9337 results for "cancer rna-seq"

in 59.58 milliseconds.

• Targeted sequencing data of breast tumors with germline BRCA1/2 mutations

  This dataset contains targeted sequencing of breast tumors with germline BRCA1/2 mutations (n = 30) and those without. Breast cancer related genes (n = 115) have been captured and sequenced.

  Dataset EGAD00001005802

• sWGS for genome-wide copy number profiling

  Shallow whole-genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of metastatic colorectal cancer patients (mCRC).

  Dataset EGAD00001006384

• Rucaparib in patients presenting a metastatic breast cancer

  Whole genome sequencing was performed on 24 patients (tumor DNA paired to constitutional DNA). WGS libraries were subjected to paired-end (2 x 100 bp) sequencing on NovaSeq (Illumina). The 96 files are in FASTQ format.

  Dataset EGAD00001006458

• Exploring the extracellular transcriptome in seminal plasma for non-invasive prostate cancer diagnosis

  mRNA capture sequencing data of 57 seminal plasma samples.

  Dataset EGAD00001007688

• High-resolution analysis for urinary DNA jagged ends

  consists 17 cases, 7 control cases and 10 cancer cases.

  Dataset EGAD00001008594

• Dataset for synovial_sarcoma-WHOLE_GENOME

  Rare cancer sequencing data of 6 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008899

• 10x Genomics Single Cell Gene Expression for SA535X6XB03099

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 6

  Dataset EGAD00001009116

• 10x Genomics Single Cell Gene Expression for SA535X4XB05462

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 4

  Dataset EGAD00001009115

• 10x Genomics Single Cell Gene Expression for SA1035X6XB03211

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 6

  Dataset EGAD00001009150

• 10x Genomics Single Cell Gene Expression for SA1035X7XB03502

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 7

  Dataset EGAD00001009151

• 10x Genomics Single Cell Gene Expression for SA1035X6XB03216

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 6

  Dataset EGAD00001009154

• 10x Genomics Single Cell Gene Expression for SA535X5XB02895

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 5

  Dataset EGAD00001009156

• 10x Genomics Single Cell Gene Expression for SA604X9XB02425

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 9

  Dataset EGAD00001009159

• Single Cell Genome Sequence for DLP+ library A96130A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA609 passage 8 on DLP+ library A96130A

  Dataset EGAD00001009454

• Single Cell Genome Sequence for DLP+ library A96161A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96161A

  Dataset EGAD00001009457

• Single Cell Genome Sequence for DLP+ library A96175A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 7 on DLP+ library A96175A

  Dataset EGAD00001009461

• Single Cell Genome Sequence for DLP+ library A96180A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 6 on DLP+ library A96180A

  Dataset EGAD00001009463

• Single Cell Genome Sequence for DLP+ library A98240A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA530 passage 3 on DLP+ library A98240A

  Dataset EGAD00001009480

• Organoid Derivation Project: WGS (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011090

• Sequencing data for oesophageal samples - Killcoyne, Gregson et al (sWGS)

  Data supporting: "Genomic copy number predicts esophageal cancer years before transformation." Killcoyne, Gregson et al. sWGS data 1000 samples BAM files

  Dataset EGAD00001006033

• Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor patient

  Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015291

• The University of Hong Kong Gastric Cancer XClone Study Single Cell CNV Data

  Single cell encapsulation and DNA libraries were prepared by Chromium™ Single Cell DNA Reagent Kits and Chromium™ Single Cell C and D Chip Kits.

  Dataset EGAD00001015383

• Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer

  This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female.

  Study phs001863

• Translating Gene-Calcium Interactions to Precision Medicine for Colorectal Cancer

  Identify functional and rare SNPs and their interactions with Ca intake levels in relation to risk of incident adenoma using whole-exome resequencing of 2468 colorectal adenoma cases and controls from PLCO. We will genotype promising rare and functional SNPs associated with incident adenoma in 570 incident cancer cases, 1,710 healthy controls, 710 adenoma recurrence cases and 966 recurrent adenoma controls from the intervention arm of PLCO to both confirm the associations with adenoma, and to identify when, in the natural history of CRC, chemoprevention by Ca-gene interactions occurs. We hypothesize that Ca-gene interactions prevent early-stage (incident adenoma) and mid-stage (adenoma recurrence) carcinogenesis as well as span the entire CRC carcinogenesis spectrum (i.e. incident CRC).

