Search Results - EGA European Genome-phenome Archive

AI_NF1glioma_RNAseq

The dataset includes 29 tumor samples from NF1-glioma patients profiled by RNA sequencing.

Dataset EGAD00001004376

Infiltrative and drug-resistant slow-cycling cells support metabolic heterogeneity in glioblastoma

Glioblastoma patient derived Fast/Slow cycling cancer stem cell RNA sequencing. Consists of 3 patient cell lines and 6 files

Dataset EGAD00001004380

t(14,18) negative diffuse follicular lymphoma with 1p36 deletion

Whole Exome Sequencing reads consisting of BAM paired end reads from Follicular Lymphoma samples.

Dataset EGAD00001004386

Anaplastic meingioma methylation

Methylation of anaplastic meningiona samples

Dataset EGAD00010001629

Identification of molecular subgroups in multiple myeloma by whole exome sequencing.

Dataset EGAD00001004408

Whole genome sequencing on HiSeq platform of tumour-normal sample pairs from 67 mucosal melanoma cases

Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 134 samples: matched tumour-normal pairs from 67 mucosal melanoma cases

Dataset EGAD00001004409

Dataset for the study - Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients

FASTQ files from sequencing to < 0.4x depth of coverage of thirteen glioma patients. Indexed sequencing libraries were prepared using a commercially available kit (ThruPLEX-Plasma Seq, Rubicon Genomics). Libraries were pooled in equimolar amounts and sequenced on a HiSeq 4000 (Illumina) generating 150-bp paired-end reads.

Dataset EGAD00001004425

Whole exome and targeted sequencing data from glioblastoma multiforme samples

Whole exome and targeted sequencing data from 11 glioblastoma multiforme patients. A total of 70 tumour specimens and 11 blood samples were used for whole exome sequencing (WES) using the Agilent SureSelectXT Human All Exon V5 Kit. Two custom targeted sequencing panels were designed using the using Agilent’s Haloplex (TES1) or Agilent SureSelect XT2 technology (TES2). Libraries were sequenced on an Illumina HiSeq2500

Dataset EGAD00001004420

FASTQ files of the RNA-Seq data for the study "Genomic landscape of lung adenocarcinoma in East Asians"

FASTQ files of the RNA-Seq data for both the normal and tumor samples for the study "Genomic landscape of lung adenocarcinoma in East Asians". For raw read count data as well as other metadata, please download from https://src.gisapps.org/OncoSG_public/study/summary?id=GIS031 by clicking the download icon next to the dataset title.

Dataset EGAD00001004421

FASTQ files of the Exome-Seq data for the study "Genomic landscape of lung adenocarcinoma in East Asians"

FASTQ files of the Exome-Seq data for both the normal and tumor samples for the study "Genomic landscape of lung adenocarcinoma in East Asians". For mutations and copy number variants called by this study, please download from https://src.gisapps.org/OncoSG_public/study/summary?id=GIS031 by clicking the download icon next to the dataset title.

Dataset EGAD00001004422

Spiradenocarcinoma (2018-10-29)

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.

Dataset EGAD00001004426

MGA-NUTM1 fusion in high grade spindle cell sarcoma Data

There is a total of 4 sample data (2 WGS and 2 RNAseq) belong to 2 patient deposited in this study.

Dataset EGAD00001004479

ChIP-Seq files for PCGP ATRX study

ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

Dataset EGAD00001004429

RNA sequencing of undifferentiated sarcomas

mRNA sequencing of 50 undifferentiated sarcoma tumour samples and 5 adjacent muscle tissue samples. BAM files are provided, with metadata specifying which samples are tumour/normal.

Dataset EGAD00001004439

ISA Nutrition 2015

Comprehensive data on lifestyle-related modifiable factors, sociodemographic, anthropometric, economic, biochemical, and genetic markers related to the occurrence of cardiometabolic diseases as part of the observational cross-sectional survey (2015 Health Survey of Sao Paulo with Focus on Nutrition (2015 ISA-Nutrition), a population-based study. Data of 805218 SNPs for 841 individuals was genotyped using the Axioma 2.0 Precision Medicine Research Array in the Thermo Fisher Scientific laboratory (Affymetrix Inc, Santa Clara, CA).

Dataset EGAD00010002678

Neuroblastoma Whole Exome Sequencing

Mapped BAM files of 162 tumor/normal WES experiments.

