Search Results - EGA European Genome-Phenome Archive

Xenograft BC WGS Dataset

We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Dataset EGAD00001001336

71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients

Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients.

Dataset EGAD00001001926

Genome and transcriptome sequence data from a breast invasive ductal carcinoma patient

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

Dataset EGAD00001004654

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004659

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

RNA-seq on patients 1-4, study of metastatic prostate cancer

Data from the study of subclonal metastatic expansion in prostate cancer. RNA-seq of twelve samples, tumour and benign tissue, from the four initial patients.

Dataset EGAD00001001345

BC WGS Dataset 4

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

Dataset EGAD00001001353

Ither2 WXS dataset - Implementation of pediatric precision oncology into clinical practice: The individualized Therapies for Children with cancer program “iTHER”

iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.

Dataset EGAD00001010178

Single cell RNA sequencing of colorectal cancer patients (KUL3)

All libraries were sequenced on Illumina HiSeq4000 until sufficient saturation was reached.

Dataset EGAD00001008584

Recalibrated whole-exome sequencing alignment data of papillary thyroid cancer of Saudi Arabia

The dataset consists of samples from papillary thyroid cancer patients. A total of 11 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset.

Dataset EGAD00001004490

UIC HNSCC RNA-Seq and miRNA-Seq Data

This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

Dataset EGAD00001004489

Single cell multiomics sequencing and analyses of human colorectal cancer

Whole genome sequencing data of tumor tissues, adjacent normal tissues, and peripheral blood from CRC patients.

Dataset EGAD00001004495

Chondrosarcoma Validation Study

Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

Dataset EGAD00001000392

Genome and transcriptome sequence data from a acute lymphoblastic leukemia tumor patient

Genome and transcriptome sequence data from a acute lymphoblastic leukemia patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

Dataset EGAD00001015285

March 2018 cumulative data release 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 2018 cumulative data release (bams,fastqs) 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

Dataset EGAD00001003963

High-resolution analysis for urinary DNA jagged ends

consists 17 cases, 7 control cases and 10 cancer cases.

Dataset EGAD00001008594

Ither2 RNA-Seq dataset - Implementation of pediatric precision oncology into clinical practice: The individualized Therapies for Children with cancer program “iTHER”

iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.

Dataset EGAD00001010179

WGS and Avenio Surveillance Panel data to previously submitted data under study number EGAS00001004276 of ALK-rearranged lung cancer

Some data was previously submitted data under study number EGAS00001004276. In this new dataset we provide additional WGS and Avenio Surveillance Panel data. We utilized 43 ALK+ NSCLC patients receiving targeted ALK therapy to evaluate ctDNA levels based on matched panel-based targeted next generation sequencing (tNGS) and untargeted shallow whole genome sequencing (sWGS). For the Avenio panel the sequencing was done on Illumina NextSeq 550 paired end 150 bp, for WGS the sequencing was done on Illumina HiSeq 4000, partly with KAPA_Hyper_Prep_Kit. In this dataset there are 132 WGS tumor samples and 134 panel sequencing data of plasma.

Dataset EGAD00001007818

Spatial transcriptome sequence data from prostate cancer needle biopsies

Spatial transcriptome sequencing data from prostate cancer needle biopsies. Dataset contains biopsies from before and after androgen deprivation therapy of 3 patients with 8 biopsies per patient in total. 2 sections (replicates) are taken from each biopsy.

Dataset EGAD00001008636

Genomic characterisation of SDH deficient renal cell carcinoma - WGS

SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

Dataset EGAD00001008469

Genomic Evolution of Breast Cancer Metastasis and Relapse

Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

Dataset EGAD00001002697

ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

Dataset EGAD00001001229

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