  Study phs002164

• CIDR Estrogen Receptor Negative Breast Cancer in African American Women: DNA Methylation, Reproductive Events, and Mammary Epithelial Cell Populations

  We conducted methylation profiling of breast tumor DNA from Formalin-Fixed Paraffin-Embedded (FFPE) samples for 1,550 cases from a cohort of Black women from the Black Women’s Health Study (BWHS), the Women’s Circle of Health Study (WCHS), and from the Pathways Study using the Illumina MethylationEPIC array. We will examine differentially methylated loci (DML) between ER+ and ER- tumors, and by age at onset of breast cancer. Combining these data with previously analyzed samples (n=385), we will consider associations between reproductive risk factors and top DML by age at diagnosis and ER status, examining the complex relationships between methylation, tumor and patient characteristics, and reproductive risk factors using structural equation modeling.

  Study phs002688

• TGS___Comprehensive_Molecular_Characterization_of_Colorectal_Cancer_Metastases__MOSAIC_

  Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression.We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity.

  Study EGAS00001000958

• Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

  This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.

  Study EGAS00001006040

• Integrative analysis of small cell lung cancer

  Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype. We conducted integrated analysis of genome sequencing, transcriptome, and copy number analysis and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million basepairs. Evidence for inactivation of TP53 and RB1 was found in all sequenced cases. Furthermore, we identified recurrent mutations in CREBBP, EP300, and MLL, observed mutations in PTEN, in SLIT2, and EPHA7, as well as focal amplifications of the FGFR1 locus. As a major feature of SCLC we found mutation in histone modifying genes, observed genome alterations that are therapeutically tractable, and provide a framework for identifying biologically relevant genes in the context of a high mutation rate. Peifer et al., 2012, Nature Genetics.

  Study EGAS00001000299

• Clonal dominance defines metastatic dissemination in pancreatic cancer

  Using patient-derived cells from a pancreatic ductal adenocarcinoma, we created orthotopic clonal replica tumors to trace in an unbiased fashion clonal lineage dynamics of unperturbed tumor expansion and dissemination over time. The model revealed the complex multifaced nature of tumor clonal expansion and uncovered brisk changes in fitness that lead to a continuous reshuffling of tumor clonal architecture and alternating clonal dominance as a distinct feature of cancer growth. Paired analysis of clonal lineages in primary and secondary sites revealed fitness in the primary tumor as a major contributor to dissemination, although other clonal intrinsic and extrinsic factors may contribute to metastatic process. Molecular characterization of lineages with differential metastatic potential identified actionable strategy to suppress dissemination at the subclonal level.

  Study EGAS00001006358

• Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer

  Tumor mutational burden (TMB) has emerged as a predictive biomarker of response to immune checkpoint inhibitors. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Here we evaluate bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples. In CheckMate 026, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne CDx™ assay. TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can therefore impact TMB calculations, highlighting the need for standardization. Encouragingly, WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90) and differences could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms and centers is achievable.

  Dataset EGAD00001005035

• Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors.

  Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 58 HGSC tumours (53 primary tumours and 5 recurrent tumours) and 53 matched normals from 53 long-term survivor patients. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche) according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009398

• EPICC: Evolutionary Predictions in Colorectal Cancer

  ATAC-seq profiling bam files from colorectal carcinoma and adenoma.

