Search Results - EGA European Genome-Phenome Archive

Sequencing data for Murtaza et al. Nature Communications 2015 (doi:10.1038/ncomms9760)

Exome and targeted amplicon sequencing data for tumor, germline and plasma samples from a patient with metastatic breast cancer.

Dataset EGAD00001002108

Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks

Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we discovered widespread heterogeneity in the chromatin landscape of CLL, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.

Dataset EGAD00001002110

Targeted Sequencing of 173 genes

Targeted sequencing of 173 genes in 2433 primary breast tumours. Data includes 2433 tumour samples, 523 adjacent normal (breast) samples and 127 blood samples. Libraries were prepared with Illumina's Nextera custom enrichment kit targetting all the exons of the most frequently mutated breast cancer genes. Libraries were multiplexed (48 libraries per lane) and sequenced on Illumina HiSeq 2000 (100bp paired-end reads). Somatic mutations were calling with a custom pipeline. We identified 40 mutation-driver (Mut-driver) genes, and determined associations between mutations, driver CNA profiles, clinical-pathological parameters and survival. We assessed the clonal states of Mut-driver mutations, and estimated levels of intra-tumour heterogeneity using mutant-allele fractions. The results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies. Referece: Pereira et al. (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nature Communications

Dataset EGAD00001002115

Whole exome sequencing of Finnish hereditary breast cancer families

Dataset contains Whole Exome Sequencing(WES) data from 37 individuals as aligned bam-files. The reads have been aligned using bowtie2 to human genome hg19 build.

Dataset EGAD00001002133

A somatic reference standard for cancer genome sequencing.

Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

Dataset EGAD00001002142

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Sequencing data for Murtaza et al. Nature Communications 2015 (doi:10.1038/ncomms9760)

Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks

Targeted Sequencing of 173 genes

Whole exome sequencing of Finnish hereditary breast cancer families

A somatic reference standard for cancer genome sequencing.

TP53 in ovarian cancer panel aligned reads Data Access Committee

Genome and transcriptome sequence data from a metastatic colon cancer patient

Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

Genome and transcriptome sequence data from a GI primary (prev breast cancer) patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a metastatic large cell neuroendocrine tumour of the lung patient

Genome and transcriptome sequence data from a rectal adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic gastric adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma of unknown primary patient

Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

Genome and transcriptome sequence data from a metastatic colon cancer patient

Genome and transcriptome sequence data from a metastatic fibrolamellar hepatocelluar carcinoma patient

Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient

Genome and transcriptome sequence data from a metastatic rectosigmoid adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic carcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient

Genome and transcriptome sequence data from a metastatic endocervical adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a medullary thyroid cancer patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a cholangiocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic carcinoma of primary unknown patient

Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of anus patient

Genome and transcriptome sequence data from a carcinosarcoma of the uterus patient

Global Anaplastic Thyroid Cancer Initiative

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a serous carcinoma of fallopian tube patient

Genome and transcriptome sequence data from a metastatic adult granulosa cell tumour patient

Genome and transcriptome sequence data from a glioblastoma multiforme patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic medullary thyroid cancer patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma presumably of ovarian origin patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a squamous cell carcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectum patient

Genome and transcriptome sequence data from a metastatic colon cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic ductal carcinoma of the breast patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from an ovarian adenocarcinoma patient