Search Results - EGA European Genome-Phenome Archive

WGS from PDAC samples

Bam files from WGS of PDAC samples described in: Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution

Dataset EGAD00001006152

WES of multi-regional CRC samples

BAM files of Whole Exome Sequencing (WES) experiment on multi-regional colorectal cancer (CRC) samples. 32 tumour and 16 normal samples corresponding to 16 patients were sequenced, which makes 32 tumour BAMs and 16 normal BAMs (48 BAMs in total).

Dataset EGAD00001006165

76 cancer and normal whole genomes from eleven SI-NET patients

This dataset comprises of 76 cancer and normal whole genomes obtained from 11 SI-NET patients, in the form of two fastq files (forward and reverse reads) for each genome containing sequences generated by Illumina NovaSeq 6000 system.

Dataset EGAD00001006161

RNA-seq of multi-regional CRC samples

BAM files of RNA sequencing (RNA-seq) experiment on multi-regional colorectal cancer (CRC) samples. 58 samples corresponding to 16 patients were sequenced and there is one BAM file for each sample.

Dataset EGAD00001006164

Whole exome sequencing analysis on patient-derived cervical cancer tissues and respective tumoroids

Whole exome sequencing (WES) was performed on the matched tumor and organoid pairs from 7 cervical cancer patients. The DNA was sequenced on NovaSeq6000 platform with 8Gb sequencing coverage. WES data was mapped against human reference genome GRCh38 by using BWA (v0.7.5) mapping tool.

Dataset EGAD00001006166

Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

Dataset EGAD00001006170

Hereditary Cancer Diagnostics with I2HCP gene panel

Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.

Dataset EGAD00001006171

Single Cell RNAseq of PBMC from renal cancer patients

Dataset EGAD00001006175

Single cell RNAseq of PBMC from bladder cancer patients

This dataset contains single cell RNA sequencing data of PBMC samples from 20 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

Dataset EGAD00001006182

Competitive selection of somatic mutant clones in normal human skin varies with body site

The risk of getting non-melanoma skin cancer varies over 40-fold across the body. Here we map mutations in normal skin in high and low risk sites in normal donors and those with an increased risk of skin cancer. The density of mutations varied widely, with evidence of positive and negative genetic selection. Regional differences in mutational signatures in high and low cancer risk sites and preferential selection of mutants of TP53 in high risk skin and FAT1 in lower risk skin were observed. 10% of clones had copy number changes in cancer associated genes and the largest had multiple driver mutations with loss of heterozygosity. In hair follicles, a proposed site of origin of skin cancers, mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. We conclude cancer risk reflects the efficiency of transformation of oncogenic mutants rather than the density of mutant clones.

Dataset EGAD00001006194

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

NICHE - DNA-seq of MMR proficient and MMR deficient early stage colon cancers

The dataset includes 174 FASTQ files from paired-end WXS sequencing on Illumina HiSeq2500 for 39 patients.

Dataset EGAD00001006041

NICHE - RNA-seq of MMR proficient and MMR deficient early stage colon cancers

The dataset includes 77 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 39 patients.

Dataset EGAD00001006042

Guardians of the genome: protecting DNA from endogenous sources of damage

Mutational signatures are imprints of cell-intrinsic and extrinsic pathophysiological processes that have occurred through tumorigenesis. Experimental efforts to explore signature etiologies have produced a compendium of signatures of exogenous mutagens previously. Here, we unearth major sources of endogenous DNA damage and the genes that are critical to mitigating this innate stream of DNA damage under normal, physiological circumstances. We performed whole genome sequencing of 173 subclones of CRISPR-Cas9 knockouts of 43 genes in a human induced pluripotent stem cell system, in the absence of any added DNA damage. We reveal substitution and indel signatures that arise from those genes which are essential guardians of the genome. By detailed dissection and comparisons to cancer-derived signatures, we demonstrate interminable sources of constitutive DNA damage, and some mechanistic knowledge into how guardian genes preserve the genome. Based on these experimental insights, we develop and benchmark a tool for clinical classification of tumor samples.

Dataset EGAD00001006055

Targeted sequencing of HGS-EOC samples

A 19-sample data set containing data from FFPE high grade serous ovarian cancer biopsies. The library was made with a custom hybridization kit (EZ-Cap, Roche) spanning 7 genes.

Dataset EGAD00001006064

Sequence of breast cancer bone metastases PDX from 2 targeted panels

Targeted sequencing analyses was made on samples of PDX engrafted with breast cancer bone metastases, 2 PDX acquired resistance to palbociclib.

Dataset EGAD00001006070

Sequence of breast cancer bone metastases PDX from WES

Exome sequencing analyses obtained from 11 samples of PDX engrafted with bone metastases, match primary tumors and/or metastases and normal tissus.

Dataset EGAD00001006071

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 of non-cancer controls

Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma from self-reporting healthy individuals (MonRec Cohort)

Dataset EGAD00001005805

Spatial whole exome sequencing of metastatic melanoma

We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

Dataset EGAD00001005819

Spatial targeted gene sequencing of metastatic melanoma

We performed deep targeted DNA sequencing for a panel of 265 cancer-related genes. This included subsampling 35 different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. Samples with cancer cell purity greater than 80% based on pathologic assessment were used for cancer gene panel DNA sequencing. Mean sequencing coverage was 861x and paired-end reads in FASTQ format were generated by the Illumina pipeline and aligned to the reference human genome hg19 build using the Burrows-Wheeler Alignment Tool (BWA, v0.7.5) with default settings. Aligned reads were further processed using GATK with best practices for removing duplicates, indel removal and recalibration.

Dataset EGAD00001005821

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