyze the genome of human melanoma cell lines and short term culture from human melanoma samples in order to identify genes that confer drug resistance to clinically relevant targeted therapies. We will perform whole-exome sequencing, copy number variation analysis and methylome analysis in a collection of human melanoma cell lines and short term culture that will be then screened for drug sensitivity/resistance through a library of clinically relevant drugs and drug combinations. By the combined analysis of the genomic lesion and the drug sensitivity/resistance profile of different cell lines, we will look for genes whose mutation is associated to the sensitivity or resistance to a specific drug in different samples.	Illumina HiSeq 2000	14
EGAD00001001216	The aim of this project is to genotype and sequence single spermatozoa from two men, one in his twenties and the other in his seventies. The resulting data is used to quantify the mutations that have arisen in the gametes of both individuals in order to better understand the effect of aging on mutation rates and modes.Project Outline. In order to quantify mutations, semen from two individuals are sequenced. 48 single sperm cells are isolated from each individual, and their DNA is extracted. The resulting genomes are amplified using PicoPlex, GenomiPhi MDA, Repli-G MDA, and MALBAC. QC step is applied to check the quality of WGA DNA using standard Sequenom plex (26 SNPs). A subset of 32 amplification products which pass the intiall QC, are genotyped using Affymetrix SNP6 chips. 12 of the genotyped amplification products are also sequenced. In addition, one multi-cell sample per individual is sequenced as a reference and for validation purposes.Altogether, 12 single cell sperm genomes and two multi-cell genomes are sequenced, coming to a total of 14 genomes. Of the single cell sperm genomes, 2 are sequenced to 50x coverage, and the other 10 to 25x coverage. Both multi-cell genomes are sequenced to 25x coverage.	Illumina HiSeq 2000	12
EGAD00001001268	H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57-66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176-85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112).This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	4
EGAD00001001316	Exome sequence analysis of individuals with severe early onset inflammatory bowel disease, and their families. Individuals are ascertained through the COLORS in IBD study, which includes centres throughout UK and Europe.	Illumina HiSeq 2000 Illumina HiSeq 2500	149
EGAD00001001317	This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	12
EGAD00001001319	The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients	Illumina MiSeq	5817
EGAD00001001320	This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000 Illumina MiSeq	138
EGAD00001001331	The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.	Illumina HiSeq 2000	24
EGAD00001001332	Development of a method for separation and parallel sequencing of the genomes and transcriptomes of single cells.	HiSeq X Ten Illumina HiSeq 2500 Illumina MiSeq	700
EGAD00001001347	Exome sequencing of a case of lethal EBV-driven LPD	Illumina HiSeq 2000	3
EGAD00001001354	Whole exome sequencing of around 700 inflammatory bowel disease cases.This data can only be used for the identification of IBD/immune-mediated disease loci.	Illumina HiSeq 2000	702
EGAD00001001363	To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	12
EGAD00001001372	All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.	Illumina HiSeq 2000	100
EGAD00001001373	The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.	Illumina HiSeq 2000	7
EGAD00001001374	The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.	Illumina HiSeq 2500	6
EGAD00001001380	All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.	Illumina HiSeq 2000	3
EGAD00001001393	The aim of this study is to assess translational changes in macrophages over a time course of Salmonella infection.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	52
EGAD00001001422	HipSci - Bardet-Biedl Syndrome - Exome Sequencing - April 2015	Illumina HiSeq 2000	3
EGAD00001001425	The objectives of this project are the identification of markers related to cancer therapy resistance in the blood of breast cancer patients and to study the genetic changes in cancer cells during this development of resistance. Whole genome amplified DNA from Circulating Tumor Cells (CTCs), selected during the course of systemic treatment from blood of metastatic breast cancer patients, will be exome sequenced . The patients selected for this study did not respond to therapy.	Illumina HiSeq 2000	149
EGAD00001001437	HipSci - Healthy Normals - Exome Sequencing - April 2015	Illumina HiSeq 2000	122
EGAD00001001438	HipSci - Healthy Normals - RNA Sequencing - May 2015	Illumina HiSeq 2000	116
EGAD00001001440	This project entailed generation of high depth WGS (30x) of 100 individuals from the general Greek population.	HiSeq X Ten	100
EGAD00001001442	This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group	Illumina HiSeq 2000	86
EGAD00001001454	Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.These data can only be used for the investigation of the genetic causes of the reported clinical phenotypes in these patients	Illumina HiSeq 2000	1
EGAD00001001460	Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2015-08-05.	Illumina HiSeq 2000	62
EGAD00001001634	This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari.	HiSeq X Ten	25
EGAD00001001636	Whole-genome sequencing at 4x of 250 samples from the Greek isolatecollection HELIC	Illumina HiSeq 2000	250
EGAD00001001637	Whole-genome sequencing at 1x of samples from the Cretan Greek isolate collection HELIC-MANOLIS. Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on an isolated population from Crete, Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.	Illumina HiSeq 2000	1003
EGAD00001001638	The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.	Illumina HiSeq 2000	5
EGAD00001001686	In the autozygosity exome sequencing of Born-in-Bradford samples of Pakistani origin there is a mother who is homozygous for an apparent truncating stop codon in PRDM9, the gene responsible for localising recombination during meiosis. We plan to deep sequence mother and child with X10, and physically phase the mother with PacBio sequencing. We will use this data to identify recombination locations, and test whether these are consistent with the known fine scale recombination map. Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group.	HiSeq X Ten Illumina HiSeq 2500	2
EGAD00001001897	15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS	HiSeq X Ten	1482
EGAD00001001928	This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500 Illumina MiSeq	61
EGAD00001001930	Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit	Illumina MiSeq	6
EGAD00001001932	HipSci - Healthy Normals - Exome Sequencing - January 2016	Illumina HiSeq 2000	123
EGAD00001001933	HipSci - Healthy Normals - RNA Sequencing - January 2016	Illumina HiSeq 2000	118
EGAD00001001949	HipSci - Monogenic Diabetes - Exome Sequencing - April 2015	Illumina HiSeq 2000	1
EGAD00001001950	HipSci - Bardet-Biedl Syndrome - Exome Sequencing - January 2016	Illumina HiSeq 2000	3
EGAD00001001951	HipSci - Monogenic Diabetes - Exome Sequencing - January 2016	Illumina HiSeq 2000	1
EGAD00001001952	HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015	Illumina HiSeq 2000	2
EGAD00001001953	HipSci - Monogenic Diabetes - RNA Sequencing - April 2015	Illumina HiSeq 2000	1
EGAD00001001954	HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016	Illumina HiSeq 2000	3
EGAD00001001955	HipSci - Monogenic Diabetes - RNA Sequencing - January 2016	Illumina HiSeq 2000	1
EGAD00001001973	Exome sequencing of 184 samples from consanguineous families with different congenital heart defects collected at KAIMRC, Riyadh, Saudi Arabia.	Illumina HiSeq 2000 Illumina HiSeq 2500	179
EGAD00001001986	This study is meant to gain further knowledge in haematological cancers. Patients samples (mainly DNAs or PCR products) from haematolocical cancer patients will be sequenced, and the outputs will be correlated to their diagnosis and/or prognosis; the findings may also add more insight into the understanding of biology in this type of tumour. We will be sequencing Primary Testicular Lymphomas (PTL) to identify genetic drivers of this rare cancer	Illumina HiSeq 2500	7
EGAD00001001999	HipSci - Embryonic Stem Cells - Exome Sequencing - April 2016	Illumina HiSeq 2000	2
EGAD00001002000	HipSci - Embryonic Stem Cells - RNA Sequencing - April 2016	Illumina HiSeq 2000	2
EGAD00001002014	Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.		6840
EGAD00001002050	In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1). This dataset contains all the data available for this study on 2016-04-20.	Illumina HiSeq 2000 Illumina MiSeq	36
EGAD00001002144	The morphology of the first humans in the Americas (Paleoamericans) differs from that of Native Americans, and has raised the question of whether or not there are also differences in origin or genetics. A few populations who survived until relatively recently have been suggested to retain Paleoamerican morphology. One of these populations is from La Jolla. Here, we have generated genome sequence data from four La Jolla individuals in order to investigate these questions This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	4
EGAD00001002158	This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2016-06-02.	Illumina HiSeq 2000	6
EGAD00001002178	The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD	Illumina HiSeq 2000	8
EGAD00001002179	Background: A rare subgroup of HIV infected individuals naturally controls infection without treatment. These ?elite controllers? constitute an important model for the natural control of HIV infection. Indeed, the study of these individuals may provide insights into strategies for the development of HIV vaccines. Although several HLA and chemokine alleles are known to be over-represented in elite controllers, only a small portion of HIV phenotypic variation is explained by known genetic variants. The elite controller phenotype is rare and distinct, representing the extreme of an infectious disease trait. As such, this phenotype may be partly explained by variation in host immune control, which may be characterized by differences in rare functional genetic variants. Genomic regions underlying elite control can be potentially identified by comparing the presence or frequency of variants in this group to that representing the opposite extreme. In this context, ?rapid progressors? is a group defined by its rapid immunological and clinical disease progression. Aim: To extend an existing study, in order to identify DNA sequence variants involved in the control of HIV infection with greater statistical resolution. Specifically, we aim to sequence up to 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (a collaboration of 25 HIV seroconversion cohort studies across Europe).	Illumina HiSeq 2000	183
EGAD00001002180	Targeted pulldown of genes known to be recurrently mutated in AML & MDS from patient and normal samples using Agilent Sureselect and for some cases also using Illumina Truseq technology.	Illumina HiSeq 2000	288
EGAD00001002181	Barrett?s oesophagus is common in the UK affecting 2 % of the population. Family history has been recorded among the 4000 Barrett's cases collected so far and have 241 families. Among them we have assessed 6 multiplex families with proven Barrett?s and defined as having 1 pro band and at least 3 affected first degree members. We propose to exome sequence the probands of these six families to assess the presence of pathogenic rare coding variants.	Illumina HiSeq 2000	6
EGAD00001002182	The BMP antagonist Grem1 has been shown to be associated with a rare human polyposis syndrome (HMPS). We have shown that there is a 40KB duplication on chrom 15 found in some patients with HMPS. Traditional serrated adenomas (rare sporadic polyps) share some morphological features with HMPS polyps and it has long been hypothesised that they are the sporadic version of HMPS polyps. We have obtained of one of these lesions and in this project we aim to characterise this tumour.	Illumina HiSeq 2000 Illumina HiSeq 2500	2
EGAD00001002183	This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	96
EGAD00001002184	Sequencing of rare human histiocytic tumour	Illumina HiSeq 2000	2
EGAD00001002185	Exome sequencing of 32 patient samples from Sri Lanka with the condition haemoglobin E beta thalassaemia	Illumina HiSeq 2000	32
EGAD00001002186	Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from large Dutch familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina MiSeq	38
EGAD00001002191	None	Illumina HiSeq 2000	28
EGAD00001002193	Single case of T-ALL carrying t(4;6), a novel translocation.	Illumina HiSeq 2000	1
EGAD00001002194	This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ We performed exome sequencing on serial samples from a patient with CMML who progressed to AML. The exome sequencing suggests that NPM1, TET2 and DNMT3a mutations were present in the dominant clone in the CMML sample and that NRAS is a new subclonal mutation in the AML sample. Diagnostic data shows the presence of a FLT3-ITD mutation in the AML sample, which is likely to have driven progression. Here we are performing re-sequencing of the putative driver and some passenger mutations which appear to be in the same clone to validate these mutations and to verify the relative quantification of these abnormalities .	Illumina MiSeq	10
EGAD00001002195	The aim of this project is to identify rare genetic variants of large effect implicated in complex diseases by focusing on the study of cardiovascular diseases and related quantitative traits in a well characterized isolated population in Cilento area, Italy. The reference panel has been selected carefully in order to maximize the imputation coverage and quality on the all population samples. The selected individuals should meet three criteria: selected individuals should be chip-genotyped and closely related to the maximum number of chip-genotyped individuals so as to maximize imputation coverage; relatedness between selected individuals should be minimal, so as to minimize redundancy in genetic information of the reference panel. We perform exome sequencing on samples from 250 individuals from the Campora and Gioi-Cardile populations.	Illumina HiSeq 2000	247
EGAD00001002196	Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq	Illumina MiSeq	6
EGAD00001002197	Recent GWAS studies have made extensive use of large eQTL data sets to functionally annotate index SNPs. With a large number of association signals located outside coding regions there has been an intense search among sequence variants affecting gene expression at the transcriptional level. However, little progress has been made in mapping regulatory variants that affect protein levels at the translational or post-translational level. It is now possible to undertake a protein QTL scan for focused sets of e.g. oxidized proteins by mass spectrometry. We have established a collaboration with a longitudinal, family-based study in France, the Stanislas cohort, which comprises circa 1000 nuclear families (4,295 individuals) and has follow up data for 10 years (three visits). We have undertaken a pilot study in a focus set of 257 subjects from 79 families with the aim to integrate GWAS, transcriptomic and DNA methylation data with proteomic data on a set of 100 proteins measured in PBMCs. We have already generated GWAS data using Illumina's core-exome chip as well as DNA methylation profiles with the 450K array. We propose to use RNA seq to generate transcriptomic data of the corresponding PBMCs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	155
EGAD00001002198	This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma.	HiSeq X Ten Illumina HiSeq 2000	7
EGAD00001002199	Sequencing of rare human histiocytic tumour	Illumina HiSeq 2000	2
EGAD00001002200	Whole exome sequencing of families with Congenital Heart Defects (182 trios). Collaboration with David Brook, University of Nottingham.	Illumina HiSeq 2000	541
EGAD00001002207	Our aim is to identify genes involved in resistance to anti-cancer therapies. In order to do this we have taken advantage of a lentiviral vector (LV)-based insertional mutagen to mutagenize cancer cell lines. LV-transduced cell lines were then treated with anti-cancer therapies and the emergence of resistant clones scored. DNA from pools of resistant clones was collected, subjected to custom capture by baits designed against the LV sequence, and then sequenced to identify the LV-genomic junction. We hope that the identification of recurrently targeted genes in resistant cell population will allow us to identify genes that mediate drug resistance.	Illumina HiSeq 2500 Illumina MiSeq	71
EGAD00001002208	Exome sequencing of short SGA children with IGF-I and insulin resistance. Collaboration with Professor David Dunger, University of Cambridge. Funded by NIHR.	Illumina HiSeq 2000	15
EGAD00001002210	Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). To date, only a single recessive gene underlying complete anosmia has been identified. Here we sequenced the exomes of 10 individuals from a single family, including three with complete anosmia, across three generations to identify the genetic basis of congenital anosmia in this family. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	10
