Search Results - EGA European Genome-Phenome Archive

GCT WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

Dataset EGAD00001003267

HGSC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

HGSC cases in the OvCaRe and CRCHUM Tumour Banks were selected according to the following criteria: (i) were administered platinum taxane based therapy; (ii) relapsed within 12 months (365 days) or had at least longer than 4.5 years (1642.5 days) follow-up data; (iii) had at least 50% tumour content by H&E staining and expert pathology review. All cases were re-reviewed by expert pathologists to confirm the diagnosis of HGSC. Germline BRCA1 and BRCA2 was determined for all patients through hereditary cancer screening programs. The design of cases selection as a discovery cohort was engineered to amplify biological differences by selecting cases from the extremes of the outcome distribution. All HGSC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

Dataset EGAD00001003268

Pancreatic Cancer OICR

ICGC DCC Release 24, PACA-CA Whole Genome sequence merged alignments

Dataset EGAD00001003270

March 2017 data update (bam/fastq) (containing H3K27ac for CEMT_87, RNA-Seq for CEMT_141, CEMT_142, CEMT_145, CEMT_146, H3K27me3, H3K9me3, H3K4me3, H3K4me1, ChIP-Seq Input for CEMT_88, CEMT_90 and CEMT_91) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

March 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

Dataset EGAD00001003272

Whole Genome Sequencing of Liver Cancers

Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers.

Dataset EGAD00001003281

Prostate WGS data (late onset)

Whole genome sequencing for 12 late onset prostate cancer tumor/control pairs (ICGC)

Dataset EGAD00001003290

oncogenic gene fusions in primary colon cancers

This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

Dataset EGAD00001003291

RNAseq SCLC Cell lines MYC

RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

Dataset EGAD00001003099

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

Dataset EGAD00001003115

EPITREAT pilot cohort

Benchmark data set containing five tumor/normal pairs of non-small cell lung cancer (NSCLC) patients. Tissue pairs were screened with bisulfite (BS) sequencing, MeDIP methylation enrichment sequencing and RNA sequencing in order to identify differentially methylated and expressed spots in the genomes.

Dataset EGAD00001003116

TP53 in ovarian cancer panel aligned reads Data Access Committee

TP53 targeted panel aligned reads consisting of BAM paired end reads from ovarian cancer tumor samples Data Access Committee

Dataset EGAD00001003119

December 2016 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

December 2016 data update (bam/fastq for WGBS on samples CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

Dataset EGAD00001003122

Inter and intra - tumor heterogeneity in Colorectal Cancer

The dataset consists of two main sample groups. 1) The inter-tumour sample group contains a total of 97 samples from 27 patients. Each patient has a single normal and primary sample as well as one or more metastases. All samples were sequenced using IonTorrent PGM and a custom colorectal cancer (CRC) panel. 2) The intra-tumour sample group contains a total of 68 samples from a single tumour as well as a normal tissue sample. All 68 samples were sequenced using IonTorrent PGM and a custom CRC panel. Shallow whole genome sequencing was additionally applied to 10 of the samples using Illumina HiSeq 4000.

Dataset EGAD00001003131

Multi-sample whole exome sequencing from 4 cases of advanced breast cancer.

Metastatic and primary tumour samples were collected from 4 patients with advanced breast cancer. Samples were collected at autopsy and also from biopsies taken during life. Tumour and germline samples are available. Whole exome sequencing was performed on all samples.

Dataset EGAD00001003137

Ovarian cancer/normal cell lines

We performed whole genome sequencing of nine OC patient-derived cell lines and one normal cell line (HOSEpiC) to analyze if the cell lines harbor OC-typical genomic aberrations absent in normal cells and to relate genomic features to drug sensitivities.

Dataset EGAD00001003146

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

Sequencing .bam files

Sequencing of untreated pancreatic cancer metastases and primary tumor sections.

Dataset EGAD00001003153

EPO2_Illumina_RNA_XEN

RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort)

Dataset EGAD00001003362

EPO2_Illumina_WXS_XEN

Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort)

Dataset EGAD00001003363

OT2_Illumina_RNA_MET

RNAseq on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003364

OT2_Illumina_RNA_MET_CELL

RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003365

OT2_Illumina_RNA_MET_XEN

RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003366

OT2_Illumina_RNA_T

RNAseq on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003367

OT2_Illumina_RNA_T_CELL

RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003368

OT2_Illumina_RNA_T_XEN

RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003369

OT2_Illumina_WGS_MET

Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003372

OT2_Illumina_WGS_MET_CELL

Whole-genome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003373

OT2_Illumina_WGS_MET_XEN

Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003374

OT2_Illumina_WGS_T

Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003375

OT2_Illumina_WGS_T_XEN

Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003376

OT2_Illumina_WXS_MET

Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003379

OT2_Illumina_WXS_MET_CELL

Whole-exome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003380

OT2_Illumina_WXS_MET_XEN

Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

Dataset EGAD00001003381

OT2_Illumina_WXS_T

Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003383

OT2_Illumina_WXS_T_XEN

Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003384

OT2_Solid_WXS_T

Whole-exome sequencing on AB 5500xl Genetic Analyzer of colorectal cancer primary tumor sample (OT2_cohort)

Dataset EGAD00001003386

Identification of differentially expressed protein-coding genes in HCC and adjacent non-cancerous tissues

Twenty samples were collected in pairs, i.e., HCC tissue and adjacent non-cancerous tissue. The collected tissue samples were stored in liquid nitrogen. First, 50 mg of tissue was lysed in TRIzol (Invitrogen) to extract RNA following the manufacturer’s instructions. Next, ribosomal RNA was depleted using a RiboZero Gold kit (Epicentre Bio-technologies). RNA integrity was assessed with an Agilent Bioanalyzer 2100. An RNA-Seq library was generated with the rRNA-depleted samples using an Illumina standard RNA Sample Prep kit according to the manufacturer’s instructions. The library was subsequently sequenced on an Illumina HiSeq2500 as 125-bp paired-ends with approximately 300-bp size selection.

Dataset EGAD00001003397

CNV detection in targeted NGS panel data

We present targeted NGS panel data from 170 samples that were processed using the TruSightTM Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed.

Dataset EGAD00001003400

June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

Dataset EGAD00001003414

TRACERx100 metastatic samples

Whole exome sequencing of 10 metastatic biopsies from four TRACERx100 patients (see EGA dataset EGAS00001002247), collected either after relapse or death. The data from these samples are initially published with Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early stage lung cancer evolution. Nature, http://dx.doi.org/10.1038/nature22364 (2017). Abstract: Earlier detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a patient-specific approach to ctDNA profiling in the first 100 lung TRACERx (TRAcking Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release in early-stage non-small cell lung cancer and perform tumor volume limit of detection analyses. Through blinded profiling of post-operative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients destined to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastases, providing a new approach for ctDNA driven therapeutic studies.

Dataset EGAD00001003301

Evolution of four ER+ breast cancers

The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.

Dataset EGAD00001003303

The molecular landscape of colorectal cancer reveals genetic mutations - COCA-CN

We collected tumor samples and adjacent nomal mucosae from 46 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

Dataset EGAD00001003304

Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

Dataset EGAD00001003305

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