Dataset EGAD00001004450

IVAC Melanoma

Whole exome and transcriptome sequencing of 12 melanoma patients (including technical replicates). linicalTrials.gov Identifier: NCT02035956. Paper: Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer - Nature volume 547, pages 222–226

Dataset EGAD00001004455

Exome sequencing of a novel cervical cancer cell line

In this work, we establish and characterized a low-passage cervix cancer cell line from a Brazilian patient with squamous cell carcinoma. The dataset contains three samples from the same patient (blood, tumor tissue and the primary cell line). The technology used was exome sequencing and the file type available is fastq files.

Dataset EGAD00001004480

Transcriptome of Ewing sarcoma tumors - RNA-seq (ICGC)

Transcriptome of Ewing sarcoma tumors (ICGC project). Fastq files of 57 RNA-seq are available (2x101bp).

Dataset EGAD00001004493

A uveal melanoma patient with MBD4 mutation

Tumour and control from a patient with uveal melanoma with a MBD4 germline mutation. Samples were whole exome sequenced.

Dataset EGAD00001004496

Single-cell RNA-seq of immune cells from Melanoma tumors (Li et al, 2018)

Single-cell RNA-seq profiling of immune cells sorted from human Melanoma tumors (and several matching PBMC samples). Contains de-multiplexed FASTQ files per plate (MARS-seq amplification batch, total 204 samples) and also de-multiplexed FASTQ files of single-cell TCRb-seq.

Dataset EGAD00001004497

Whole Exome Sequencing

Whole exome sequencing data of 19 snap-frozen peritoneal mesothelioma (tumor) samples and 16 matched normal samples. Sequencing library was prepared using Ion AmpliSeq Exome RDY Library Preparation. Samples were sequenced on the Ion Proton System using the Ion PI Hi-Q Sequencing 200 Kit and Ion PI v3 chip.

Dataset EGAD00001004503

Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

In this dataset there are 55 whole genome sequencing samples of epithelial ovarian carcinoma (bam files).

Dataset EGAD00001004532

Whole Transcriptome Sequencing

RNA-seq data of 15 snap-frozen tissue of peritoneal mesothelioma. The strand specific RNA library prepared using TruSeq (Illumina) and pair-end sequencing performed in Illumina HiSeq 4000. The datasets contains paired fastq files for each of 15 tumor samples.

Dataset EGAD00001004504

Whole genome sequencing of metastatic cutaneous squamous cell carcinoma

This dataset includes somatic small variant calling files derived from fifteen metastatic samples from cutaneous squamous cell carcinoma matched to normal blood samples. These samples were whole-genome sequenced by HiSeq X Ten and the resulting reads were mapped against the human genome (hg37) using BWA-MEM 0.7.10-r789. Somatic variant calling was then performed using strelka 1 (version 2.0.17).

Dataset EGAD00001004530

RNAseq profiling of pediatric osteosarcoma

Primary pediatric osteosarcoma samples were collected and profiled using RNAseq. When possible, germline and tumor samples were collected. For some patients, multiple tumor tissues were collected and sequenced. Some of the samples were used to derive PDTX models, which were also profiled with RNAseq. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

Dataset EGAD00001004538

WGS profiling of pediatric osteosarcoma

Primary pediatric osteosarcoma samples were collected and profiled using WGS. When possible, germline and tumor samples were collected. For some patients, multiple tumor tissues were collected and sequenced. Some of the samples were used to derive PDTX models, which were also profiled with WGS. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

Dataset EGAD00001004537

RNA-seq of hepatocellular carcinoma xenografts established from needle biopsies

RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.

Dataset EGAD00001004541

Comprehensive genetic analysis of uveal melanoma heterogeneity during metastatic progression

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Despite improvement of diagnosis and treatment of the primary tumor, there is no effective treatment of metastatic disease and approximately half of patients will die within one year or less following metastases detection. Tumor heterogeneity has been proposed as a key factor of drug resistance. However, it has been scarcely studied in UM. The present project aims searching for specific drivers of the metastatic progression, describing the genomic and transcriptomic landscape of metastatic UM, exploring tumor heterogeneity and investigating its role in drug resistance. Thus whole exome sequencing and transcriptomics have been performed on constitutional, primary tumor and metastatic samples from 28 UM patients.