  Dataset EGAD00001008140

• RNA Sequencing of Pulmonary Arterial Endothelial Cells in Pulmonary Hypertensive Patients and Controls

  The transcriptome of pulmonary arterial endothelial cells from healthy lungs and from lungs of patients with idiopathic pulmonary arterial hypertension have been analyzed and specific differences in disease-relevant pathways were identified. The genes identified as altered in these patients have direct effects on pulmonary arterial endothelial cell function. This finding may underlie the inability of the pulmonary vasculature to respond to and repair the damage observed in pulmonary hypertension.

  Study phs000998

• Airway Epithelial Cell Culture RNA Expression

  This study seeks to characterize airway epithelial mRNA and miRNA expression under a variety of experimental conditions. Samples are available from primary human cell cultures as well as cell lines grown under a variety of experimental conditions as documented in the phenotype and conditions associated with each individual sample. For some experiments, cells on plastic were exposed to cigarette smoke condensate to evaluate the effects of smoking. FOSL1 is a target gene for regulation by MIR34A family microRNAs.

  Study phs002472

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  To investigate the relationship between transcriptome profile and genetic background in a large series of adrenocortical tumors and to identify new potential pathogenetic mechanisms, we performed transcriptome profiling by high-throughput sequencing. We collected snap-frozen tissue from patients with adrenocortical tumors (n = 59) with known genetic background: 26 adenomas with Cushing syndrome, 17 adenomas with mild autonomous cortisol secretion, 9 endocrine-inactive adenomas, 7 adrenocortical carcinomas. Additionally, we sequenced 4 control samples.

  Study EGAS00001004533

• Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 45 low-risk myelodysplastic syndrome cases

  Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 45 low-risk myelodysplastic syndrome (LRMDS) cases. Gene expression profiles (GEPs) of the 45 LRMDS have been compared to GEPs derived from likewise highly purified mesenchymal cells obtained from bone marrow specimens of healthy donors for the identification of inflammatory signatures. Additionally, an overlap in inflammatory signatures has been determined by comparing the GEPs of these 45 LRMDS cases to the GEPs of 4 Shwachman-Diamond syndrome and 3 Diamond-Blackfan anemia cases, both representing different subclasses of congenital pre-leukemia syndromes with a tendency of leukemic progression and perturbed niche compartment. Finally, the GEPs and gene expression signatures have been utilized for prognostication and the prediction of leukemic progression.

  Dataset EGAD00001002658

• Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 10 healthy donors

  Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 10 healthy donors (HDs). This data set is used as a baseline control to observe the differences between gene expression profiles (GEPs) of pre-leukemia cases (45 low-risk myelodysplastic syndrome, 4 Shwachman-Diamond and 3 Diamond-Blackfan anemia patients) and gene expression patterns observed in a normal, healthy context. Through differential expression and gene set enrichment analysis we determined that inflammatory signaling pathways are significantly more active in mesenchymal cells of pre-leukemia cases compared to their healthy counterparts. Finally, we determined through statistical modelling of healthy donor's GEPs which pre-leukemia cases have significantly more active inflammatory signaling and demonstrated a strong relation to survival statistics.

  Dataset EGAD00001002659

• Genome-wide genotyping data and exome sequencing of 100 European-descent and 100 African-descent Belgians used in the EGAS00001001895 study

  We recruited 100 healthy, male donors of self-reported European descent (EUB) and 100 of self-reported African descent (AFB) (Ghent, Belgium). For each participant, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on Ficoll-Paque density gradients. Monocytes were then positively selected with magnetic CD14 microbeads and exposed for 6 hours to different ligands activating TLR4 (LPS), TLR1/2 (Pam3CSK4), TLR7/8 (R848) and to a human seasonal influenza A virus (IAV). High-quality RNA was obtained from unstimulated and stimulated monocytes for 970 of the 1000 samples (200 x 5 conditions), and was sequenced on an Illumina HiSeq2000. On average, 34 million 101-bp single-end reads were obtained per sample.