EGAD00001002211	Given the central importance of Africa to studies of human origins, genetic diversity and disease susceptibility, large-scale and representative characterisation of genetic diversity in Africa is needed. Analyses of ancient DNA from Africa would complement sequencing of modern African populations and provide unique opportunities to transform our understanding of the pre-history of the region. This approach would greatly refine our understanding of population structure and gene flow in Africa and globally, including genetic signatures of ancient admixture. This low coverage sequencing experiment will allow us to test and refine our pipeline for ancient DNA sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	6
EGAD00001002212	Non-syndromic cases of congenital heart defects (CHD) exhibit variable modes of inheritance (Mendelian and non-Mendelian). Several studies have identified strong candidates in humans by taking a candidate gene approach as well as by using whole exome next generation sequencing (NGS). So far these studies could only explain a minor fraction of the observed phenotype in humans, most of them in syndromic cases and no single study has focused on the subset of cases with left ventricular outflow tract obstruction (LVOTO). To discover novel disease-causing genes a large cohort of patients with LVOTO, approximately 100 cases, 25 families and 100 trios have been exome sequenced. This study based on NGS sequencing data yielded several known and novel compelling candidate genes, such as MYH6, NR2F2 and MYH11, but also novel ones, such as ITGB4. To evaluate the significance of our findings in a replication cohort we assembled another 1614 cases with an LVOTO phenotype from our collaborators in Toronto, Berlin and Amsterdam. Targeted resequencing in this additional cohort will help to find additional cases with mutations in the identified candidate genes to strengthen genotype-phenotype association. We will use control data from the INTERVAL project for case/control analyses The pulldowns will be performed as 24-plex ISC with 192 or greater indexes, and the sequencing will be performed with 192 samples per lane, requiring 9 lanes of sequencing.	Illumina HiSeq 2000	1376
EGAD00001002213	This study involves exome sequencing of blood/bone marrow DNA from patients with myeloid malignancies. Blood DNA samples have been taken from patients at different timepoints of disease phenotype. We hope to elucidate mechanisms of clonal evolution in these patients.	Illumina HiSeq 2000	32
EGAD00001002221	Whole exome sequencing of a subset of participants from the INTERVAL study.	Illumina HiSeq 2000	4502
EGAD00001002225	This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancy a. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina MiSeq	147
EGAD00001002226	1. Odors are detected, firstly, by olfactory sensory neurons (OSNs) in the olfactory epithelium of the nose. This neurons then project directly to the olfactory bulb in the brain. Olfaction depends on cellular regeneration of the OE, olfactory bulb and hippocampus, and on their continual re-wiring. The olfactory neural pathway includes regions of the frontal, temporal and limbic brain, which in turn overlap with brain areas involved in brain disorders. OSNs are the only aspect of the human brain exposed to the external environment. This not only makes them vulnerable to environmental changes, but also accessible for biomedical studies. We have already sequenced and developed a protocol for analyzing the transcriptome of mouse main olfactory epithelium and single OSNs. We propose here to perform a similar study for samples from the human olfactory epithelium. We have developed a minimally invasive method for obtaining human OSNs, among other cells from the nasal epithelium. In this experiment, we have obtained cell samples from the olfactory epithelium, including OSN, from healthy volunteers. We would like to further characterize them by RNA sequencing. This will give us valuable insight into human olfaction. It will also provide a first step into a new avenue to study, and find biomarkers for, brain diseases though the analysis of these easily available neurons. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	8
EGAD00001002227	In collaboration with Dr David Savage, we have identified a patient with a very unusual phenotype, lacking almost all visceral fat, but showing a massive accumulation of white fat tissue behind her neck and significantly elevated liver fat. Whole exome sequencing of the proband and her unaffected parents and brother has been run previously, however no causative variant has been found and the sequencing coverage was generally poor. We propose to conduct whole genome sequencing of all 4 family members at a depth of 30X.	HiSeq X Ten	3
EGAD00001002228	Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). Here we obtained genomic DNA from families with multiple individuals with anosmia, suggesting they are congenital. These include those inherited in a manner consistent with dominant and recessive alleles. We have sequenced the exomes of both affected and unaffected family members on the Illumina platform.	Illumina HiSeq 2000	24
EGAD00001002230	Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growth This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	96
EGAD00001002231	Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shred by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	HiSeq X Ten	80
EGAD00001002233	RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	24
EGAD00001002235	Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	80
EGAD00001002251	Exome sequencing of families with Congenital Heart Defects of diverse sub-phenotypes. Comprises both parent-offspring trios for sporadic cases and multiplex families. Collaboration with David Brook, University of Nottingham. Funded by the British Heart Foundation.	Illumina HiSeq 2000	646
EGAD00001002729	Haplotype Reference Consortium Release 1.1 - subset for release via the EGA		11227
EGAD00001002742	Whole-genome sequencing data from Chad and Lebanon.	HiSeq X Ten Illumina HiSeq 2500	15
EGAD00001002743	These samples comprise both melanoma cases and controls sequenced for a selection of loci linked to disease susceptibility. These bams are a subset of the sequencing restricted specifically to the GRCh37 coding areas of the BAP1 gene.		3186
EGAD00001003097	High-coverage sequencing data from 47 Yemenis samples	HiSeq X Ten	47
EGAD00001003098	Low-coverage sequencing data from 99 Lebanese samples	Illumina HiSeq 2500	99
EGAD00001003145	Sensory neurons are nerve cells that are activated by sensory input such as heat, light and convey information to the brain. Although a key cell type in complex organisms, human sensory neurons are challenging to study because they are impossible to obtain from living donors. We have collaborated with the Neucentis Pharmaceutical Research Unit to differentiate sensory neuron like cells from human induced pluripotent stem cells derived as part of the Human Induced Pluripotent Stem Cells Initiative. We will sequence RNA from 100 IPS lines derived from healthy individuals and perform RNA-seq on the differentiated cells to identify noncoding variants that alter gene expression in human sensory neurons.	Illumina HiSeq 2000 Illumina MiSeq	123
EGAD00001003161	HipSci - Bardet-Biedl Syndrome - Exome Sequencing - October 2016	Illumina HiSeq 2000 Illumina HiSeq 2500	3
EGAD00001003180	HipSci - Monogenic Diabetes - RNA Sequencing - October 2016	Illumina HiSeq 2000 Illumina HiSeq 2500	1
EGAD00001003181	HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016	Illumina HiSeq 2000 Illumina HiSeq 2500	3
EGAD00001003204	Understanding how cells sense and respond to their environment, and how these responses are modulated by genetic variation, are fundamental biological problems, particularly for understanding how pathogenic organisms invade and manipulate the cells of the human immune system. Macrophages recognize and respond to many important human pathogens including HIV-1, Mycobacteria tuberculosis and Salmonella. This study will focus on the cellular response of human macrophages to Salmonella infection and how this response is modulated by the genetic bacground of the individual as well as additional pro-inflammatory stimulus (interferon-gamma priming). We will acquire 100 human induced pluripotent stem cell lines from the HipSci project, differentiate the cells in vitro into macrophages and expose them to four environmental conditions: (i) no stimulation, (ii) interferon-gamma (18h), (iii) Salmonella typhimurium SL1344 (5h), (iv) interferon-gamma (18h) + Salmonella (5h).Subsequently, we will isolate RNA from the samples for sequencing.	Illumina HiSeq 2500	236
EGAD00001003213	The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and started to investigate the olfactory transcriptome in primates for evidence of selection at the level of receptor gene choice. Having collected this data from two primates, we now wish to extend the analysis to humans. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	9
EGAD00001003215	This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.	Illumina HiSeq 2000 Illumina HiSeq 2500	-
EGAD00001003237	Primary mucosal melanomas (MMs) arise from melanocytes located in mucosal membranes lining the respiratory, gastrointestinal and urogenital tracts. MMs frequently present late and have a poor prognosis; the 5-year survival rate is only 14%. MM makes up only ~1.4% of all melanomas and it is this rarity that makes knowledge of the genetic changes that contribute to its pathogenesis limited to a small number of exome/genome studies and other targeted studies. Thus to investigate the somatic alterations and mutation spectra in MM genomes, we have extracted genomic DNA from formalin-fixed, paraffin-embedded (FFPE) human MMs, and subjected them to whole exome sequencing. Given the propensity of MM to metastasize, we will also be sequencing metastatic MM lesions; primary and metastatic lesions from the same individual represent an excellent opportunity to identify potential drivers of metastasis in MM. Finally we will sequence 'normal' DNA from the same individual, where possible, to exclude germline variations.	Illumina HiSeq 2000	110
EGAD00001003241	Toxoplasmosis is a zoonotic disease caused by a ubiquitous protozoan parasite called Toxoplasma gondii, which can infect all mammal and bird species throughout the world. seroprevalence varies widely between countries. Studies have estimated that between 7-34% of people in the UK have been infected with T. gondii. The vast majority of these people will not have noticed any symptoms, however about 10% of people develop a mild to moderate self limiting flu-like illness. Following the acute active stage of the infection the parasite persists in the body in the form of cysts, particularly in heart and skeletal muscle and nervous system tissues, for many years, and usually for life. In immunocompetent persons these cysts do not pose a health risk. We will use RNA-seq to quantify the transcriptional response of macrophages to T gondii infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	18
EGAD00001003244	We aim to sequence the mRNA transcriptome of 22 human melanoma cell lines in biological triplicate in order to define the gene expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2000	66
EGAD00001003245	We aim to sequence the small RNAs of 22 human melanoma cell lines in biological triplicate in order to define the microRNAs expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	66
EGAD00001003250	1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.	Illumina HiSeq 2000	55
EGAD00001003260	The cell lines in this study are a combination of internally sequenced (cosmic) and externally sequenced cell lines known to be “double-wild-type” (lacking BRAF and NRAS somatic mutations). These sequences were realigned in this data set for consistency.		22
EGAD00001003294	Integrated callset of high coverage Ethiopian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)		5
EGAD00001003295	Integrated callset of high coverage Egyptian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)		3
EGAD00001003296	Integrated callset of low coverage Ethiopian and Egyptian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)		220
EGAD00001003307	In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1). This dataset contains all the data available for this study on 2017-04-27.	Illumina HiSeq 2000 Illumina MiSeq	40
EGAD00001003308	This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2017-04-27.	Illumina HiSeq 2000	10
EGAD00001003329	The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. This dataset contains all the data available for this study on 2017-05-11.	Illumina HiSeq 2000 Illumina HiSeq 2500	3188
EGAD00001003331	Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2017-05-11.	Illumina HiSeq 2000 Illumina HiSeq 2500	78
EGAD00001003347	This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-05-24.	Illumina HiSeq 2000	75
EGAD00001003354	From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.	Illumina HiSeq 2500	27
EGAD00001003355	From 17 patients undergoing knee joint replacement surgery for osteoarthritis, we collected 4 samples each: intact cartilage, degraded cartilage, synovium, and meniscus. We also collected blood for DNA analysis. Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.	Illumina HiSeq 2500	72
EGAD00001003407	Whole-genome sequencing and phasing of admixed Aboriginal Australian genomes and Papua New Guinean genomes using 10x Genomics Chromium technology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-06-27.	HiSeq X Ten	4
EGAD00001003514	HipSci - Healthy Normals - Exome Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	123
EGAD00001003515	HipSci - Bardet-Biedl Syndrome - Exome Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	3
EGAD00001003516	HipSci - Monogenic Diabetes - Exome Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	1
EGAD00001003517	HipSci - Alport Syndrome - Exome Sequencing - July 2017	Illumina HiSeq 2500	7
EGAD00001003518	HipSci - Battens Disease - Exome Sequencing - July 2017	Illumina HiSeq 2500	4
EGAD00001003519	HipSci - Bleeding and Platelet Disorders - Exome Sequencing - July 2017	Illumina HiSeq 2500	7
EGAD00001003520	HipSci - Congenital Hyperinsulinia - Exome Sequencing - July 2017	Illumina HiSeq 2500	5
EGAD00001003521	HipSci - Hereditary Cerebellar Ataxias - Exome Sequencing - July 2017	Illumina HiSeq 2500	11
EGAD00001003522	HipSci - Hereditary Spastic Paraplegia - Exome Sequencing - July 2017	Illumina HiSeq 2500	1
EGAD00001003523	HipSci - Hypertrophic Cardiomyopathy - Exome Sequencing - July 2017	Illumina HiSeq 2500	18
EGAD00001003524	HipSci - Kabuki Syndrome - Exome Sequencing - July 2017	Illumina HiSeq 2500	6
EGAD00001003525	HipSci - Macular Dystrophy - Exome Sequencing - July 2017	Illumina HiSeq 2500	3
EGAD00001003526	HipSci - Primary Immune Deficiency - Exome Sequencing - July 2017	Illumina HiSeq 2500	8
EGAD00001003527	HipSci - Retinitis Pigmentosa - Exome Sequencing - July 2017	Illumina HiSeq 2500	2
EGAD00001003528	HipSci - Usher Syndrome - Exome Sequencing - July 2017	Illumina HiSeq 2500	27
EGAD00001003529	HipSci - Healthy Normals - RNA Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	118
EGAD00001003530	HipSci - Monogenic Diabetes - RNA Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	1
EGAD00001003531	HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017	Illumina HiSeq 2000 Illumina HiSeq 2500	3
EGAD00001003532	HipSci - Alport Syndrome - RNA Sequencing - July 2017	Illumina HiSeq 2500	7
EGAD00001003533	HipSci - Battens Disease - RNA Sequencing - July 2017	Illumina HiSeq 2500	4
EGAD00001003534	HipSci - Congenital Hyperinsulinia - RNA Sequencing - July 2017	Illumina HiSeq 2500	5
EGAD00001003535	HipSci - Kabuki Syndrome - RNA Sequencing - July 2017	Illumina HiSeq 2500	6
EGAD00001003536	HipSci - Primary Immune Deficiency - RNA Sequencing - July 2017	Illumina HiSeq 2500	8
EGAD00001003537	HipSci - Hereditary Spastic Paraplegia - RNA Sequencing - July 2017	Illumina HiSeq 2500	6
EGAD00001003538	HipSci - Hereditary Cerebellar Ataxias - RNA Sequencing - July 2017	Illumina HiSeq 2500	11
EGAD00001003539	HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017	Illumina HiSeq 2500	7
EGAD00001003540	HipSci - Hypertrophic Cardiomyopathy - RNA Sequencing - July 2017	Illumina HiSeq 2500	18
EGAD00001003541	HipSci - Macular Dystrophy - RNA Sequencing - July 2017	Illumina HiSeq 2500	1
EGAD00001003542	HipSci - Retinitis Pigmentosa - RNA Sequencing - July 2017	Illumina HiSeq 2500	2
EGAD00001003543	HipSci - Usher Syndrome - RNA Sequencing - July 2017	Illumina HiSeq 2500	27
EGAD00001003556	We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome. This dataset contains all the data available for this study on 2017-08-10.	Illumina HiSeq 2500	25
EGAD00001003564	The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-08-16.	Illumina HiSeq 2500	46
EGAD00001003565	The project is focused on the axonal forms of Charcot-Marie-Tooth (CMT) disease. We have selected 13 families (7 from Spain and 6 from Czech Republic) that have been indepth clinically assessed and previously tested for mutations in known CMT genes without causal variants characterised. In these patients we expect to discover several CMT2 genes. Thus, we requested for exome sequencing of 45 DNAs:27 exomes in families from Spain and 18 exomes in the families from Czech Republic. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-08-16.	Illumina HiSeq 2500	45
EGAD00001003596	The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients. This dataset contains all the data available for this study on 2017-08-29.	Illumina HiSeq 2000	125
EGAD00001003747	Optimisation of ex vivo Memory B cell Expansion/Differentiation for Interrogation of Rare Peripheral Memory B Cell Subset Responses 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13.	Illumina MiSeq	38
EGAD00001003748	Sequencing of B-cell receptor repertoires in healthy individuals and patients with chronic lymphocytic leukemia. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13.	Illumina MiSeq	387