Dataset EGAD00001004554

WGBS files for PCGP NBL_MYCN_ATRX

WGBS files for PCGP NBL_MYCN_ATRX paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

Dataset EGAD00001004559

Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

Dataset EGAD00001004565

WES files for Newman MAP3K8 melanoma

WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

Dataset EGAD00001004566

RNASeq files for Newman MAP3K8 melanoma

RNASeq files for MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

Dataset EGAD00001004567

Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient

Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004598

Somatic mutations in facial skin from countries of contrasting skin cancer risk

The incidence of non-melanoma skin cancer is 17-fold lower in Singapore compared to the UK1, despite Singapore receiving 2-3 times more year-round ultraviolet radiation (UV)2,3. The ageing epidermis of the skin comprises competing somatic mutant clones4,5, from which such cancers develop. We question if differences in keratinocyte skin cancer incidence are reflected in the mutational landscape by comparing ageing facial epidermis from donors of Singapore and the UK. We find UK skin to be a highly competitive, densely mutated landscape with 4-fold greater mutation burden compared to Singaporean skin and differences in clonal selection by country. We disproportionately observe multiple features common to keratinocyte skin cancers6,7,8 in UK skin, such as UV mutagenesis, copy number aberration and hotspot mutations (in particular TP53 R248W). We conclude that keratinocyte skin cancer incidence is reflected in the somatic clones of non-cancerous epidermis. Finally, we re-analyse squamous cell carcinoma exomes from Korea9 to show, even in low incidence populations, carcinogenesis is driven by UV damage.

Dataset EGAD00001009666

The mutational landscape of skin tumours in CYLD cutaneous syndrome determined

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.

Dataset EGAD00001004573

Genome and transcriptome sequence data from a non-small cell adenocarcinoma patient

Genome and transcriptome sequence data from a non-small cell adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004600

Metabolic reprogramming towards OXPHOS identifies a novel therapeutic target for mantle cell lymphoma

Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways to overcome resistance, an urgent clinical need in all relapsed/refractory cancers, remains difficult. Through genomics analysis of clinical specimens, we show that metabolic reprogramming towards oxidative phosphorylation (OXPHOS) and glutaminolysis is associated with therapeutic resistance to the Bruton’s tyrosine kinase inhibitor ibrutinib in mantle cell lymphoma (MCL), an incurable B-cell lymphoma with poor clinical outcomes. Inhibition of OXPHOS with a novel, clinically applicable small molecule, IACS-010759, which targets complex I of the mitochondrial electron transport chain, results in significant growth inhibition in vitro and in vivo in ibrutinib-resistant patient-derived cancer models. This work suggests that targeting metabolic pathways to subvert therapeutic resistance is a clinically viable approach to treat highly refractory malignancies.

Dataset EGAD00001004577

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

Chronic liver injury predisposes to cirrhosis and hepatocellular carcinoma, but how somatic mutations accumulate in liver disease is unexplored. We sequenced whole genomes of 400 microdissections of 100-500 hepatocytes from 5 normal and 6 cirrhotic livers. Compared to normal liver, cirrhotic liver had higher mutation burden, especially structural variants, including chromothripsis. Cirrhotic nodules were oligoclonal; sometimes entirely derived from a single, recent common ancestor. Clonal expansions millimeters in diameter occurred in cirrhosis in the absence of known driver mutations. Endogenous mutational processes predominated, although signatures of polycyclic aromatic hydrocarbon and aristolochic acid exposure occurred in some samples. Up to 10-fold within-patient variation in activity of exogenous signatures existed between adjacent cirrhotic nodules, with both clone-specific and microenvironmental forces shaping this heterogeneity. Synchronous hepatocellular carcinomas drew from the same repertoire of mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.

Dataset EGAD00001004578

WGS files for Newman MAP3K8 melanoma

WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

Dataset EGAD00001004579

Ewing's Sarcoma Whole Genome Sequencing

54 WGS Ewing's sarcoma samples sequenced at The Hospital for Sick Children Toronto (Adam Shlien's lab) and published on Science 2018. Reference Anderson et al. "Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors"

Dataset EGAD00001004589

EORTC study on the evolution of driver mutations and MGMT promotor methylation in glioblastomas treated with standard of care: Correlation with survival and impact on trial design

Precision medicine trials in glioblastoma should be conducted at tumor recurrence. However, second surgery for recurrent GBMs is not routinely performed and therefore molecular data is predominantly derived from primary samples. This study aims to establish the frequency of driver changes at tumor recurrence.

Dataset EGAD00001004593

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