  Dataset EGAD00001002714

• The Transcriptional Landscape of SHH Medulloblastoma

  To further understand the biology of Sonic hedgehog medulloblastoma and its molecular subtypes, we studied 250 human Shh-MB using strand-specific RNA sequencing. We identified novel alterations within the cAMP dependent pathway and found that 18% of tumors have genetic events that directly target the abundance and/or stability of MYCN. We also discovered an extensive network of fusions in focally amplified regions, and several loss-of-function fusions in tumor suppressor genes PTCH, SUFU and NCOR1. Molecular convergence on a core of specific genes by nucleotide variants, copy number aberrations, and gene fusions highlights key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma.

  Dataset EGAD00001006305

• Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

  We investigated 10 female and 14 male SARS-CoV-2 positive children (age range: 0.8 to 18 years). Based on the WHO guidelines, 15 patients were classified as having mild COVID-19, while 7 children were classified as moderate COVID-19 cases. Two children were asymptomatic. 8 female and 10 male SARS-CoV-2 negative children were included as controls (age range: 4 to 16). 12 SARS-CoV-2 positive female and 9 male adults were included ( age range: 27 - 76) together with 13 female and 10 male SARS-CoV-2 negative adult controls (age: 24 - 77). 10 adult COVID-19 patients had mild disease, while 12 had moderate COVID-19. We performed single-cell RNA sequencing experiments.

  Dataset EGAD00001007969

• Fastq files for the single cell RNAseq data of Follicular lymphoma study

  Fastq files for the single cell RNAseq data of Follicular lymphoma study. This dataset includes the paired single cell RNA sequencing data for 23 samples.

  Dataset EGAD00001008595

• Blood Transcriptome Profiling Links Immunity to Disease Severity in Myotonic Dystrophy Type 1 (DM1)

  Here, we explore the molecular signatures in RNA sequencing data from blood associated with disease severity as measured in Myotonic dystrophy type 1 (DM1) patients with less than 400 CTG-repeat length size in the DMPK gene in blood. These DM1 patients participated in the OPTIMISTIC study. This approach involved stratifying those within the OPTIMISTIC study into different patient groups with different degrees of disease severity (as measured by the muscle-impairment rating scale (MIRS)) and assessed at baseline. Patients were divided into groups with mild (MIRS 1–2) and severe (MIRS 3–5) neuromuscular symptoms with different DMPK repeat length characteristics. Therefore these .Bam files are baseline samples from this study.

  Dataset EGAD00001010010

• Targetable NOTCH1 rearrangements in reninoma - RNA

  Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

  Dataset EGAD00001010889

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015377

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015379

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015378

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015376

• Genomic Profiling of Relapsed and Refractory Childhood Cancers

  Through clinical trials focused on molecularly guided therapy in pediatric cancers (NCT01355679, NCT01802567, NCT02162732), the Beat Childhood Cancer Consortium performed paired tumor/normal whole exome sequencing and/or tumor mRNA sequencing for 202 pediatric or adolescent young adult patients with rare, relapsed and refractory cancers (including neuroblastoma, Ewing sarcoma, osteosarcoma, rhabdomyosarcoma, ependymoma, glioma, and other rare solid tumors). A subset of these patients had multiple biopsies sequenced, including longitudinal profiling.

  Study phs002238

• Transcriptomic and Epigenetic Profiling of SCLC Patient Samples

  Small cell lung cancer (SCLC) is an aggressive disease with poor outcomes and limited treatment options. Recent studies have identified transcriptionally defined subsets of SCLC that may allow for the personalization of treatment. Here we use transcriptomic sequencing and methylation profiling (RRBS) of biopsy and cfDNA to develop a highly accurate DNA methylation-based classifier to distinguish SCLC subtypes. These results demonstrate the clinical feasibility of molecular subtyping of SCLC.

  Study phs003416

• Whole-exome sequencing of Helicobacter pylori-uninfected normal gastric gland

  Recent studies showed that somatic mutations accumulate in normal tissues with age; however, mutation accumulation in the Helicobacter pylori-uninfected normal gastric mucosa has not been reported. A total of 18 biopsied gastric mucosa were obtained from nine subjects without Helicobacter pylori-infection or gastric cancer. Gastric epithelia were manually dissociated from the lamina propria. Subsequently, single glands were picked up under a stereomicroscope. Genomic DNA isolated from each gland was subjected to whole-exome sequencing.