EGAD00001003749	Isotype-resolved sequencing of B cell receptor in measles virus infection 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13.	Illumina MiSeq	182
EGAD00001003750	This is the first whole exome sequencing analysis of a primary meningeal melanocytic tumour (MMT) alongside the patients germline. Here we report the CRAM files from the tumour and germline.	Illumina HiSeq 2500	2
EGAD00001004037	Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naive CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel. . This dataset contains all the data available for this study on 2018-03-14.	Illumina HiSeq 2500	123
EGAD00001004038	Identification of genes involved in congenital disorders of glycosylation and 3-methylglutaconic aciduria. There are more than 100 genes known for congenital disorders of glycosylation and new disorders are discovered each year. WE included patients with a so far unsolved glycosylation disease. The diagnostic group 3-methyglutaconic aciduria is a heterogenous group of disorders mostly caused by abnormal phospholipid synthesis or in association with mitochondrial dysfunction. We included patients with a so far unsolved disease and 3-methylglutaconic aciduria. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-03-14.	Illumina HiSeq 2500	31
EGAD00001004039	Albinism is genetically heterogeneous rare genetic condition affecting 1:17000 in the Western world (but more frequent in Africa) whose main feature is a profound visual impairment, characterised by foveal hypoplasia, abnormal chiasmatic connections, nystagmus and photofobia. All these features result in severly altered visual acuity (<0,1), absent depth perception and poor night vision. People with albinism are primarily visually handicapped. In addition, for some types of albinism, the visual phenotype can be presented with partial or total hypopigmentation, hence resulting in a secondary phenotype which can lead to skin cancer if skin is not adequately protected. Recently a new syndrome has been described, FHONDA, with the same visual abnormalities of albinism but without pigment alteration. The traditional classification differentiates Oculoculatenous albinism (OCA), where hypopigmentation involves hair, skin and eyes versus Ocular Albinism (OA), where hypopigmentation only affects the eyes. These are non-sydrimic types of albinism. Some syndromic forms (Hermansky-Pudlak=HPS, Chediak-Higashi=CHS) affect cells beyond pigment cells, present in the lungs, immune system, platelets and intestines, resulting in more severe phenotypes that can be fatal. Mutations in at least 19 genes are assocaited with the corresponding types of albinism. Most hospitals will only diagnose the most frequent cases using traditional Sanger, MLPA approaches. Some will use CGH arrays. We aim to diagnose all cases of albinism through the Albinochip proposal, which combines a Sequenom first step of known mutations combined with subsequent NGS approaches. In some cases we fail to find a second mutation, these are good candidates for further full exome analyses. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-03-14.	Illumina HiSeq 2500	48
EGAD00001004040	Whole Exome Sequencing of trios (proband + parents) or probands only with Neonatal Diabetes Mellitus (NDM) or Congenital Hyperinsulinism of Infancy (CHI) of unknown genetic origin. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-03-14.	Illumina HiSeq 2500	57
EGAD00001004150	This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-06-06.	Illumina HiSeq 4000	-
EGAD00001004151	A case-control series of melanoma cases from Leeds, UK have been sequenced in the Fluidigm platform to identify genetic variants associated with sporadic melanoma development. Samples in which potentially contributing variants have been detected are being sequenced in an orthogonal platform for variant confirmation. . This dataset contains all the data available for this study on 2018-06-06.	Illumina HiSeq 4000	201
EGAD00001004153	Gastric neuroendocrine tumors (gNETs) occur with an estimated frequency of 2 per 100,000 in the general population. Type I gastric neuroendocrine tumors (NETs) represent the 75% of gNTEs and arise from gastric enterochromaffin-like (ECL) cells. They have late age of onset and usually benigh course. Classically, hypergastrinemia in patients who have autoimmune atrophic gastritis, causes hyperplasia of gastric ECL cells that progresses into type I gastric NETs and parietal cell (PC) destruction. The genetic bases in families with this disease are unknown. We performed an exome sequencing study of an atypical aggressive familial gNETs case (with early age onset, nodal infiltrations and gastric adenocarcinomas) that followed a recessive model. We identified a deleterious mutation in homozygosis in the ATP4A gene, which encodes the proton pump responsible for acid secretion by gastric parietal cells. This mutation lead to achlorhydria first, and hypergastrinemia and gNET developing as consequence (Calvete et al. 2014). Recently, two more families with gNETs, classical clinical traits and recessive model have been studies by WES but we didn't find any mutation in the ATP4a gene. However, putative mutations affecting genes that contribute to the development and the integrity of PC have been found suggesting that genetic alterations associated to this disorder target to a unique cell type (parietal cells). In order to cinfirm this hypothesis, it is necessary the search for new genes implicated in the gNETs, more familial cases are needed to be studied. We have identified four more new familial gNETs cases. Here, we propose their study by WES. The first family is formed by thress siblings with gNETs. The other families include two siblings with gNETs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-06-06.	Illumina HiSeq 2500	7
EGAD00001004169	PBMCs were purified from blood samples of 8 HTLV-1 infected individuals, and cryo-preserved in fetal calf serum containing 10% DMSO. DNA from each samples was extracted using Qiagen Blood & Tissue kit according to the manufacturer's protocol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ .	HiSeq X Ten Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina MiSeq NextSeq 500	97
EGAD00001004199	This dataset was made to verify the computational reconstruction of B cell reseptors from single-cell RNA-seq using BraCeR. The dataset contains BCR-derived reads from single-cell RNA-seq from 13 cells using the Smart-seq2 protocol, as well as targeted BCR-sequencing data from the same cells.		26
EGAD00001004266	Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 2000	72
EGAD00001004272	We will sequence at 15X coverage the genomes of 960 IBD patients. These samples are currently onsite at Sanger and made available for sequencing via our collaboration with the UK IBD Genetics consortium. During the next quinquennium we intend to sequence the genomes of many thousand IBD patients and these 960 represent the first stage of this effort. Ultimately we will perform association tests comparing these genomes to similar numbers of control genomes to identify rare and low-frequency variants underlying IBD. . This dataset contains all the data available for this study on 2018-08-03.	HiSeq X Ten	1432
EGAD00001004273	In this project we have sequenced the exome of skin moles (melanocytic naevi) and also normal skin from young and old people. We are interested in looking at the clonality of these lesions and the burden of UV mutations . This dataset contains all the data available for this study on 2018-08-03.	Illumina HiSeq 2500	184
EGAD00001004274	1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference. . This dataset contains all the data available for this study on 2018-08-03.	Illumina HiSeq 2000 Illumina HiSeq 2500	71
EGAD00001004293	Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). . This dataset contains all the data available for this study on 2018-08-13.	Illumina HiSeq 2000 Illumina HiSeq 2500	110
EGAD00001004294	This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-08-13.	Illumina HiSeq 2500 Illumina MiSeq	92
EGAD00001004295	Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-08-13.	Illumina HiSeq 2000 Illumina HiSeq 2500	105
EGAD00001004304	We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. . This dataset contains all the data available for this study on 2018-08-20.	Illumina HiSeq 2500	1290
EGAD00001004305	As part of the Human Cell Atlas we will study fetal tissue. . This dataset contains all the data available for this study on 2018-08-20.	Illumina HiSeq 2500 Illumina HiSeq 4000	27
EGAD00001004332	Familial adenomatous polyposis (FAP) and MUTYH‐associated polyposis (MAP) are inherited disorders associated with multiple colorectal adenomas that lead to a very high risk of colorectal cancer. The somatic mutations that drive adenoma development in these conditions have not been investigated comprehensively. In this study we performed analysis of paired colorectal adenoma and normal tissue DNA from individuals with FAP or MAP, sequencing 14 adenoma whole exomes (eight MAP, six FAP), 55 adenoma targeted exomes (33 MAP, 22 FAP) and germline DNA from each patient.	Illumina Genome Analyzer II Illumina HiSeq 2000	121
EGAD00001004413	There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.	Illumina HiSeq 2500	18
EGAD00001004414	There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.	Illumina HiSeq 2500	12
EGAD00001004415	There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.	Illumina HiSeq 2500	9
EGAD00001004416	There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.	Illumina HiSeq 2500	9
EGAD00001004426	Spiradenocarcinoma is a rare cutaneous sweat gland adnexal cancer with potential for aggressive behaviour. They are classified histologically into low- and high-grade tumours, with morphologically low-grade tumours thought to behave more favourably. However, limited information is available, with only 18 published cases. We have collected morphologically low-grade spiroadenocarcinomas (one with a lung metastasis) and high-grade spiroadenocarcinomas, as well as some spiradenomas (benign lesions), cylindromas (another type of malignant cutaneous sweat gland adnexal tumour) and hybrid spiradenoma-cylindromas. H&E-stained sections were reviewed, follow-up was obtained, and immunohistochemistry for Ki-67, p53 and, MYB has been performed. The tumours were solitary, measuring 0.8-7?cm (median: 2.7?cm), with a predilection for the head and neck of elderly patients (median age: 72 years; range 53-92) without gender bias. Histologically, the tumours were multinodular and located in deep dermis and subcutis. A pre-existing spiradenoma was present in all cases. The malignant component was characterized by expansile growth with loss of the dual cell population, up to moderate cytological atypia and increased mitotic activity (median: 10/10 HPF; range 1-28). Additional findings included squamoid differentiation (n=9), necrosis (n=7), and ulceration (n=5). P53 expression was variable and no significant differences were noted in the benign compared with the malignant parts of the tumours. In contrast, in the malignant components the Ki-67 proliferative index was slightly increased, and MYB expression was lost. Follow-up (median: 67 months; range: 13-132) available for 16 patients (84%) revealed a local recurrence rate of 19% but no metastases or disease-related mortality. Here we wish to exome sequence these cases to define the first genomic landscape for this malignancy. This dataset contains all the data available for this study on 2018-10-29.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000	164
EGAD00001004570	Repeated clinical malaria episodes are associated with modification of the immune system in children.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/. . This dataset contains all the data available for this study on 2019-01-17.	Illumina HiSeq 2500	113
EGAD00001004573	Patients with germline mutations in CYLD can develop hundreds of benign skin tumours called cylindromas. The development of multiple tumours within a single patient at sun-protected and sun-exposed sites, varying tumour histological patterns and grades of malignancy allow for the testing of several genetic hypothesis in relation to cutaneous carcinogenesis. By adopting the unprecedented approach of whole genome sequencing of multiple benign skin tumours within individuals in multigenerational families, we set out to study the impact of mutational diversity on models such as multistep carcinogenesis as well as non-sequential carcinogenesis. Using non-negative matrix factorisation (NMF) to discover mutational signatures, we found distinct mutational signatures in identical benign tumours (N=2 patients; n=11 tumours) at sun exposed and sun protected skin tumours within a mother and her daughter. We found recurrent mutations in epigenetic modifying genes in CCS tumours which are known to have an oncogenic dependency on Wnt signalling. We also demonstrate that cutaneous tumours that metastasize to the lung carry a a UV signature, supporting the origin from the skin. Distinct malignant tumours, such as BCC and malignant spiradenocarcinoma carried unique driver mutations. These findings add new dimensions to the existing paradigms of UV-induced skin cancer and highlight the utility of studying rare disease to gain novel insights into genetic mechanisms of tumour formation.	HiSeq X Ten	13
EGAD00001004581	This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies: 1. 3781 British Pakistani/British Bangladeshi adults from East London Genes and Health 2. 2791 British South Asian mothers from Born in Bradford 3. 1428 British South Asian adults from Birmingham 4. 86 individuals (mixed ancestries) from families with rare diseases, from Queen Mary University London All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866. Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 \|\| FS > 30 \|\| MQ < 40.0 \|\| MQRankSum < -12.5 \|\| ReadPosRankSum < -8.0" Indels: "QD < 2.0 \|\| FS > 30 \|\| ReadPosRankSum < -20.0"		-
EGAD00001004583	Whole-genome-sequencing (WGS) of human tumours has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational-signatures in 324 WGS of human induced pluripotent stem cells (iPSCs) following exposure to known or suspected environmental carcinogens. 79 agents were tested with or without metabolic activation at concentrations that produced measurable cytotoxicity; 41 yielded characteristic substitution mutational signatures. Some exhibit similarity with signatures found in human tumours. Additionally, 6 agents produced double-substitution signatures and 8 produced indel signatures. Investigating mutation asymmetries across genome topography reveals fully functional mismatch and transcription-coupled repair pathways in iPSCs. Primary adducts induced by environmental carcinogens can be resolved by disparate repair/replicative pathways, resulting in an assortment of signature outcomes even for a single mutagen. This compendium of experimentally-induced mutational-signatures permits further exploration of roles of environmental agents in cancer aetiology, and underscores how human stem cell DNA is directly vulnerable to environmental agents.	HiSeq X Ten	324
EGAD00001004777	RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-02-15.	Illumina HiSeq 2000 Illumina HiSeq 2500	71
EGAD00001004786	Whole genome sequencing (WGS) detects all mutations in a cancer. “Mutational signatures” are patterns of mutations that report the DNA damage and subsequent DNA repair processes that have occurred in cancers. We present a patient with Xeroderma Pigmentosum that developed metastatic angiosarcoma, unresponsive to all lines of sarcoma therapy. Primary tumour WGS revealed a hypermutated tumour, including clonal ultraviolet light-induced mutational patterns (Signature 7) and subclonal signatures of activating mutations of DNA Polymerase-epsilon (POLE)(Signature 10). These signatures are associated with response to immune-checkpoint blockade. Immunohistochemistry confirmed high PD-L1 expression in metastatic deposits. The patient was commenced on anti-PD-L1 therapy and has responded.	HiSeq X Ten	2
EGAD00001004797	Twenty-seven Tibetan samples from China were whole-genome sequenced to investigate high-altitude adaptation, population genetics and demographic history.	HiSeq X Ten	43
EGAD00001004828	This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs). The final quality filtered set included 91 individuals with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq.	Illumina HiSeq 2500 Illumina MiSeq	242
EGAD00001004829	This dataset includes whole genome sequence data for ATAC-seq (42 samples) of human stimulated and cultured CD4+ Treg cells.	Illumina HiSeq 2500	49
EGAD00001004830	This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole transcriptome data for141 samples. The final quality filtered set included 123 individuals with RNA-seq data.	Illumina HiSeq 2500	141
EGAD00001004831	We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed ATAC sequencing to assess the chromatin accessability in different cytokines treated cells. These cellular profiles were used to map risk variants to the cytokine-induced cell states relevant for autoimmune diseases. . This dataset contains all the data available for this study on 2019-03-11.	Illumina HiSeq 2500 Illumina MiSeq	183
EGAD00001004839	PAGE Dataset Apr 2018 (Ref: PAGE Lancet 2019)		1812
EGAD00001004840	PAGE Dataset Apr 2018 (Ref: PAGE Lancet 2019)		1813
EGAD00001004841	PAGE Dataset Apr 2018 (Ref: PAGE Lancet 2019)		610
EGAD00001004842	PAGE2 Dataset Nov 2017 (Ref: PAGE2 GIM 2018)		81
EGAD00001004843	PAGE2 Dataset Nov 2017 (Ref: PAGE2 GIM 2018)		81
EGAD00001004844	PAGE2 Dataset Nov 2017 (Ref: PAGE2 GIM 2018)		27
