Search Results - EGA European Genome-Phenome Archive

A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome

We previously reported the whole-genome sequencing of the well-studied human malignant melanoma cell line, COLO-829, and a lymphoblastoid cell line from the same individual, providing the first comprehensive catalogue of somatic mutations from an individual cancer (Pleasance et al. (2010) Nature 463, 191). This initial study was carried out using the Illumina Genome Analyzer II, largely using paired-end reads of 75 bases from standard Illumina paired-end libraries. Here we report the results of sequencing the genomes of COLO-829 and its matched lymphoblastoid sample using HiSeq2000 with v3 cluster-generation and sequencing chemistries. This has significantly improved the evenness and completeness of genomic coverage, particularly in areas of extreme sequence composition that were underrepresented in the initial study.

Study EGAS00001000245

WES and RNA-seq raw sequence data for HIFI project

WES sequence data from 15 samples, RNA-seq sequence data from 19 samples, all sequence data are raw pair-end sequence data in fastq format, sequenced by Illumina platform.

Dataset EGAD00001004799

RNA sequencing data of high-grade serous ovarian cancer samples

RNA sequencing data of over 200 HGSOC samples at diagnosis, after chemotherapy and during progression.

Dataset EGAD00001006456

ATAC-seq

ATAC-seq data. Dataset includes FASTQ files, BAM files, and analysis files with the ATAC-seq peaks determined using MACS2.

Dataset EGAD00001008962

Targeted sequencing of brain AVMs

Targeted sequencing data to look for the involvement of genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others, in brain AVMs

Dataset EGAD00001009695

Genetic landscape of Extranodal NK/T-cell lymphoma

Whole-exome sequence (WES) data of tumor-normal pairs from 40 ENKTCL patients and RNA sequence (RNA-seq) data of tumors from 20 ENKTCL patients.

Dataset EGAD00001009852

Cam_121 RNA-Seq data

This dataset contains RNA-Seq data from 204 primary melanomas and 177 regional lymph nodes. More details can be found in the manuscript: "Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study"

Dataset EGAD00001006401

Paired Biopsy Project: West Coast Dream Team

This project contains the 16 WGS tumor samples and the corresponding 15 WGS normal tissue samples (germline control) not yet deposited in the public domain (e.g., EGA, dbGaP) at the time of submission of the manuscript (Zhu et al.)

Dataset EGAD50000000473

Oncoprint GSCCs

This dataset contains DNA sequencing data from 7 GSCCs (data for BT569 is not available). We performed focused exome sequencing (43 most mutated genes in GBM), combined with OneSeq analysis (Agilent) on the GSCCs and identified both shared and GSCC-specific mutations. For CME038, whole genome sequencing was performed.

Dataset EGAD00001011276

BAM files from whole-genome sequencing of 3 agressive B-cell lymphoma tumour and non-tumor samples

This dataset contains BAM files from whole-genome sequencing (WGS) of 3 agressive B-cell lymphoma tumour samples for cases 1, 6, and 7 as well as the corresponding non-tumor whole-genome sequencing BAM files.

Dataset EGAD50000000800

ATAC-seq in colon normal mucosa

ATAC-seq

Dataset EGAD00001007690

GATCI whole genome sequencing fastqs

Raw whole genome sequencing data (fastq) for the GATCI project

Dataset EGAD00001005926

Somatic mutations and single cell transcriptomes reveal the root of malignant rhabdoid tumours

Like many childhood cancers, malignant rhabdoid tumours (MRT) are thought to arise from aberrant foetal development. Although MRT predominantly exhibit a mesenchymal phenotype, it has been suggested that the foetal root of MRT lies in neural crest development. Here, we combine phylogenetic analyses of MRT, single cell mRNA assays, and functional experiments in patient-derived MRT organoids, to define the embryological origin of MRT and explore therapeutic avenues that may drive MRT differentiation. Phylogenetic analyses from the distribution of somatic mutations revealed that MRT were related to neural crest-derived, but not to mesodermal tissues, providing direct evidence of the neural crest origin of MRT in humans. In MRT organoids, reversal of the principal driver event underpinning MRT, SMARCB1 loss, induced differentiation along mesenchymal pathways. Together, these findings placed MRT cells on a developmental trajectory of neural crest to mesenchyme conversion, and defined the transcriptional changes underpinning MRT differentiation. Searching perturbation databases for agents that mimic these mRNA changes, we identified HDAC and mTOR inhibition as potential differentiation agents. Treatment of MRT organoids with this drug combination induced proliferation arrest with transcriptional changes akin to SMARCB1 re-expression. Our study defines the embryological root of MRT and proposes a differentiation treatment for this often fatal childhood cancer.

Dataset EGAD00001006296

Efficacy of CDK4/6i in preclinical models of malignant pleural mesothelioma

Assessment of antitumor activity of CDK4/6 inhibitors using in vitro and in vivo preclinical models of MPM using RNA-sequencing. We also include the genomic characterization (whole exome sequencing) of patient-derived cell lines used in the in vitro experiments.

Study EGAS00001005352

Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (WGS)

Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. WGS (BAM files)

Dataset EGAD00001006349

WGS data from the MESOMICS project (French project of molecular characterization of malignant pleural mesothelioma)

The dataset includes cram files from WGS of 115 tumor samples as well as 43 matched normal tissue or blood. The sequencing was done with HiSeq X Five instrument.

Dataset EGAD00001007023