  Study JGAS000313

• Complex structural variation patterns in pediatric solid tumors

  In this study, we performed systematic characterization of chromoplexy, chromothripsis and extrachromosomal DNA across five types of pediatric solid tumors: neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma. Almost half of all tumors had at least one complex SV and we identified candidate pathogenic events that affect genes or chromosomal alterations known to be relevant in these cancer types. In conclusion, complex SVs are prevalent and highly pathogenic in pediatric solid tumors.

  Study EGAS00001007565

• Whole-genome sequencing analysis of low-grade astrocytomas within the ICGC PedBrain Tumor Project

  In order to investigate the full range of genetic alterations contributing to the tumourigenesis of low-grade astrocytoma, we have conducted a next-generation sequencing-based analysis on a large series of matched tumor-normal pairs. This study, conducted by the International Cancer Genome Consortium PedBrain Tumor Project (ICGC PedBrain, http://www.pedbraintumor.org/), has revealed multiple new insights into the biological basis of this tumor entity.

  Study EGAS00001000381

• Korean Young Age Diffuse Gastric Cancers

  The incidence of diffuse gastric cancers (DGC) remains steadily high, but relatively small numbers of DGCs have been evaluated with whole exome sequencing (WES). Clinicopathological features of DGC vary according to age, but the molecular basis for these variations is unclear. To identify genomic alteration in this unique subset of gastric cancers, whole exome and SNP6 analyses were performed using frozen cancer tissue. The same analyses were also performed using blood of the same patients.

  Study EGAS00001001711

• sWGS of Pap test smears from healthy donors and HGSOC patients and matched tumor tissue

  Shallow whole genome sequencing was performed on Pap test smears considering at least 10 M reads per sample. The cohort consists of 77 samples from healthy women, i.e. no tumor diagnosis, and 65 samples from women with a diagnosis of high-grade serous ovarian cancer (HGSOC) taken months or years before diagnosis. 44 primary tumor samples matched to the respective HGSOC patients were sequenced in the same manner as the Pap test smears.

  Study EGAS00001007084

• Whole-exome sequencing of ovarian clear cell carcinoma in clinical outliers

  Whole-exome sequencing dataset for the Australian Ovarian Cancer Study (AOCS) and The Jikei University School of Medicine (JIKEI) ovarian clear cell carcinoma (OCCC) clinical outliers project, representing 10 donors. Although OCCC are commonly resistant to platinum based chemotherapy, good clinical outcomes are observed in a subset of patients. Exome sequencing was performed in 10 patients who had either unusually long survival (N=5) or had a very short time to progression (N=5).

  Study EGAS00001004248

• Molecular subtypes of malignant peritoneal mesothelioma

  Malignant Peritoneal Mesothelioma (PeM) is a rare but frequently fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, and no targeted therapies for PeM yet exist. This study performs comprehensive integrative analysis of genome, transcriptome, and proteome of treatment-naive PeM tumors with the aim of identifying mesothelioma-related molecular alterations and potentially identifying novel treatment strategies.

  Study EGAS00001002820

• Identification of recurrent mutations in Cushing’s disease

  The overall goal of the Identification of recurrent mutations in Cushing’s disease project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices. The aims of Project are to implement and establish the feasibility of WES in patients with USP8 wild-type corticotroph adenomas; to develop a framework for understanding of the molecular mechanism of the pathogenesis of corticotroph adenoma.

  Study EGAS00001003029

• Whole-genome sequencing reveals genomic signatures associated with the inflammatory microenvironments in Chinese NSCLC patients

  Chinese lung cancer patients have distinct epidemiologic and genomic features, highlighting the presence of specific etiologic mechanisms other than smoking. We integrate genomic (whole-genome sequencing, WGS) and transcriptome (polyA-enriched RNASeq) sequencing from 92 NSCLC cases and comprehensively identified the distinct genomic features of Chinese NSCLC patients. We reveal that inflammatory infiltration may contribute to the accumulation of EGFR mutations, especially in never-smokers.