EGAD00001004852	We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed K27Ac ChM sequencing to assess the chromatin activity in different cytokines treated cells. These cellular profiles were used to map risk variants to the cytokine-induced cell states relevant for autoimmune diseases. . This dataset contains all the data available for this study on 2019-03-19.	Illumina HiSeq 2500 Illumina MiSeq	192
EGAD00001004880	We will sequence at 15X coverage the genomes of 1536 IBD patients. These samples are currently onsite at Sanger and made available for sequencing via our collaboration with the UK IBD Genetics consortium. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-01.	HiSeq X Ten	3124
EGAD00001004881	Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage. . This dataset contains all the data available for this study on 2019-04-01.	Illumina HiSeq 2500	18
EGAD00001004888	We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep. . This dataset contains all the data available for this study on 2019-04-03.	Illumina HiSeq 2500	5
EGAD00001004890	The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.	HiSeq X Ten Illumina HiSeq 4000	26
EGAD00001004892	High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-03.	HiSeq X Ten	5
EGAD00001004894	In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-04-03.	HiSeq X Ten	60
EGAD00001004942	Gastroschisis (MIM 230750) is a herniation of the intestines through a defect of the abdominal wall lateral to the umbilicus (usually on the right side), and it is not covered by a membrane [Ledbetter, 2012]. Gastroschisis is a congenital anomaly with increasing incidence, easy prenatal diagnosis and extremely variable postnatal outcomes. On the basis of clinical manifestations, epidemiologic charateristics, and the presence and type of additional malformations, gastroschisis could be considered a heterogeneous condition with no gene/s discovered yet. This congenital anomaly affects approximately 1-3 infancts per 10,000 live births [Calzolari et al.1995;Parker et al.,2010] Current knowledge about causative mutations/variants. To date, no single gene has been linked to gastroschisis. Some publications have tried to link this malformation to variants in genes (such as AEBP1 (adipocyte enhancer binding protein) gene [Feldkamp et al,. 2012] or the VEGF-NOS3 pathway [Lammer et al., 2008]. Previously, a Scribble mutant mouse model (circletail) was reported to exhibit gastroschisis, however recent studies demonstrated that the Scribble knockout fetus exhibits exomphalos phenotype of gastroschisis [Carnagham et al., 2013]. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-08.	Illumina HiSeq 2500	30
EGAD00001004951	Whole-genome sequencing of human individuals from Polynesian and Native American populations, as well as 10x Genomics Chromium data from Polynesian, Native American and Aboriginal Australian populations, allowing for experimental phasing of haplotypes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-11.	HiSeq X Ten	68
EGAD00001004952	Small-molecule inhibitors targeting the most commonly activated pathway in melanoma, MAPK pathway (either alone or in combination) are already given to melanoma patients for few years, and initially reduce tumour burden dramatically, eventually melanomas become resistant and tumours progress while on treatment. Resistance to this treatment occurs by acquisition of additional mutations or other alterations that affect the mitogen-activated protein kinase (MAPK) pathway by either direct or indirect signalling. Many resistance mechanisms somehow lead to reactivation of extracellular signal-regulated kinase (ERK), thereby restoring signalling of the oncogenic BRAF/MEK/ERK pathway. In addition, PI3K pathway activation contributes to resistance to BRAF inhibition. Less frequent but equally important to the phenomenon of targeted drug resistance is the observation that B15-20% of BRAF mutant melanoma patients fail to respond to BRAF inhibition already early on treatment, owing to intrinsic resistance. These patients have little therapeutic options, unless immunotherapy can be given. To better understand the resistance mechanisms in MAPK inhibitor-treated melanoma patients and melanoma biology, our lab generated a big panel of MAPK inhibitor resistant melanoma cell lines by continuous drug exposure. The understanding of the genetic landscape and gene expression as well as cross resistance to other treatment regimens, and other aspects of melanoma biology such as phenotype switch, will allow us to better exploit new therapeutic strategies for melanoma patients. . This dataset contains all the data available for this study on 2019-04-11.	Illumina HiSeq 4000	34
EGAD00001004955	The aim of this project is to test whether HPV oncogenes and /or interferon induce the APOBEC mutational signature in vitro, and to test the role of APOBEC3A in this process. . This dataset contains all the data available for this study on 2019-04-11.	HiSeq X Ten	20
EGAD00001005002	This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ATAC-seq (114 samples) The final quality filtered set included 73 individuals with ATAC-seq.	Illumina HiSeq 2500 Illumina MiSeq	114
EGAD00001005006	PAGE Dataset Mar 2019		2595
EGAD00001005007	PAGE Dataset Mar 2019		2595
EGAD00001005008	PAGE Dataset Mar 2019		875
EGAD00001005020	The incidence of brain metastases in breast cancer (BCBM) patients is increasing. These patients have a very poor prognosis and therefore identification of blood-based biomarkers, such as circulating tumor cells (CTCs) and understanding the genomic heterogeneity could help to personalize treatment options. In this study, DNA from individual CTCs as well as corresponding primary tumors and brain metastases were analyzed by next generation sequencing (NGS) in order to evaluate copy number aberrations and single nucleotide variations (SNVs).	Illumina HiSeq 2000	28
EGAD00001005064	Bronchoscopies were collected from healthy and asthma volunteers. Cohort inclusion criteria for all subjects were: age between 40 – 65 years and history of smoking < 10 pack years. For the asthmatics, inclusion criteria were: age of onset of asthmatic symptoms ≤12 years, documented history of asthma, use of inhaled corticosteroids with(out) β2-agonists due to respiratory symptoms and a positive provocation test (i.e. PC20 methacholine ≤8mg/ml with 2-minute protocol). For the non-asthmatic controls, the following criteria were essential for inclusion: absent history of asthma, no use of asthma-related medication, a negative provocation test (i.e. PC20 methacholine >8 mg/ml and adenosine 5'-monophosphate >320 mg/ml with 2-minute protocol), no pulmonary obstruction (i.e. FEV1/FVC ≥70%) and absence of lung function impairment (i.e. FEV1 ≥80% predicted). Asthmatics stopped inhaled corticosteroid use 6 weeks prior to all tests. All subjects were clinically characterised with pulmonary function and provocation tests, blood samples were drawn, and finally subjects underwent a bronchoscopy under sedation. If a subject developed upper respiratory symptoms, bronchoscopy was postponed for ≥6 weeks. Fibreoptic bronchoscopy was performed using a standardised protocol during conscious sedation. Six macroscopically adequate endobronchial biopsies were collected for this study, located between the 3rd and 6th generation of the right lower and middle lobe. Extracted biopsies were processed directly thereafter, with a maximum of one hour delay. The medical ethics committee of the Groningen University Medical Center Groningen approved the study, and all subjects gave their written informed consent.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000	4087
EGAD00001005065	Human lung tissue was obtained from deceased organ donors from whom organs were being retrieved for transplantation. Informed consent for the use of tissue was obtained from the donors’ families (REC reference: 15/EE/0152 NRES Committee East of England - Cambridge South). Fresh tissue from the peripheral parenchyma of the left lower lobe or lower right lobe of the lung was excised within 60 minutes of circulatory arrest and preserved in University of Wisconsin (UW) organ preservation solution (Belzer UW® Cold Storage Solution, Bridge to Life, USA) until processing.	Illumina HiSeq 4000	11
EGAD00001005072	We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient.	HiSeq X Ten	3
EGAD00001005073	Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.	Illumina HiSeq 2500	15
EGAD00001005084	Whole genome sequencing of participants from the INTERVAL study. . This dataset contains all the data available for this study on 2019-06-12.	HiSeq X Ten	5112
EGAD00001005085	15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase II. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-06-12.	HiSeq X Ten	5592
EGAD00001005086	15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase III. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-06-12.	HiSeq X Ten	-
EGAD00001005215	The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). We will obtain diseased and non-diseased cartilage as well as other disease-relevant tissue following TJR, coupled with a blood sample. We will generate genotype data and will characterise the pairs of diseased and non-diseased tissue samples in terms of methylation, transcription (RNASeq) and expression (quantitative proteomics). We will apply integrative approaches to combine information across the omics levels to characterise genes, pathways, and networks that underlie osteoarthritis progression. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-01.	Illumina HiSeq 2500	210
EGAD00001005235	DNA and RNA isolated from FFPE blocks of patients who received immune checkpoint inhibition (ICI) are sequenced with the aim to identify therapeutically tractable vulnerabilities in tumors to prevent ICI resistance. . This dataset contains all the data available for this study on 2019-08-07.	Illumina HiSeq 2500	141
EGAD00001005236	ost adults with intellectual disabilities (ID) do not undergo genetic diagnostic investigation as part of their clinical care and have 'missed the boat' with regard to the WES and WGS genetic testing that is now being provided for children with ID. There is a dramatically increased risk of psychistric disorders in adults with ID, e.g. the risk of psychoses is 10X higher than in the general population. It remains an open question as to how much of adult ID is genetic in origin and how similar the genetic forms of adult ID are to those being diagnosed in children, in part due to survivor bias. There is also the opportunity to identify adults with treatable forms of ID, of which over 80 have been described, thus improving their clinical management. Furthermore, analysis of medical records of adults with genetic forms of ID can help to characterise the 'natural history' of individual disorders, resulting in more accurate prognoses for diagnosed children and identifying opportunities for improved management and possibly therapeutic intervention (e.g. optimal anti-epileptic therapy). Here we propose to exome sequence (to ~50X coverage) 200 adults with ID and co-morbid psychiatric disorders. This cohort has previously been assayed with chromosomal microarrays (Wolfe et al 2017 EJHG, 25, 66-72) identifying a diagnostic yield of ~11% which is comparable to the CNV diagnostic yield in various child ID cohorts (10-15%). The authors observed no substantive biases in diagnostic yield between different psychiatric diagnostic classes. The WES data will be analysed using the diagnostic workflows developed in the DDD study to ensure comparability between child and adult ID datasets. This study is intended as a pilot study to demonstrate the value of WES in adults with ID. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-07.	Illumina HiSeq 4000	200
EGAD00001005251	Retinoblastoma (RB), the commonest eye cancer in children was the first cancer for which a genetic cause was identified: the Rb1 gene is a tumour suppressor gene that is mutated in RB. The Rb1 gene defect alone does not predict the clinical outcome. We propose to study other possible mechanisms: 1. Stepwise further mutations occur in RB, increasing its carcinogenesis. We will sequence the whole genome in RB tissue, and relate the different genes expressed to the treatments used. 2. Extracellular matric proteins contribute to a tumour permissive environment for RB to continue to grow. This includes Samll Leucine Rich Proteoglycans (SLRP), a family of 15 secreted extracellular matrix proteins involved in eye development. 3. Cancer stem cells (CSC), a subpopulation of treatment resistant cells, drive RB tumours, and whether these stem cells can be manipulated for new therapies. The aim of this study is to assist finding targeted diagnostic techniques and treatments for RB. . This dataset contains all the data available for this study on 2019-08-14.	HiSeq X Ten	47
EGAD00001005253	This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-14.	Illumina HiSeq 4000	1574
EGAD00001005254	Whole genome sequences at 15X depth of patients with Inflammatory Bowel Disease. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-14.	HiSeq X Ten	2546
EGAD00001005255	In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.	HiSeq X Ten	2
EGAD00001005263	Primary T cell immunodeficiency disorders have a heterogeneous genetic basis. This study will focus on one case characterised by severe T cell lymphopenia in the index case. We aim to sequence the complete exomes of this individual, her three unaffected siblings and parents in an effort to identify the causative genetic mutation responsible for this disorder. We will perform exome capture using Agilent SureSelect system, followed by sequencing on the HiSeq platform. Our study has the potential to uncover genes important for T cell development and novel therapeutic strategies to treat T cell immunodeficiencies. . This dataset contains all the data available for this study on 2019-08-19.	Illumina HiSeq 2000	-
EGAD00001005264	The objective of this study is to identify the causative genes in two unrelated congenital neutropenia families. We aim to whole exome sequence the affected individuals, unaffected siblings and parents in both cases in an effort to idenitfy the causative genetic mutation. Exome capture will be performed using Agilent SureSelect system. Subsequently, exome libraries will sequenced using the Illumina HiSeq platform. Sequence variant calling will be done in house and common variants excluded using public databases and data from unaffected family members. . This dataset contains all the data available for this study on 2019-08-19.	Illumina HiSeq 2000	8
EGAD00001005265	We plan to sequence the exomes of 4 AML cases (tumour and germline) in an effort to discover new mutations in this disease that could improve our understanding of leukaemogenesis and guide the development of new targeted therapies. The Sanger Institute will sequence the exomes of 4 Acute Myeloid Leukaemia cases including tumour and germline DNA so that somatically-acquired, AML-specific mutations can be accurately designated. . This dataset contains all the data available for this study on 2019-08-19.	Illumina HiSeq 2000	6
EGAD00001005266	Deep whole genome sequencing of sampels from the Cilento isolates. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.	HiSeq X Ten	20
EGAD00001005267	Whole genome sequencing of sampels from the NSPHS cohort. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.	HiSeq X Ten	20
EGAD00001005268	Whole genome sequencing of sampels from an isolated population from the Val Borbera valley in Italy. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.	HiSeq X Ten	20
EGAD00001005269	Deep whole genome sequencing of sampels from the Orkney Complex Disease Study (ORCADES), each with data on up to 300 quantitative traits and other risk factors associated with cardiovascular, metabolic and other complex diseases. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.	HiSeq X Ten	20
EGAD00001005273	50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, processed with the FAIRE assay in order to generate maps of open chromatin. . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	78
EGAD00001005274	50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, subjected to Chromatin Immunoprecipitation using an antibody for H3K4me1. H3K4me1 peaks mark distal regulatory elements. . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	174
EGAD00001005275	The objective is to identify new disease genes involved in calcific aortic valve stenosis (CAVS) by screening newly identified candidate genes. The recruitment of patients with CAVS has been achieved by l’institut du thorax (Nantes, France). DNA from the selected patients has been analysed by targeted capture (Agilent SureSelect) and massively parallel sequencing (Illumina). . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	485
EGAD00001005276	These samples include exome sequences of samples from patients who suffered Sudden Unexplained Death in Epilepsy. They all are of European descent. . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	28
EGAD00001005277	This project is a pilot study, in collaboration with Maria Grazia Spillantini and Mariangela Iovino (Cambridge Centre for Brain Repair), to investigate the utility of IPS-derived neurons for the study of neurodegenerative disorders. Our aim is to characterise the transcriptional consequences of tauopathies using neurons derived from differentiated IPSCs as a model system. We will use IPS cells derived from six individuals, four with known mutations in the tau protein, 2 without. RNA will be extracted at Day 0 and Day 65 of differentiation by which time the neuronal tauopathy is apparent. RNA will be extracted and the transcriptome of each line characterised using RNAseq. We will then search for genes that are differentially expressed between the transcriptomes of individuals with tau mutations versus those in controls. My lab will analyse the RNAseq data, comparing both affected and controls and both time-points, to establish candidate genes. Darren Logan’s lab, along with our collaborators, will experimentally verify and further investigate these genes in additional lines and animal models. From this analysis we will generate a list of candidate genes that are differentially expressed between cases and controls. This study will not only help us understand the molecular basis of tauopathies, but also identify gene candidates for biomarkers of neurodegenerative disease. It will serve as a proof of principle for future planned studies into generating and transcriptomically analysing an allelic series of Tau mutations in IPSCs with a controlled genetic background. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	11
EGAD00001005278	We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We would like to exome sequence these samples to gain a snap shot of the mechanisms of resistance that are operative. . This dataset contains all the data available for this study on 2019-08-21.	Illumina HiSeq 2000	42
EGAD00001005290	Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated condition, as well as in the presence of Th2, iTreg and Th17 polarizing cocktail. To characterize the efficacy of cytokine induced porization and subpopulation specific response, we profiled single cell transcriptome five days following polarization using 10x platform (3' v2).	Illumina HiSeq 4000	16
EGAD00001005291	Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated conditions, as well as in the presence of Th1, Th2, Th17 and iTreg cocktail. In addition, T cells were stimulated in the presence of IL-10, IL-21, IL-27, IFNb and TNFa. We performed bulk RNA sequencing to assess impact of different disease-relevant cytokines upon T cell response.	Illumina HiSeq 2500	141
EGAD00001005298	This project aims to evaluate the transcriptional response to disease measured in whole blood of participants who developed enteric fever after challenge and, importantly, those who were challenged but stayed well throughout the challenge period. This data will provide unique coverage of the transcriptome and will yield invaluable insight after integration with a wealth of clinical data collected during this trial. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-28.	Illumina HiSeq 2000	195
EGAD00001005299	This study involves exome sequencing of blood/bone marrow DNA from patients with myeloid malignancies. Blood DNA samples have been taken from patients at different timepoints of disease phenotype. We hope to elucidate mechanisms of clonal evolution in these patients. . This dataset contains all the data available for this study on 2019-08-28.	Illumina HiSeq 2000 Illumina MiSeq	46
EGAD00001005300	Study to stimulate WT and IL-10RB mutant macrophages with LPS in presence or absence of recombinant IL-10 and compare their gene expression profiles by RNASeq These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-08-28.	Illumina HiSeq 2000	32
EGAD00001005311	This study entails whole genome sequencing of an interleukin (IL)-12 b-1 receptor-deficient individual who presented with a chronic systemic Salmonella Enteritidis infection that did not resolve with standard IFNg and antibiotic treatment. Whole genome sequencing of the patient's parents are also included. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-09-05.	HiSeq X Ten	3
EGAD00001005351	Analysis of mutational signatures caused by exposure to known mutagens in human induced pluripotent stem (iPS) cells. A reference human iPS cell-line will be exposed to 100 chemicals known or proposed to be mutagenic. Following exposure to mutagen, cells will undergo a period of recovery before sub clones are generated and sequenced. The progenitor "parental" IPS cell-line will be used to generate reference sequence data, in order to determine the mutational signatures acquired as a result of exposure to different mutagens.	HiSeq X Ten	6
EGAD00001005421	These are 21 metastatic melanoma exomes matched with 7 germlines from 7 multisite metastatic melanoma cases.	Illumina HiSeq 2000	-
EGAD00001005431	Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn’s disease, Behçet’s disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and—in particular—isotype use. An increase in clonality in systemic lupus erythematosus and Crohn’s disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune- mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.	Illumina MiSeq	167
EGAD00001005466	Whole genome sequencing of 100 unrelated Uzbeks in order to impute genotypes into PE cases and controls from Uzbekistan and to provide genetic data and infrastructure for future genetic studies in Uzbekistan and Central Asia more generally and to fill a gap in worldwide information as Central Asia is not adequately represented in available genomic data. This dataset is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology.	Illumina HiSeq 2000	100
EGAD00001005467	Whole genome sequencing of 100 unrelated Kazakhs in order to impute genotypes into PE cases and controls from Kazakhstan and to provide genetic data and infrastructure for future genetic studies in Kazakhstan and Central Asia more generally and to fill a gap in worldwide information as Central Asia is not adequately represented in available genomic data. This dataset is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator)	Illumina HiSeq 2000	100
EGAD00001005469	This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies: 1. 5236 British Pakistani/British Bangladeshi adults from East London Genes and Health (ELGH) 2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani) (BiB) 3. 1061 British South Asian adults from Birmingham (mostly Pakistani) (Birm) All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866. In the sample list file, the columns of interest to most people will be: vcf.id - sample ID from the vcf cohort - which cohort they're in sex.assigned - sex inferred from coverage on the X and Y chromosomes. Individuals for whom this did not match their reported sex have been discarded total, chrX and chrY - coverage within bait regions across all chromosomes, chrX and chrY respectively Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 \|\| FS > 30 \|\| MQ < 40.0 \|\| MQRankSum < -12.5 \|\| ReadPosRankSum < -8.0" Indels: "QD < 2.0 \|\| FS > 30 \|\| ReadPosRankSum < -20.0"		-
EGAD00001005483	These are caveman, pindel, battenberg and brass calls for index patients' metastatic melanoma genomes within this study.		-
EGAD00001005487	These are caveman, pindel and sequenza calls for the metastatic melanoma exomes within this study.		-
EGAD00001005736	In the brain the cells that control inflammation are called a type of white blood cell called microglia. Microglia are located throughout the brain and spinal cord and account for 10–15% of all cells found within the brain. As the resident white blood cells, they are the main active immune defence in the central nervous system (CNS). Microglia are part of an important class of cells known as macrophages that have two main states: M1 and M2. M1 cells are pro- inflammatory, leading to more inflammation, while M2 are anti-inflammatory, and drive wound healing. In this study, we will collect primary microglia from surgical biospies of 100 individuals. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/		-
EGAD00001005741	When comparing the differentiation capacities of pluripotent stem cell lines that have different genetic backgrounds, batch to batch experimental variablility poses a significant challenge, especially when trying to identify smaller effects. One way to address this issue is to differentiate several different lines in the same culture dish, thereby elimating experimental variation. In addition, it allows researchers to analyze many more lines with less experiments. Parallel single cell RNA-Seq exploits that individual cells are tagged and hence each cell can be reliably assigned to the donor of origin based on the genetic variants it contains. In addition, analyzing the genetic signature of single cells within a differentiating population can reveal differentation stages that are not easily detected in bulk RNAseq data. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	13433
EGAD00001005788	We will be testing the hypothesis that MBD4 PTV germline carriers also show an increased number of C toT germline mutations in their offspring. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-01-15.	HiSeq X Ten	39
EGAD00001005790	Falciparum malaria is clinically heterogeneous and yet in most cases the risk of life-threatening disease dramatically declines after the first few infections of life because children rapidly acquire disease tolerance (resistance to severe malaria without improved control of parasite burden). Identifying the factors that determine clinical outcome in a malaria-naive host is therefore paramount to reduce malaria mortality. However, the relative contribution of disease-causing variants of the Plasmodium var gene family versus pathogenic inflammatory cytokine cascades remains fiercely debated - we sought to reconcile these conflicting arguments by studying their interaction in vivo. To this end, two human challenge models were used to reveal the parasite-host interactions that underpin variation in falciparum malaria. To capture the diversity of human immune responses, each individual was analysed independently by tracking dynamic changes in their whole blood transcriptome through time. And to uncover evidence of preferential expansion of disease-causing variants, var gene expression was tracked in vivo from the start to end of infection. In this way, we could show that group A var genes are always expressed upon liver egress but in a minority population that does not increase over 10-days of blood cycling; there is no selection of disease-causing variants in the naive host. In fact, parasites do not respond in any way to differences or changes in host environment. On the other hand, host-intrinsic variation determines the intensity of inflammation and progression to clinical malaria. And furthermore, regulation of the interferon signaling network controls host fate. These data emphasise the role of human immune decision-making in shaping course & outcome of infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-01-15.	Illumina HiSeq 2500	30
EGAD00001005816	This dataset includes whole genome sequence data for ChIPmentation assays (18 H3K4me3, 20 H3K27ac and 3 input samples) of human stimulated and cultured CD4+ Treg cells.	Illumina HiSeq 2500 Illumina MiSeq	1
EGAD00001005964	This dataset includes whole transcriptome data of human stimulated and cultured CD4+ Treg cells (39 samples).	Illumina HiSeq 2500	39
EGAD00001005981	These are the raw sequencing files for the 50 brain tumour, 3 extracranial tumour and 34 matched normals for the patients in the discovery cohort.	Illumina HiSeq 4000	87
EGAD00001005982	These are the variant calls for the 50 brain tumour samples in the discovery cohort.	Illumina HiSeq 4000	50
EGAD00001005983	These are the Sequenza copy number calls for the 30 brain tumour samples within the discovery cohort.	Illumina HiSeq 4000	30
EGAD00001005984	Raw sequencing files for the 18 (brain tumour-only) samples within the external validation cohort.	Illumina HiSeq 4000	18
EGAD00001005985	These are the raw sequencing files for the orthogonal validation brain tumour samples in the discovery cohort.	Illumina HiSeq 4000	31
EGAD00001005993	The aim of this study is to define the mutational landscape of human liver tumours. . This dataset contains all the data available for this study on 2020-02-20.	HiSeq X Ten	6
EGAD00001006055	Mutational signatures are imprints of cell-intrinsic and extrinsic pathophysiological processes that have occurred through tumorigenesis. Experimental efforts to explore signature etiologies have produced a compendium of signatures of exogenous mutagens previously. Here, we unearth major sources of endogenous DNA damage and the genes that are critical to mitigating this innate stream of DNA damage under normal, physiological circumstances. We performed whole genome sequencing of 173 subclones of CRISPR-Cas9 knockouts of 43 genes in a human induced pluripotent stem cell system, in the absence of any added DNA damage. We reveal substitution and indel signatures that arise from those genes which are essential guardians of the genome. By detailed dissection and comparisons to cancer-derived signatures, we demonstrate interminable sources of constitutive DNA damage, and some mechanistic knowledge into how guardian genes preserve the genome. Based on these experimental insights, we develop and benchmark a tool for clinical classification of tumor samples.	HiSeq X Ten	173
EGAD00001006061	Whole genome and whole exome sequencing data supporting the manuscript 'Somatic evolution in the non-neoplastic IBD affected colon' by Sigurgeir Olafsson et al.	HiSeq X Ten Illumina NovaSeq 6000	693
EGAD00001006118	In this study we will perform targeted sequencing on the bulk samples of in vitro colonies. This dataset contains all the data available for this study on 2020-05-05.	Illumina HiSeq 4000 Illumina NovaSeq 6000	595
EGAD00001006139	Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-12.	Illumina HiSeq 4000 Illumina NovaSeq 6000	49
EGAD00001006157	The impact of genetic variants on molecular pathways that give rise to neurodegenerative diseases such as Alzheimer's and Parkinson's is best elucidated in the appropriate cell types and molecular contexts. Existing studies have focused on bulk profiling of mixed cell types, but have ignored assaying genetic effects across development and cell differentiation. At the core of this proposal is the idea to use single-cell assays to study genetic effects during differentiation of dopaminergic and cortical neurons to identify the sequence of molecular events from variants to healthy and diseased cell states in a cell-specific manner. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-18.	Illumina HiSeq 4000	42
EGAD00001006249	This study aims to use RNAseq to identify differentially expressed transcripts in human melanoma cells that over-express the cell surface protein, LRRN4CL, relative to empty-vector control cells, to provide mechanistic insight into how LRRN4CL over-expression confers enhanced pulmonary metastatic colonisation abilities.	Illumina HiSeq 2500	48
EGAD00001006331	Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.		9
EGAD00001006431	Background: The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable suggesting alternative pathways to malignancy. Methods: We applied comprehensive whole genome sequencing (WGS) and transcriptomics to sporadic retinoblastomas derived from twenty patients attending our clinic, contrasting these results to that obtained through customary clinical testing. We sought RB1 and other driver mutations, investigated mutation burden, mutational signatures and phylogenetic relatedness in one case of bilateral retinoblastoma. Results: At least one RB1 mutation was identified in all retinoblastomas. We confirmed RB1 mutations previously identified by clinical screening, identified three new RB1 mutations and provided clarity to the mechanism behind a further six mutations. Eight tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Potential driver mutations included mutations in BCOR (5/20) and amplification of MYCN (2/20) and MDM4 (1/20). We show that RB1 mutations are not mutually exclusive of MYCN amplifications, and further reveal that all tumours demonstrate increased MYCN expression suggesting a universal role in retinoblastoma tumorigenesis. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. In-keeping with previous WGS of paediatric cancers, the mutation burden in retinoblastomas was extremely low. Mutational signature analysis showed a predominance of signatures associated with cell division and an absence of ultraviolet-related DNA damage. In a tumour exposed to chemotherapy prior to enucleation, a profound platinum-related mutational signature was observed. Conclusions: WGS provides a complete picture of the genomic landscape of retinoblastomas, allowing the discovery of mutations otherwise undetected by conventional clinical screening approaches. The presence of at least one RB1 mutation in all retinoblastomas and the relative paucity of driver mutations in other genes suggests mutations beyond RB1, MYCN and BCOR are rare. Whilst most RB1 mutations are identifiable by clinical screening, the increased resolution and ability to detect otherwise elusive rearrangements of RB1 by WGS, confirming whether they are somatic or germline, has important repercussions on clinical management and advice on recurrence risks.	HiSeq X Ten	41
EGAD00001006610	We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Sorted Tcons were activated using a titration of anti-CD3 and anti-CD28 in combination as well as individually. As a control we cultured cells in the same conditions but without the stimuli. In total, we defined seven conditions from four individuals for sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.	Illumina HiSeq 2500	74
EGAD00001006611	We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Isolated memory and naïve T cells were activated using anti-CD3, anti-CD28 or both in combination. As a control we cultured cells in the same conditions but without the stimuli. We carried Chipmentation using the H3K27ac antibody on 200,000 cross-linked cells. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 2500	18
EGAD00001006612	We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Sorted Tcons were activated using a titration of anti-CD3 and anti-CD28 in combination as well as individually. As a control we cultured cells in the same conditions but without the stimuli. In total, we defined seven conditions from four individuals for sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 2500	30