  Study EGAS00001002954

• DO NOT USE - Whole genome sequencing of SI-NETs from five patients

  Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several intestinal tumors centered around a regional lymph node metastasis, yet the typical path of evolution of these lesions remains unclear. Here, we determined the complete genome sequences of 37 tumors from 5 patients with multifocal SI-NET, allowing elucidation of phylogenetic relationships between multiple intestinal tumors and metastases in individual patients.

  Study EGAS00001004435

• UROMOL 2020 - SNP data

  The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we performed a large integrative multi-omics analysis of patients diagnosed with NMIBC (n=834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters.

  Study EGAS00001004862

• PELICAN45 RNAseq Dataset

  To better understand the biology of prostate cancer, we performed RNAseq in cancerous (primary and metastatic) and noncancerous tissues in the PELICAN45 cohort. The PELICAN45 RNAseq samples include androgen-deprived metastasis samples from the PELICAN33 consenting rapid autopsy study participants, whose identifiers are A1, A2, etc. The PELICAN45 RNAseq dataset also includes data from non-androgen deprived metastases in an additional 12 men. These samples are identified as PB50, PB133, etc.

  Study EGAS00001006959

• Lung cancer organoids

  Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term culture conditions of human airway epithelial organoids that contain all major cell populations and allow personalized human disease modelling. We collected macroscopically inconspicuous lung tissue from non-small-cell lung cancer (NSCLC) patients undergoing medically indicated surgery and isolated epithelial cells to engineer 3D organoids. We exploit the potential to derive sub-clones from AOs to demonstrate the feasibility of CRISPR gene editing. Finally, we show that AOs readily allow modelling of viral infections such as RSV and for the first time demonstrate the possibility to study neutrophil-epithelium interaction in an organoid model. Taken together, we anticipate that human AOs will find broad applications in the study of adult human airway epithelium in health and disease.

  Dataset EGAD00001004013

• Direct transcriptional consequences of somatic mutation in breast cancer

  The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation.

  Dataset EGAD00001002236

• Lung cancer organoids addition

  Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term culture conditions of human airway epithelial organoids that contain all major cell populations and allow personalized human disease modelling. We collected macroscopically inconspicuous lung tissue from non-small-cell lung cancer (NSCLC) patients undergoing medically indicated surgery and isolated epithelial cells to engineer 3D organoids. We exploit the potential to derive sub-clones from AOs to demonstrate the feasibility of CRISPR gene editing. Finally, we show that AOs readily allow modelling of viral infections such as RSV and for the first time demonstrate the possibility to study neutrophil-epithelium interaction in an organoid model. Taken together, we anticipate that human AOs will find broad applications in the study of adult human airway epithelium in health and disease.

  Dataset EGAD00001004943

• Somatic mutation and clonal evolution in premalignant lung disease - WGS (2020-01-15)

  Cancer is a genetic disease caused by an accumulations of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from the lung tissue of individuals with a variety of lung diseases (COPD, UIP, IPF, Emphysema, pulmonary hypertension). This will allow us to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. Smoking is a large risk factor for developing many of these lung diseases so we are particularly keen to determining whether there is evidence of a smoking signature in these patients. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005786

• Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

  This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.

  Dataset EGAD00001008589

• Lung cancer, healthy control and non-cancerous plasma cfDNA samples

  The dataset contains 106 lung cancer, 12 healthy control and 11 non-cancerous lesion plasma cfDNA sample. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001008321

• TGS - Comprehensive Molecular Characterization of Colorectal Cancer Metastases (2015-07-02)[MOSAIC]

  Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression. We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity. This dataset contains all the data available for this study on 2015-07-02.

  Dataset EGAD00001001426

• Detection of cancer cell transcriptomes

  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.