EGAD00001006648	Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1,191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. This dataset includes CRISPR screening of cancer cell lines, RNA sequencing studies of cancer cell lines and also data from the sequencing of tumour xenografts collected from mice.	Illumina HiSeq 2500	27
EGAD00001006649	Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1,191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. This dataset includes CRISPR screening of cancer cell lines, RNA sequencing studies of cancer cell lines and also data from the sequencing of tumour xenografts collected from mice.	Illumina HiSeq 4000 Illumina NovaSeq 6000	55
EGAD00001006784	This study aims to identify novel candidate variants from human Y-chromosomal genes DAZ, BPY2 and CDY1/2 by resequencing the coding regions of these genes from male patients with spermatogenic impairment. The coding regions of the genes plus a selection of phylogenetically informative Y-chromosomal markers have been amplified by standard PCR, amplicon lengths range from 178 to 486 bp. Amplicons were quantified by gel electrophoresis and pooled in approx. equimolar concentrations per patient. For each of the 480 submitted samples, approx. 1 microgram of amplified DNA pool was provided in a total volume of 120 microlitres. The samples were indexed and libraries prepared for PE250bp Illumina MiSeq runs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina MiSeq	480
EGAD00001006786	Multi region samples are collected from patients, with consent, immediately after resection of the tumour. Samples are digested and sorted using FACS as single cells into lysis buffer. Cells are then stored until further processing for G&T-seq. After sequencing, we will explore intra-tumour heterogeneity using computational approaches to integrate RNA and DNA data onto the tumour phylogeny This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 4000	672
EGAD00001006924	Plasmodium vivax offers unique challenges for control and elimination, and may prove a tougher hurdle to overcome than Plasmodium falciparum. And yet compared to P. falciparum we know very little about the innate and adaptive immune responses that need to be harnessed to reduce disease and transmission. We recently generated a blood bank of a new clonal field isolate of P. vivax (PvW1) for human challenge studies and used systems immunology tools to track the host response throughout infection and convalescence. As part of this study, RNA-sequencing was used to resolve changes in whole blood gene expression through time in 6 volunteers (7-9 time-points per volunteer). In summary, these data show that P. vivax induces two distinct transcriptional programmes in whole blood during and after infection. During infection, transcriptional profiling reveals the rapid mobilisation of an emergency myeloid response, which leads to systemic inflammation and the recruitment of all major T cell subsets into lymphoid tissues. Six days after infection, this innate response subsides and a transcriptional signature of proliferation is revealed. This most likely represents widespread activation of lymphocytes, which return to the circulation after parasite clearance - transcriptional profiling of T cells at this time-point could therefore reveal the outcomes of critical cell-cell interactions that take place within the spleen during infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 2500	54
EGAD00001006931	De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up. . This dataset contains all the data available for this study on 2021-02-02.	Illumina HiSeq 4000	26
EGAD00001007029	Human Induced Pluripotent Stem Cells (hiPSC) are an established patient-specific model system where opportunities are emerging for cell-based therapies. We compared and contrasted hiPSCs derived from different tissues, skin and blood, in the same individual. We show extensive single-nucleotide mutagenesis in all hiPSC lines, although fibroblast-derived hiPSCs (F-hiPSCs) are particularly heavily mutagenized by ultraviolet (UV)-related damage. We utilized genome sequencing data on 454 F-hiPSCs and 44 blood-derived hiPSCs (B-hiPSCs) to gain further insights. Across 324 whole genome sequenced (WGS) F-hiPSCs derived by the Human Induced Pluripotent Stem Cell Initiative (HipSci), UV-related damage is present in ~72% of cell lines, sometimes causing substantial mutagenesis (range 0.25-15 per Mb). Furthermore, we find remarkable genomic heterogeneity between independent F-hiPSC clones derived from the same reprogramming process in the same donor, due to oligoclonal populations within fibroblasts. Combining WGS and exome-sequencing data of 452 HipSci F-hiPSCs, we identify 272 predicted pathogenic mutations in cancer-related genes, of which 21 genes were hit recurrently three or more times, involving 77 (17%) lines. Notably, 151 of 272 mutations were present in starting fibroblast populations suggesting that more than half of putative driver events in F-hiPSCs were acquired in vivo. In contrast, B-hiPSCs reprogrammed from erythroblasts show lower levels of genome-wide mutations (range 0.28-1.4 per Mb), no UV damage, but a strikingly high prevalence of acquired BCOR mutations in ~57% of lines, indicative of strong selection pressure. All hiPSCs had otherwise stable, diploid genomes on karyotypic pre-screening, highlighting how copy-number-based approaches do not have the required resolution to detect widespread nucleotide mutagenesis. This work strongly suggests that models for cell-based therapies require detailed nucleotide-resolution characterization prior to clinical application.	HiSeq X Ten	86
EGAD00001007033	De- and trans-differentiation is a rare and only poorly understood phenomenon in cutaneous melanoma. To study this disease more comprehensively we have retrieved 11 primary cutaneous melanomas from our pathology archives showing biphasic features characterized by a conventional melanoma and additional areas of de-/trans-differentiation as defined by a lack of immunohistochemical expression of all conventional melanocytic markers (S-100 protein, SOX10, Melan-A and HMB-45). The clinical, histologic and immunohistochemical findings were recorded and follow-up was obtained. The patients were mostly elderly (median: 81 years; range: 42-86 years) without significant gender predilection, and the sun-exposed skin of the head and neck area was most commonly affected. The tumors were deeply invasive with a mean tumor thickness of 7 mm (range: 4-80 mm). The dedifferentiated component showed atypical fibroxanthoma-like features in the majority (7), while additional rhabdomyosarcomatous and epithelial transdifferentiation was noted histologically and/or immunohistochemically in two tumors each. The background conventional melanoma component was of desmoplastic (4), superficial spreading (3), nodular (2), lentigo maligna (1) or spindle cell (1) types. For the 7 patients with available follow-up data (median follow-up period of 25 months; range: 8-36 months), 2 died from their disease and 3 developed metastases. Next-generation sequencing of the cohort revealed somatic mutation of established melanoma drivers including mainly NF1 mutations in the conventional component (5 cases), which were also detected in the corresponding de-/trans-differentiated components. In summary, the diagnosis of de-/trans-differentiated melanoma is challenging and depends on the morphologic identification of the conventional melanoma component. Molecular analysis is diagnostically helpful as the mutated gene profile is shared between the conventional and de-/trans-differentiated components. Importantly, de-/trans-differentiation does not appear to confer a more aggressive behavior.	Illumina HiSeq 4000	21
EGAD00001007034	De- and trans-differentiation is a rare and only poorly understood phenomenon in cutaneous melanoma. To study this disease more comprehensively we have retrieved 11 primary cutaneous melanomas from our pathology archives showing biphasic features characterized by a conventional melanoma and additional areas of de-/trans-differentiation as defined by a lack of immunohistochemical expression of all conventional melanocytic markers (S-100 protein, SOX10, Melan-A and HMB-45). The clinical, histologic and immunohistochemical findings were recorded and follow-up was obtained. The patients were mostly elderly (median: 81 years; range: 42-86 years) without significant gender predilection, and the sun-exposed skin of the head and neck area was most commonly affected. The tumors were deeply invasive with a mean tumor thickness of 7 mm (range: 4-80 mm). The dedifferentiated component showed atypical fibroxanthoma-like features in the majority (7), while additional rhabdomyosarcomatous and epithelial transdifferentiation was noted histologically and/or immunohistochemically in two tumors each. The background conventional melanoma component was of desmoplastic (4), superficial spreading (3), nodular (2), lentigo maligna (1) or spindle cell (1) types. For the 7 patients with available follow-up data (median follow-up period of 25 months; range: 8-36 months), 2 died from their disease and 3 developed metastases. Next-generation sequencing of the cohort revealed somatic mutation of established melanoma drivers including mainly NF1 mutations in the conventional component (5 cases), which were also detected in the corresponding de-/trans-differentiated components. In summary, the diagnosis of de-/trans-differentiated melanoma is challenging and depends on the morphologic identification of the conventional melanoma component. Molecular analysis is diagnostically helpful as the mutated gene profile is shared between the conventional and de-/trans-differentiated components. Importantly, de-/trans-differentiation does not appear to confer a more aggressive behavior.		18
EGAD00001007520	In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.	Illumina HiSeq 2000	2731
EGAD00001007572	This data set contains single cell transcriptomes generated using the chromium 10X platform from both fresh cells and nuclei. The samples measured are derived from children with Wilms tumour, Clear Cell Sarcoma of the Kidney (CCSK), or Malignant Rhabdoid Tumours.	Illumina HiSeq 4000 Illumina NovaSeq 6000	55
EGAD00001007718	Single-cell data gene expression data set (5’Chromium 10X) of healthy paediatric volunteers, and paediatric and adult COVID-19 patients. Gene expression was determined from samples of nasal, tracheal and bronchial brushings and blood (PBMCs). In addition to gene expression, PBMC’s were assayed by CITE-seq. A subset of samples have VDJ sequencing data for T cell receptors (TCR) and B cell receptors (BCR).	Illumina NovaSeq 6000	268
EGAD00001007815	Genotyped data for 28,022 British individuals with South Asian ancestry from the Genes and Health cohort (Feb2020), which were imputed with the GenomeAsia pilot reference panel.		28022
EGAD00001007853	We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.	HiSeq X Ten	3
EGAD00001007854	We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.	Illumina HiSeq 4000 Illumina NovaSeq 6000	8
EGAD00001007909	HCA Endometrium_LM The endometrium regenerates monthly and its transformation is executed through dynamic changes in states and interactions of multiple cell types. Using transcriptomics methods we seek to profile changes of the endometrium across the menstrual cycle. Our map will have implications in women's health and cancer, by enabling the interpretation of GWAS analyses or the studying functional consequences of somatic mutations. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina NovaSeq 6000	7
EGAD00001007982	Single-cell analysis of the transcriptome, T cell immune receptors, and surface proteome (CITE-seq) from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with pre-existing autoimmune diseases (rheumatoid arthritis n = 5, psoriasis n = 4, or multiple sclerosis n = 3), as well as COVID-19 patients without pre-existing autoimmunity as controls (n = 10) to investigate altered immune responses.	Illumina NovaSeq 6000	27
EGAD00001008015	We performed bulk RNA-sequencing on peripheral blood collected from 4,732 blood donors recruited as part of the INTERVAL study. Using these data, we mapped gene expression and splicing quantitative trait loci (QTLs). Then, we integrated these data with protein, metabolite and lipid QTLs in the same individuals. The study aimed to identify the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans.	Illumina NovaSeq 6000	1
EGAD00001008197	We isolated naive and memory CD4+ T cells from 119 healthy individuals and stimulated the cells using anti-CD3/anti-CD28 coated beads. We profiled gene expression using single cell RNA-seq (10X-Genomics 3’ v2 kit) at resting state and three time points of activation (16h, 40h and 5 days post stimulation) and mapped expression quantitative trait loci.	Illumina HiSeq 4000 Illumina MiSeq	167
EGAD00001008345	Using the chromium 3' expression assay, we generated an atlas of neuroblastoma and the human fetal adrenal gland. These data were complemented with whole genome sequencing of normal and tumour DNA from the neuroblastoma samples.	Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina MiSeq Illumina NovaSeq 6000	32
EGAD00001008360	Mutational burden and profiles to be studied in approx. 500 human primary melanomas with matched normal samples, part of the Leeds melanoma cohort. New custom design targeted capture panel covering melanoma-specific copy number alterations, promoter mutations, gene fusions, coding genes, HLA regions and IFNg/JAK/STAT pathway genes.	Illumina HiSeq 4000	1
EGAD00001008361	RNA-seq transcriptomics of whole blood samples from longitudinal follow-up of a cohort of visceral leishmaniasis (VL) patients with and without HIV coinfection, from active disease through apparent cure and potential relapse. Analysis will identify potential correlates of relapse to identify immune mechanisms underlying the high rate of relapse in HIV/VL coinfection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .	Illumina HiSeq 4000	249
EGAD00001008541	In other analysis in the current manuscript, we find a similar gene signature (to dissociation based artifacts in mouse and human tissue) is present in post-mortem microglia and astrocytes, across all snRNA-seq datasets analyzed, although it is highly variable between subjects. Using acutely-resected neurosurgical tissue, we performed single-nucleus RNA-seq and reveal that a similar signature can be detected in microglia following prolonged exposure to room temperature. Tissue handling and methods details, as well as sequencing and analysis details) can be found in the methods section of related manuscript (Marsh et al., 2022). Together, these results suggest that the presence of this signature in post-mortem brain samples may be the result of a combination of acute pre-mortem (agonal state, cause of death, comorbidities, etc.) and post-mortem (post-mortem interval (PMI), storage time, RNA quality, etc.) variables and may not represent normally present cell state.	Illumina NovaSeq 6000	4
EGAD00001008575	Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single cell omics analyses in CVID discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.	Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	2838
EGAD00001008661	Whole-genome sequencing (WGS) genotype data generated as part of the Interval project. The data are reported, separately per chromosome, in variant call format (VCF). The genotypes are denoted in diploid format (for chrY the genotype 1 denoted as 1/1 and 0 denoted as 0/0). Note that multi-allelic variants are present in the data, but encoded to appear on separate, consecutive lines. The data are reported in following versions - unphased, phased, phased with imputation, sites only. Note: the unphased version has additional genotype information, while the phased versions only contain the genotypes.		1
EGAD00001008730	Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 34 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected on the first, third and/or fifth day following ICU admission. RNA was extracted from leukocytes isolated at the bedside using LeukoLOCK kits. We have previously identified sepsis response signatures (SRSs), transcriptomic endotypes that are associated with differential early mortality (Davenport et al, Lancet Respir Med, 2016; Burnham et al, AJRCCM, 2017) and response to treatment in a clinical trial (Antcliffe et al, AJRCCM, 2018). We generated RNA sequencing data on 903 samples, including 134 samples repeated from our previously released microarray data. Libraries were prepared using NEB Ultra II Library Prep kits (Illumina) and sequenced on a NovaSeq 6000. Reads were aligned to the reference genome (GRCh38) using STAR and gene counts quantified using featureCounts (annotation Ensembl v99). Counts were TMM-normalised and log-transformed. Following QC, processed data were available on 864 samples from 667 unique patients.	Illumina NovaSeq 6000	909
EGAD00001008736	This data set contains whole exome sequences of individuals from 8086 (mostly British Pakistani/British Bangladeshi, mostly self-reported parentally related) individuals from the following studies: 1. 5236 British Pakistani/British Bangladeshi adults from East London Genes & Health, now known as Genes & Health 2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani) 3. 1061 British South Asian adults from Birmingham (mostly Pakistani) This dataset contains all the exome sequence data available for this study on 2022-04-26		1
EGAD00001009005	Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.	HiSeq X Ten Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	15