  Dataset EGAD00001009005

• Monotherapy Breast Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Dataset EGAD00001000349

• Whole genome sequence of liver cancers displaying biliary phenotype

  RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype

  Dataset EGAD00001000809

• EPITREAT extended cohort

  Data set of 22 tumor/normal pairs of non-small cell lung cancer (NSCLC) patients. All tissue pairs were screened with MeDIP methylation enrichment sequencing and validations were performed with targeted bisulfite re-sequencing.

  Dataset EGAD00001003944

• Whole genome sequencing of osteosarcoma from patients seen at UT MD Anderson Cancer Center.

  Whole genome sequencing of 35 osteosarcoma patients (primary, relapsed, and metastatic) with matched normals. Tumors were sequenced at target 60X and matched normals at target 30X.

  Dataset EGAD00001005389

• Bulk RNAseq fastq files

  RNAseq FASTq files from 15 samples from patients with ovarian cancer, 5 samples for each of the 3 tumor immune phenotypes (Infiltrated, Excluded and Desert).

  Dataset EGAD00001006975

• Lowpass whole genome sequencing of single circulating tumor cells (CTCs) in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Lowpass whole genome sequencing of 43 single CTCs and one tumor biopsy

  Dataset EGAD00001007700

• COIN_CRC_GWAS

  Genotype data of 1,950 individuals from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).

  Dataset EGAD00010002186

• Target pilot trial

  In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer

  Dataset EGAD00001008358

• Clinical data

  Clinical data from this cohort of patients, including hormone sensitive or castration resistant prostate cancer, overall survival, NMF subtypes, tumor TMB, prior treatment status, PD-L1 IC and TC scores from SP142 and SP263 as well as percentage of CD8 IHC at tumor center.

  Dataset EGAD00001008761

• Dataset for breast_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 12 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008867

• Dataset for cancer_of_unknown_primary-WHOLE_GENOME

  Rare cancer sequencing data of 46 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008869

• SA501X3F direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for third-passage patient-derived primary triple-negative breast cancer xenograft SA501X3F.

  Dataset EGAD00001003149

• SA501X4F direct library preparation (DLP) single-cell genomes

  Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for fourth-passage patient-derived primary triple-negative breast cancer xenograft SA501X4F.

  Dataset EGAD00001003150

• RNAseq - Colorectal organoids and tumoroids (2017-05-04)

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer This dataset contains all the data available for this study on 2017-05-04.

  Dataset EGAD00001003320

• 10x Genomics Single Cell Gene Expression for SA1035X5XB03021

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 5

  Dataset EGAD00001009153

• Single Cell Genome Sequence for DLP+ library A95618B

  Single Cell Genome Sequence for Triple negative breast cancer patient-derived xenograft SA609 passage 3 on DLP+ library A95618B

  Dataset EGAD00001009316

• Single Cell Genome Sequence for DLP+ library A96141A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96141A

  Dataset EGAD00001009513

• WGS of a Li-Fraumeni patient's HSPCs

  WGS data of clonally expanded HSPCs from a Li-Fraumeni patient at the time of second cancer (Burkitt lymphoma and <5% t-MN) after primary osteosarcoma diagnosis and a reference MSC bulk.

  Dataset EGAD00001011257

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 9 part 1)

  Whole genome sequencing data of 6 high-grade serous carcinoma (HGSC) patients (11 samples) sequenced with MGISEQ-2000

  Dataset EGAD00001011353

• Dataset for soft_tissue_tumor-RNA

  Rare cancer sequencing data of 243 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008859

• Influence of Genomic Landscape on Cancer Immunotherapy for Newly Diagnosed Ovarian Cancer: Biomarker Analyses from the IMagyn050 Randomized Clinical Trial

  The IMagyn050 trial (NCT03038100), which evaluated the efficacy of Atezo vs placebo (Pla) with carboplatin, paclitaxel and bevacizumab (CPB) in front line ovarian cancer patient (pts), did not meet its co-primary endpoints of PFS in ITT or PD-L1+ (Moore et al. JCO 2021). The aim of this exploratory study was to evaluate whether patients with BRCA1/2-mutated or homologous recombination-deficient (HRD) ovarian cancers benefitted from atezolizumab in the phase III IMagyn050 (NCT03038100) trial. Methods: Patients with newly diagnosed ovarian cancer were randomized to either atezolizumab or placebo with standard chemotherapy and bevacizumab. PD-L1 status of tumor-infiltrating immune cells was determined centrally (VENTANA SP142 assay). Genomic alterations, including deleterious BRCA1/2 alterations, genomic loss of heterozygosity (gLOH), tumor mutation burden (TMB), and microsatellite instability (MSI), were evaluated using the FoundationOne assay. HRD was defined as gLOH ≥16%, regardless of BRCA1/2 mutation status. Potential associations between progression-free survival (PFS) and genomic biomarkers were evaluated using standard correlation analyses and log-rank of Kaplan-Meier estimates. Results Among biomarker-evaluable samples, 22% (234/1050) harbored BRCA1/2 mutations and 46% (446/980) were HRD. Median TMB was low irrespective of BRCA1/2 or HRD. Only 3% (29/1024) had TMB ≥10 mut/Mb and 0.3% (3/1022) were MSI-high. PFS was better in BRCA2-mutated versus BRCA2-non-mutated tumors and in HRD versus proficient tumors. PD-L1 positivity (≥1% expression on immune cells) was associated with HRD but not BRCA1/2 mutations. PFS was not improved by adding atezolizumab in BRCA2-mutated or HRD tumors; there was a trend toward enhanced PFS with atezolizumab in BRCA1-mutated tumors. Conclusion Most ovarian tumors have low TMB despite BRCA1/2 mutations or HRD. Neither BRCA1/2 mutation nor HRD predicted enhanced benefit from atezolizumab. This is the first randomized double-blind trial in ovarian cancer demonstrating that genomic instability triggered by BRCA1/2 mutation or HRD is not associated with improved sensitivity to immune checkpoint inhibitors.

  Study EGAS00001006838

• Helleday_HRAS_Project

  This experiment is looking at the mutational signatures generated by engineered HRAS mutations by using whole genome sequence generated on massively parallel next generation sequencers.

  Study EGAS00001000332

• Single_Cell_Targeted_Sequence_Capture

  This study is to ascertain whether it is feasible to extract single cell from a tumour, perform amplification, generate a library and sequence a targeted pulldown.

  Study EGAS00001000435

• The molecular landscape of colorectal cancer （17 cases）

  We performed whole-exome sequencing of tumor samples and adjacent normal mucosae from 17 cases to characterize the genetic alterations in china.

  Study EGAS00001002174

• The molecular landscape of colorectal cancer reveals genetic mutations.

  We performed whole-exome sequencing of tumor samples and adjacent normal mucosae from 46 patients to characterize the genetic alterations in China.

  Study EGAS00001001893

• Microdissection_sequencing_of_normal_human_prostate

  Histology sections from pathologically benign human prostates were prepared and microdissections retrieved from Laser-Capture Microdissection are submitted to low-input whole-genome sequencing.

  Study EGAS00001003049

• WGS_of_AML_during_PARPi_therapy

  We will require WGS on Illumina X10 machines of three samples, along with storage and computational power to perform the relevant analysis.

  Study EGAS00001002274

• The molecular landscape of colorectal cancer （5 cases）

  We performed whole-exome sequencing of tumor samples and adjacent normal mucosae from 5 patients to characterize the genetic alterations in china.

  Study EGAS00001002374

• Sequencing of cell-free DNA from breast cancer patients

  To assess the utility of high coverage whole genome sequencing analysis of cell-free DNA to detect tumour-specific genomic changes

  Study EGAS00001004960

• EGAD00010000558

  SNP 6.0 arrays of small cell lung cancer

  Dataset EGAD00010000558

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors.

  Dataset EGAD00001000641