EGAD00001009161	Children with ALL treated with anti-CD19 therapy occasionally develop a phenotypically distinct AML. However, the precise clonal origin of such class switch leukemias remains unresolved. Here, we reconstructed the evolution of leukemia in a child with primary ALL, two ALL relapses and AML after treatment with anti-CD19 CAR-T and blinatumomab through whole-genome sequencing. The phylogeny revealed that the AML was a monoclonal outgrowth descending from the initial ALL and harbored biallelic loss of CDKN2A, PAX5 and TP53. However, none of the ALL or AML relapses directly descended from one another, suggesting the presence of a reservoir of persistent clones. Our findings suggest anti-CD19 treatment selects pre-existing clones, with many key genetic alterations underpinning the lineage switch detectable prior to treatment.	Illumina NovaSeq 6000	8
EGAD00001009304	Genomic profiling at diagnosis of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification and treatment decisions. Patients for which diagnostic screening fails to identify disease defining or risk stratifying lesions are classified as B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) on paired tumor-normal samples. For 52 B-other patients we compared WGS findings to data from clinical and research cytogenetics. WGS identifies a cancer associated event in 51/52 cases, this includes an established subtype defining genetic alteration in 5/52 that were previously missed by standard-of-care genetics. Of the 47 true B-other ALL we identified a recurrent driver in 87% (41). Complex karyotype by cytogenetics emerges as a heterogeneous group, underlied by distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r, IGK::BCL2). For a subset of 31 cases, we integrate findings from RNA-sequencing (RNA-seq) analysis to include fusion gene detection, and classification by gene expression. Compared to RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes, however RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrate that WGS can identify clinically relevant genetic abnormalities missed by standard-of-care testing and identify leukemia driver events in virtually all cases of B-other ALL.	HiSeq X Ten	115
EGAD00001009305	Genomic profiling at diagnosis of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification and treatment decisions. Patients for which diagnostic screening fails to identify disease defining or risk stratifying lesions are classified as B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) on paired tumor-normal samples. For 52 B-other patients we compared WGS findings to data from clinical and research cytogenetics. WGS identifies a cancer associated event in 51/52 cases, this includes an established subtype defining genetic alteration in 5/52 that were previously missed by standard-of-care genetics. Of the 47 true B-other ALL we identified a recurrent driver in 87% (41). Complex karyotype by cytogenetics emerges as a heterogeneous group, underlied by distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r, IGK::BCL2). For a subset of 31 cases, we integrate findings from RNA-sequencing (RNA-seq) analysis to include fusion gene detection, and classification by gene expression. Compared to RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes, however RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrate that WGS can identify clinically relevant genetic abnormalities missed by standard-of-care testing and identify leukemia driver events in virtually all cases of B-other ALL.	Illumina HiSeq 4000	33
EGAD00001009386	Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10551	Illumina NovaSeq 6000	28
EGAD00001009387	Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10570	Illumina NovaSeq 6000	8
EGAD00001009388	Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-11708	Illumina NovaSeq 6000	4
EGAD00001009773	116,958 single-cell transcriptomes from samples of peripheral blood mononuclear cells (PBMCs) from five CVID patients at three distinct stages of the SARS-CoV-2 infection: 1) baseline, before viral infection, 2) progression, during viral infection, and 3) convalescence, once the viral infection had been resolved and the patient was PCR negative. CVID patients were under regular immunoglobulin replacement therapy and displayed only mild symptoms during SARS-CoV-2 infection.	Illumina NovaSeq 6000	12
EGAD00001009800	This dataset was used to compare gene expression profiles of ex vivo isolated classical CD14+ monocytes from patients with moderate COVID-19 to those of healthy individuals. Blood samples were taken from patients with moderate COVID-19 admitted to hospitals in London (Hammersmith Hospital, Charing Cross Hospital, Saint Mary’s Hospital) 3-14 days after disease onset and 0-2 days after hospitalization and positive PCR, and before study treatment initiation. Moderate patients displayed mild or moderate COVID-19 pneumonia, defined as grade 3 or 4 WHO severity. Samples were collected from March 2020 to February 2021. Healthy donors were Imperial College staff with no prior diagnosis of or recent symptoms consistent with COVID-19, and where possible, were matched in age and sex distribution with COVID-19 patients. None of the participants of this study were COVID-19 vaccinated. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll Hypaque (GE Healthcare) gradient centrifugation <4 hours after blood collection. CD14+ monocytes were isolated using a positive selection magnetic sorting kit (StemCell Technologies, UK) from total PBMC and stimulated with vehicle, UV-inactivated SARS-CoV-2 (CoV-2). RNA was isolated using the RNeasy Micro Plus Kit (QIAGEN) following the manufacturer’s guidelines. RNA-sequencing was performed by the Oxford Genomics Centre. PolyA-enriched strand- specific libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits (Illumina). All samples were pooled together and 150bp PE reads were sequenced on a Novaseq 6000 system.	Illumina NovaSeq 6000	42
EGAD00001009801	The primitive streak emerges during the 14th day of human development and establishes dorsoventral and antero-posterior (craniocaudal) body axes. Segmentation along the craniocaudal axis is governed by Hox genes; four clusters of transcription factors whose 3’ to 5’ expression correlates with position along the axis. The precise utilisation of Hox genes in different cell types remains incompletely characterised in humans. In this study, we applied single-cell and spatial transcriptomics to contiguous regions of the human fetal spine between the 5th and 13th post-conception weeks. We built a detailed developmental atlas to examine the segmental expression of Hox genes across different cell types, observing that the Hox code was displayed by all anatomically fixed cell types along the craniocaudal axis. By contrast, mature derivatives of neural crest cells retained the anatomical Hox code of their origin within the crest, a pattern reproduced across neural crest derivatives in other human fetal organs. These findings indicate that scars of Hox gene expression persist in crest cells which may serve as barcodes of neural crest migration.	Illumina NovaSeq 6000	1
EGAD00001009851	A collection of four induced pluripotent stem cell models (iPSC) derived from patients diagnosed with Spinocerebellar ataxia 15 (SCA15) . Spinocerebellar ataxia 15 (SCA15) is a neurological condition characterised by progressive gait and limb ataxia as well as abnormalities in eye movement and difficulties with balance, speech and swallowing (Synofzik et al., 2011). Whole Genome Sequencing was performed to confirm the presence of a heterozygous deletions in the inositol 1,4,5-triphosphate receptor gene (ITPR1), characteristic of the disease. Cell models names: HPSI0216i-vieg_5 or Vieg_5 (WTSIi472-A), HPSI0216i-vieg_3 or Vieg_3 (WTSIi472-B), HPSI0216i-dacv_6 or Dacv_6 (WTSIi554-A), HPSI0216i-boho_3 or Boho_3 (WTSIi502-A). All iPSC models are available via ECACC-Culture Collections.	Illumina NovaSeq 6000	1
EGAD00001010017	This dataset is part of a study that aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. This specific dataset includes scRNA-seq and snRNA-seq data from trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) together with EVT differentiation media. This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells. Data for primary trophoblast organoids is available under E-MTAB-12650.	Illumina NovaSeq 6000	6
EGAD00001010037	This dataset is part of a study that aims to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. This dataset contains snucRNAseq; from three human implantation sites (between 8 and 12 post-conceptional weeks, PCW) from medical hysterectomies.	Illumina NovaSeq 6000	11
EGAD00001010038	This dataset is part of a study that aims to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. This dataset contains 10x multiome snRNA-seq/snATAC-seq from human implantation sites, decidual and placental samples from 8-9 PCW.	Illumina NovaSeq 6000	6
EGAD00001010050	Dataset includes 1) RNAseq for Bob_Ngn2 cell differentiation from iPSC to iNeuron stage (time point 0, 24, 48 and 96 hours). 2) Bob_Ngn2 cell line chip-seq (H3K4me3, H3K4me1, H3K27me3, H3K9me3, H3K27ac, H3K36me3) for both iPSC and iNeuron stage with 3 replicates at each time point. 3) Single cell CRISPR activation experiment with 96 endogenous genes.	Illumina HiSeq 4000 Illumina NovaSeq 6000	38
EGAD00001010126	Melanoma is the most aggressive type of skin cancer, causing about 75% of dermatological cancer deaths. Acral lentiginous melanoma (ALM) is the most common subtype of melanoma in admixed Latin American populations, but very few tumour genomes and exomes, all from European-descent individuals, have been analysed across several studies. Because of this, the genomic landscape of ALM is mostly unknown. Our aim in this project is to define this landscape and identify driver somatic alterations by whole-exome sequencing a collection of ALM germline/tumour paired FFPE samples from the National Cancer Institute of Mexico. . This dataset contains all the data available for this study on 2023-03-09.	Illumina HiSeq 4000	1
EGAD00001010298	One of the most dangerous forms of DNA damage are interstrand crosslinks (ICLs), which covalently crosslink the two strands of the DNA double helix. The repair of these lesions is crucial for cellular survival due to their ability to block transcription and DNA replication. Initially, the major pathway that has been described in ICL repair involves a network of 22 genes that are mutated in a severe human genetic disease known as Fanconi Anemia (FA). Using synthetic lethality screens in the near-haploid human HAP1 cell line, we recently identified two potentially novel regulators of ICL repair, C1orf112 and THAP12. Loss of C1orf112 and THAP12 causes hypersensitivity to ICL-inducing DNA damaging agents, such as Mitomycin C (MMC). Additionally, C1orf112-depleted cells show elevated levels of micronuclei and accumulation of DNA damage in S-phase. To better understand how C1orf112 and THAP12 mediate the repair of ICLs, we want to perform mutational signature analysis, using the BotSeq method. Therefore, WT, C1orf112 and THAP12 knockout cells were cultured in vehicle or MMC treated conditions for 10 days and the genomic DNA was isolated. FANCA and FANCD2 knockout cells are taken along as controls in this experimental setting. . This dataset contains all the data available for this study on 2023-04-20.		18
EGAD00001011131	This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.	Illumina NovaSeq 6000	376
EGAD00001011265	Data from sequencing of microbiopsies of keratinocytes isolated via laser capture microscopy from lesional and non-lesonal skin biopsies from psoriasis patients.	Illumina NovaSeq 6000	1211
EGAD00001011379	HLA sequence data and final calls for VaccGene and 1000Gp3 African populations		1
EGAD00001011815	Primary sclerosing cholangitis (PSC) is a T-cell mediated, chronic inflammatory condition of the biliary tree that is strongly associated with inflammatory bowel disease. Genome-wide association studies have identified 22 non-HLA genetic risk variants associated PSC. Identifying the genes impacted by these variants has proven difficult as the majority lie in non-coding regions of the genome. Knowledge of the genes and biological pathways these non-coding variants are perturbing is vital to understanding the disease biology. One means of assessing the impact of non-coding variants within disease associated loci upon genes is via colocalisation with eQTL. Many eQTL are cell-type specific, requiring the analysis of disease relevant cell types to detect colocalisation. We have collected PSC-relevant T-cell-subtypes from the peripheral blood of PSC patients via fluorescence activated cell sorting in preparation for RNA sequencing and mapping of eQTL. Samples were collected at the Norfolk and Norwich University Hopital, for which local ethical approval has been granted. Lysed cell samples will be transferred to WTSI and DNA/RNA will be extracted from lysed cell samples by T143 before genotyping (DNA) and custom library preparation and sequencing (RNA). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 2500	12
EGAD00001012227	Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection.	Illumina NovaSeq 6000	1
EGAD00001015345	In this study, we investigate differences in the cellular landscape and functionality of ex vivo cultured nasal epithelial cells in response to SARS-CoV-2 infection across different age groups: paediatric (<12y), adult (30-50y), and older adults (>70y). We unravel, that while ciliated cells serve as primary sites for viral replication consistently across all age groups, a distinctive goblet inflammatory subtype emerges in infected paediatric cultures, characterized by heightened expression of interferon-stimulated genes and incomplete viral replication. Conversely, older adult cultures infected with SARS-CoV-2 exhibit a proportional surge in basaloid-like cells, which not only facilitate viral dissemination but also demonstrate associations with altered epithelial repair pathways.	Illumina NovaSeq 6000	17
EGAD00001015367	Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract DNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted DNA will be used for exome sequencing.	Illumina HiSeq 4000 Illumina NovaSeq 6000	156
EGAD00001015368	Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract RNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted RNA will be used for RNA sequencing.	Illumina NovaSeq 6000	1
EGAD00001015369	This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 35 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected over the first five days of ICU admission to investigate how host genetics affects the individual repsonse to sepsis. DNA was extracted from buffy coat or whole blood samples using the Qiagen DNA extraction protocol, the automated Maxwell Blood purification kit (Promega), or the QIAamp Blood Midi kit protocol (Qiagen). Genotyping data were generated using the Illumina HumanOmniExpress BeadChip (295 patients), the Infinium CoreExome BeadChip (655 patients), and the Infinium Global Screening Array BeadChip (307 patients). Genotyping QC and imputation into the Haplotype Reference Consortium was perfomed within each batch. The datasets were combined and following post-imputation filtering data were available on 1168 samples.		1
EGAD00001015384	T cells develop from circulating precursor cells, which enter the thymus and migrate through specialised sub-compartments that support their maturation and selection. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the micro-anatomical underpinnings of this process in pre- and early postnatal stages, we established a novel quantitative morphological framework for the thymus, the Cortico-Medullary Axis, and used it to perform a spatially resolved analysis. By applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics, and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions within the first trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and uncover divergence in the timing of medullary entry between CD4 vs. CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation, and Organ Axis construction (TissueTag), which can be applied to any tissue.	Illumina NovaSeq 6000	-
EGAD00001015407	This is a study of 100 patients with the aim to provide transcriptomic sequencing data analysis of cells isolated from bronchioalveolar lavage and blood samples from critically ill patients with pneumonia on an intensive care unit in order to investigate the host contribution to disease. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/	Illumina HiSeq 4000	1
EGAD00010000124	Psoriasis cases as part of WTCCC2 phase 2	Illumina_670k - Illuminus	2622
EGAD00010000150	WTCCC2 project samples from Ankylosing spondylitis Cohort	Illumina_670k - Illuminus	2005
EGAD00010000230	WTCCC2 samples from Hypertension Cohort	- Illuminus	2943
EGAD00010000232	WTCCC2 samples from Type 2 Diabetes Cohort	- Illuminus	2975
EGAD00010000234	WTCCC2 samples from 1958 British Birth Cohort	Illumina HumanExome-12v1_A-GenCall, zCall	12241
EGAD00010000236	WTCCC2 samples from Coronary Artery Disease Cohort	- Illuminus, GenoSNP	3125
EGAD00010000246	Coeliac disease cases and control samples. (1958BC samples excluded)	GenoSNP Illumina ImmunoBeadChip - Illuminus	10758
EGAD00010000248	1958BC control samples	GenoSNP Illumina ImmunoBeadChip - Illuminus	6812
EGAD00010000250	NBS control samples	GenoSNP Illumina ImmunoBeadChip - Illuminus	3030
EGAD00010000262	WTCCC2 project Schizophrenia (SP) samples	Affyemtrix 6.0 - CHIAMO	3019
EGAD00010000264	WTCCC2 project samples from Ischaemic Stroke Cohort	Illumina_670k - Illuminus	4205
EGAD00010000282	Pharmacogenomic response to Statins samples (Genotypes/Phenotypes)	Affymetrix 6.0 - CHIAMO	4134
EGAD00010000284	NBS control samples only (Hap300)	Illumina (Various)	2500
EGAD00010000286	All cases and controls (Hap550)		11950
EGAD00010000288	All cases and Finnish, Dutch, Italian control samples (Hap550)		6313
EGAD00010000290	NBS control samples only (Hap550)		2276
EGAD00010000292	All cases and Finnish, Dutch, Italian control samples (Hap300)		10339
EGAD00010000294	1958BC control samples only (Hap300)		2436
EGAD00010000296	1958BC control samples only (Hap550)		2224
EGAD00010000298	All cases and controls (Hap300)		13761
EGAD00010000506	WTCCC2 BO (Barretts oesophagus) samples	Illumina_670k-Illuminus	1991
EGAD00010000516	Samples from the Pomak Villages in Greece, Pomak isolate	HumanExome_12v1.1_A -GenCall, zCall	1046
EGAD00010000518	Samples from the Greek island of Crete, MANOLIS cohort	HumanExome_12v1.1_A -GenCall, zCall	1280
EGAD00010000522	Samples from the Greek island of Crete, MANOLIS cohort	HumanOmniExpress-12 v1.1 BeadChip-GenCall	1364
EGAD00010000564	HipSci - Healthy Normals - Expression Array - May 2014		120
EGAD00010000566	HipSci - Healthy Normals - Genotyping Array - May 2014		120
EGAD00010000568	HipSci - Healthy Normals - Methylation Array - May 2014		-
EGAD00010000584	WTCCC2 Glaucoma samples using Illumina 670k array	Illumina 670k (custom Illumina Human660W-Quad)	2765
EGAD00010000594	SCOOP severe early-onset obesity cases		1720
EGAD00010000602	WTCCC2 Reading and Mathematics ability (RM) samples from UK using the Affymetrix 6.0 array		3665
EGAD00010000610	Samples from the Greek island of Crete, MANOLIS cohort		221
EGAD00010000628	The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica.		1
EGAD00010000630	The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica.		436
EGAD00010000632	WTCCC2 People of the British Isles (POBI) samples using Illumina 1.2M array		2912
EGAD00010000634	WTCCC2 People of the British Isles (POBI) samples using Affymetrix 6.0 array		2930
EGAD00010000636	WTCCC2 Visceral Leishmaniasis samples from Brazil using Illumina 670k	0	1
EGAD00010000638	WTCCC2 Visceral Leishmaniasis samples from Indial using Illumina 670k	0	1
EGAD00010000640	WTCCC2 Visceral Leishmaniasis samples from Sudanl using Illumina 670k	0	1
EGAD00010000650	Genotypes from Omni2.5 chip		1213
EGAD00010000664	Finnish population cohort genotyping_B		-
EGAD00010000722	Pilot experiment on functional genomics in osteoarthritis (coreex)		1
EGAD00010000724	Pilot experiment on functional genomics in osteoarthritis (methyl)		-
EGAD00010000730	WTCCC2 Psychosis Endophenotype samples from UK, Germany, Holland, Spain and Australia using the Affymetrix 6.0 array		1
EGAD00010000740	Osteoarthritis cases genotyped on Illumina HumanOmniExpress from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.		674
EGAD00010000742	Subset 1 of osteoarthritis cases genotyped on Illumina610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.		5383
EGAD00010000744	Subset 2 of osteoarthritis cases genotyped on Illumina 610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with consent for osteoarthritis studies only.		2326
EGAD00010000766	We have established a mechanism for the collection of postal DNA samples from consenting National Joint Registry for England and Wales (NJR) patients and have carried out genotyping genome-wide in 903 patients with the condition Developmental Dysplasia of the Hip (DDH) on the Illumina CoreExome array		903
EGAD00010000768	Replication data for HipSci normal samples using both HumanCoreExome-12_v1 and HumanOmni2.5-8 BeadChips		-
EGAD00010000771	HipSci - Healthy Normals - Methylation Array - April 2015		-
EGAD00010000773	HipSci - Healthy Normals - Genotyping Array - November 2014	Illumina	580
EGAD00010000775	HipSci - Healthy Normals - Expression Array - November 2014	Illumina	580
EGAD00010000777	HipSci - Bardet-Biedl Syndrome - Genotyping Array - November 2014		-
EGAD00010000779	HipSci - Monogenic Diabetes - Genotyping Array - November 2014	Illumina	9
EGAD00010000781	HipSci - Bardet-Biedl Syndrome - Methylation Array - April 2015		-
EGAD00010000783	HipSci - Bardet-Biedl Syndrome - Expression Array - November 2014		-
EGAD00010000785	HipSci - Monogenic Diabetes - Expression Array - November 2014		-
EGAD00010000807	Illumina HumanCoreExome genotyping data from the British Society for Surgery of the Hand Genetics of Dupuytrenâ€™s Disease consortium (BSSH-GODD consortium) collection		4201
EGAD00010000817	HipSci - Monogenic Diabetes - Methylation Array - April 2015		-
EGAD00010000854	WTCCC3 UK maternal cases of pre-eclampsia	Illumina Human670-QuadCustom_v1	3980
EGAD00010000874	Understanding Society Sequenom genotypes	Sequenom	8590
EGAD00010000883	The ARGO-Larissa GWAS.	Illumina HumanCoreExome-24v1-0	859
EGAD00010000890	Understanding Society GWAS, all samples	Illumina HumanCoreExome-12v1-0	20926
EGAD00010000891	Understanding Society GWAS, samples that passed quality control	Illumina HumanCoreExome-12v1-0	19888
EGAD00010000901	Russian Tuberculosis samples using Affymetrix 6.0	Affymetrix Genome-Wide Human SNP Array 6.0 Genotypes	11937
EGAD00010000909	HipSci - Embryonic Stem Cells - Methylation Array - April 2016	Illumina	2
EGAD00010000910	HipSci - Embryonic Stem Cells - Expression Array - April 2016	Illumina	2
EGAD00010000911	HipSci - Embryonic Stem Cells - Genotyping Array - April 2016	Illumina	2
EGAD00010000918	Understanding Society GWAS, samples that passed quality control, imputed to UK10K + 1000 Genomes combined reference panel	Illumina HumanCoreExome-12v1-0 chip, UK10K + 1000 Genomes combined reference panel imputed	19888
EGAD00010000922	Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with broader consent.	Illumina HumanCoreExome-24v1-0	494
EGAD00010000923	Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with consent for osteoarthritis studies only.	Illumina HumanCoreExome-12v1-0	463
EGAD00010000924	Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with consent for osteoarthritis studies only.	Illumina HumanCoreExome-12v1-1	991
EGAD00010000925	Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with broader consent.	Illumina HumanCoreExome-12v1-0	855
EGAD00010000926	Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with broader consent.	Illumina HumanCoreExome-12v1-1	3075
EGAD00010000927	Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with consent for osteoarthritis studies only.	Illumina HumanCoreExome-24v1-0	248
EGAD00010000928	WTCCC3_Primary Biliary Cirrhosis Replication Post-QC	Illumina ImmunoChip	2861
EGAD00010000929	WTCCC3_Primary Biliary Cirrhosis Replication	Illumina ImmunoChip	2981
EGAD00010000950	WTCCC2 Bacteraemia Susceptibility (BS) smaples using Affymetrix 6.0	Affymetrix 6.0	4924
EGAD00010001004	WTCCC1 project samples from 1958 British Birth Cohort	Infinium 550K	1504
EGAD00010001005	Illumina HumanCoreExome-12v1-1_A chip typing in a Greek adolescent population	Illumina Human Core Exome 12v1.1	120
EGAD00010001034	WTCCC3 Anorexia Nervosa GWAS	Illumina Human670-QuadCustom_v1_A	1696
EGAD00010001040	Methylation changes in OA patients with chronic exposure to cobalt and chromium	Illumina HumanMethylation450	68
EGAD00010001043	WTCCC3 Anorexia Nervosa Infinium-HumanCoreExome	Illumina HumanCoreExome-12v1-0_A and HumanCoreExome-24v1-0_A	925
EGAD00010001101	Genotype data from Chad, Lebanon, and Yemen	Illumina HumanOmni2.5-8 v1.1 B	-
EGAD00010001102	Genotype data from Chad, Lebanon, and Yemen	Illumina HumanOmni2.5-8 v1.2 A	-
EGAD00010001103	Genotype data from Chad, Lebanon, and Yemen	Illumina HumanOmni2.5-8 v1.1 B	-
EGAD00010001139	HipSci - Healthy Normals - Methylation Array - October 2016	Illumina	181
EGAD00010001143	HipSci - Healthy Normals - Expression Array - September 2016	Illumina	613
EGAD00010001145	HipSci - Bardet-Biedl Syndrome - Methylation Array - October 2016	Illumina	45
EGAD00010001147	HipSci - Healthy Normals - Genotyping Array - September 2016	Illumina	613
EGAD00010001149	HipSci - Monogenic Diebetes - Methylation Array - October 2016	Illumina	35
EGAD00010001157	Genotyping of additional Inflammatory Bowel Disease cases - 2014 (QC pass samples)	Illumina Human Core Exome 12v1-1_a	9247
EGAD00010001158	Genotyping of additional Inflammatory Bowel Disease cases - 2014 (all samples)	Illumina Human Core Exome 12v1-1_a	11767
EGAD00010001211	Inverse variance weighted fixed effect meta-analysis of three European GWAS studies of the offspring of Pre-eclampsia affected births (2658 Cases and 308267 Controls).		-
EGAD00010001212	Genetic studies of pregnancy-related cardiometabolic disorders in Central Asian, Northern European, and Colombian populations	Illumina HumanOmniExpress-12v1_J	-
EGAD00010001216	Melanoma cell lines CNV by SNP6	SNP6	22
EGAD00010001221	Illumina Omni 2.5M SNPchip data (build37) of Ethiopian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)	Illumina HumanOmni2-5_8v1_A	124
EGAD00010001223	Illumina Omni 2.5M SNPchip data (build37) of Egyptian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)	Illumina HumanOmni2-5M-8v1-1_B	100
EGAD00010001285	Genotyping of knee osteoarthritis patients who have undergone total joint replacement	Illumina InfiniumCoreExome-24v1-1_A	17
EGAD00010001287	Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement	Illumina HumanMethylation450K	68
EGAD00010001289	Resolving the Genetic Architecture of Aseptic Loosening After Total Hip Replacement	Illumina InfiniumCoreExome-24v1-1_A	2880
EGAD00010001291	Methylation profiling of hip osteoarthritis patients who have undergone total joint replacement	Illumina HumanMethylation450K	27
EGAD00010001292	Genotyping of hip osteoarthritis patients who have undergone total joint replacement	Illumina InfiniumCoreExome-24v1-1_A	9
EGAD00010001326	Papuan Genotyping	Illumina Multi-EthnicGlobal_A1	380
EGAD00010001328	HipSci - Healthy Normals - Genotyping Array - July 2017	Illumina	-
EGAD00010001330	HipSci - Healthy Normals - Expression Array - July 2017	Illumina	1
EGAD00010001332	HipSci - Bardet-Biedl Syndrome - Genotyping Array - July 2017	Illumina	1
EGAD00010001334	HipSci - Monogenic Diabetes - Genotyping Array - July 2017	Illumina	1
EGAD00010001340	HipSci - Bardet-Biedl Syndrome - Expression Array - July 2017	Illumina	1
EGAD00010001342	HipSci - Monogenic Diabetes - Expression Array - July 2017	Illumina	1
EGAD00010001344	HipSci - Hereditary Cerebellar Ataxias - Genotyping Array - July 2017	Illumina	1
EGAD00010001346	HipSci - Hereditary Spastic Paraplegia - Genotyping Array - July 2017	Illumina	1
EGAD00010001348	HipSci - Kabuki Syndrome - Genotyping Array - July 2017	Illumina	1
EGAD00010001350	HipSci - Usher Syndrome - Genotyping Array - July 2017	Illumina	1
EGAD00010001352	HipSci - Alport Syndrome - Genotyping Array - July 2017	Illumina	1
EGAD00010001354	HipSci - Congenital Hyperinsulinia - Genotyping Array - July 2017	Illumina	1
EGAD00010001356	HipSci - Hypertrophic Cardiomyopathy - Genotyping Array - July 2017	Illumina	1
EGAD00010001358	HipSci - Primary Immune Deficiency - Genotyping Array - July 2017	Illumina	23
EGAD00010001360	HipSci - Bleeding and Platelet Disorders - Genotyping Array - July 2017	Illumina	1
EGAD00010001362	HipSci - Macular Dystrophy - Genotyping Array - July 2017	Illumina	1
EGAD00010001364	HipSci - Retinitis Pigmentosa - Genotyping Array - July 2017	Illumina	1
EGAD00010001366	HipSci - Battens Disease - Genotyping Array - July 2017	Illumina	1
EGAD00010001368	HipSci - Hereditary Cerebellar Ataxias - Expression Array - July 2017	Illumina	1
EGAD00010001370	HipSci - Hereditary Spastic Paraplegia - Expression Array - July 2017	Illumina	1
EGAD00010001372	HipSci - Kabuki Syndrome - Expression Array - July 2017	Illumina	1
EGAD00010001374	HipSci - Usher Syndrome - Expression Array - July 2017	Illumina	1
EGAD00010001376	HipSci - Alport Syndrome - Expression Array - July 2017	Illumina	1
EGAD00010001378	HipSci - Congenital Hyperinsulinia - Expression Array - July 2017	Illumina	1
EGAD00010001380	HipSci - Hypertrophic Cardiomyopathy - Expression Array - July 2017	Illumina	1
EGAD00010001382	HipSci - Primary Immune Deficiency - Expression Array - July 2017	Illumina	1
EGAD00010001384	HipSci - Bleeding and Platelet Disorders - Expression Array - July 2017	Illumina	1
EGAD00010001386	HipSci - Macular Dystrophy - Expression Array - July 2017	Illumina	1
EGAD00010001388	HipSci - Retinitis Pigmentosa - Expression Array - July 2017	Illumina	1
EGAD00010001390	HipSci - Battens Disease - Expression Array - July 2017	Illumina	1
EGAD00010001470	Himalayan population genetic study raw data (Himalaya)	Illumina HumanOmniExpress-12-v1-0	170
EGAD00010001471	Himalayan population genetic study QC filtered data	Illumina HumanOmni1-Quad_v1-0, HumanOmniExpress-12-v1-0, humanomniexpress-24-v1-1, HumanOmni25-8v1-2_A1	738
EGAD00010001472	Himalayan population genetic study raw data (Himalaya)	Illumina HumanOmni1-Quad_v1-0	565
EGAD00010001473	Himalayan population genetic study raw data (Tibet)	Illumina humanomniexpress-24-v1-1	148
EGAD00010001484	Genetic Overlap between Metabolic and Psychiatric disease	Illumina HumanCoreExome-12v1-0	2611
EGAD00010001521	Bisulfite Converted DNA obtained from Whole Blood analysed on IlluminaHumanMethylationEPIC BeadChip microarrays processed with bigmelon R package	IlluminaHumanMethylationEPIC	1175
EGAD00010001622	Human Core Exome Genotyping for 1471 samples from the STudy Into Lean and Thin Subjects (STILTS) cohort	Illumina humancoreexome-12v1-1_a	1471
EGAD00010001623	Human Core Exome Genotyping for 1456 severe early onset obesity cases (SCOOP)	Illumina humancoreexome-12v1-1_a	1456
EGAD00010001624	Genetics of thinness compared to obesity - summary statistics	Illumina humancoreexome-12v1-1_a	2927
EGAD00010001717	This is the affymetrix gene expression data of the metastatic tumours related to this study.	Human Clariom D Arrays	11
EGAD00010001746	Functional genomics approaches to understand osteoarthritis	Illumina HumanCoreExome-24v1-1	77
EGAD00010001848	Genotype data obtained using the coreExome Illumina SNP chip array for all the individuals included in the study of gene expression regulation in human primary regulatory CD4+ T cells (Tregs)	coreExome Illumina SNP chip array	120
EGAD00010001867	Yemen and Chad Genotyping	Unknown HumanOmni25-8v1-2	1
EGAD00010001868	Yemen and Chad Genotyping	Unknown HumanOmni25-8v1-2_A1	258
EGAD00010001870	Lebanon_Genotyping	Unknown HumanOmni25M-8v1-1	126
EGAD00010001917	GWAS genotype data for maternal and fetal (baby) cases of preeclampsia and controls from Uzbekistan. This dataset is a component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium members in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology	Unknown HumanOmni25M-8v1-1	180
EGAD00010001918	GWAS genotype data for maternal and fetal (baby) cases of preeclampsia and controls from Uzbekistan. This dataset is a component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium members in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology	Unknown HumanOmni2-5-8-v1-1-C	2658
EGAD00010001919	GWAS genotype data for maternal and fetal (baby) cases of preeclampsia and controls from Uzbekistan. This dataset is a component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium members in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology	Unknown HumanOmni25-8v1-1	58
EGAD00010001945	Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes lllumina 2.5-8 genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).	llumina 2.5-8	3004
EGAD00010001947	Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes OmniExpress genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).	OmniExpress	2305
EGAD00010001949	Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes Infinium GSA genotyping of maternal, paternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).	Infinium GSA	2321
EGAD00010001983	Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Europe (UK, Iceland, Norway, and Denmark) and Central Asia (Kazakhstan and Uzbekistan).		4
EGAD00010001984	Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Europe (UK, Iceland, Norway, Denmark and Finland).		12
EGAD00010001985	Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).		4
EGAD00010001986	Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Europe (UK, Iceland, Norway, and Denmark).		10
EGAD00010001987	Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).		4
EGAD00010001988	Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Europe (UK, Iceland, Norway, Denmark and Finland) and Central Asia (Kazakhstan and Uzbekistan).		4
EGAD00010002291	Blood samples were obtained from 119 healthy individuals of British ancestry. Genomic DNA was isolated from a suspension of PBMCs from each individual using a DNA isolation kit (Qiagen). Genotyping was then performed using the Infinium CoreExome-24 (v1.3) chip (Illumina).	Infinium CoreExome-24 (v1.3) chip (Illumina)	127
EGAD00010002577	VaccGene HLA imputation panel variants and HLA allele calls for all individuals across all tested sequence platforms and countries, and the high quality direct genotypes for these individuals (with genotype data available) across the MHC in PLINK format	Illumina HumanOmni25M-8v1-1	2499
EGAD00010002578	Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 1391 individuals from EMaBS in Entebbe, Uganda.	Illumina HumanOmni25-8v1-1	1391
EGAD00010002579	Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - X chromosome.	Illumina HumanOmni25M-8v1-1	353
EGAD00010002580	Genotype data and (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 750 individuals from Respiratory and Meningeal Pathogens Unit in Soweto, South Africa - X chromosome.	Illumina HumanOmni25M-8v1-1	755
EGAD00010002581	Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - autosomes.	Illumina HumanOmni25M-8v1-1	353
EGAD00010002582	Genotype data and (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 750 individuals from Respiratory and Meningeal Pathogens Unit in Soweto, South Africa - autosomes.	Illumina HumanOmni25M-8v1-1	755
EGAD00010002583	Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 1391 individuals from EMaBS in Entebbe, Uganda - X chromosome.	Illumina HumanOmni25-8v1-1	1391
EGAD00010002633	Genetic characterisation of primary sclerosing cholangitis	Illumina Omni2.5-8Exome BeadChip	1