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• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• Clonal cultures of T memory cells

  Sequence data (bam files) of two RRBS samples for paper "A comprehensive analysis of 195 DNA methylomes reveals shared and cell specific features of partially methylated domains". Short Description: CD4+ T memory cells (CD3+ CD4+ CD45RA- CD45RO+ CD25-) from donors were sorted by flow-cytometry either as a bulk culture ('ex vivo' sample) or in a single-cell format into 96 well-plates ('clone' sample) in the presence of a TCR stimulus.

  Dataset EGAD00001004303

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• LINE luminal breast cancer Neoadjuvant Chemotherapy Study (2019-08-28)

  A targeted gene screen of 365 known cancer genes in luminal breast cancer samples pre-chemotherapy and at resection post-chemotherapy to evalaute clonal expansion of chemotherapy cancer cells. . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005297

• Targeted DNA sequencing dataset for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  We performed deep targeted DNA sequencing with a panel of 74 selected cancer-related genes previously identified to be recurrently mutated in EBV associated DLBCL. Sequencing was performed on a HiSeq platform (Illumina) with 250 bp paired-end reads. There are 68 FFPE samples in this targetedDNAseq-dataset with 46 unpaired tumors and 22 normals used as a panel of normals.

  Dataset EGAD00001009396

• WGBS of CD14 monocytes dataset of covid19 patients from Quebec, Canada

  this dataset contains the raw data generated for CD14 monocytes WGBSof 7 covid19 hospitalized patients sampled at various time points (Admission, Day 5 and Day 15) in total 15 biospecimen are available. WGBS libraries have been sequenced on Illumina NovaSeq 6000.

  Dataset EGAD00001008718

• DAC for EGA study: "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma"

  This DAC regulates access to the whole-exome sequence data for the study "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma".

  Dac EGAC50000000706

• Dataset for transcriptome sequencing of forebrain organoids from Lissencephaly patients

  This dataset contains transcriptome sequencing for 16 samples of forebrain organoids from Lissencephaly patients. The sequencing was performed on Illumina NextSeq 6000 . The sequencing was always paired.

  Dataset EGAD00001015688

• DAC for the "Study on the proliferation history of colorectal adenomas"

  Dac EGAC00001000209

• Dataset for manuscript titled: Spatial Intra-Tumour Heterogeneity and Treatment-Induced Genomic Evolution in Oesophageal Adenocarcinoma: Implications for Prognosis and Therapy

  Dataset for manuscript titled: Spatial Intra-Tumour Heterogeneity and Treatment-Induced Genomic Evolution in Oesophageal Adenocarcinoma: Implications for Prognosis and Therapy

  Dataset EGAD00001015373

• Anaplastic Thyroid Cancer somatic variants (MuTect)

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header.

  Dataset EGAD00001004129

• Aligned whole genome bisulfite sequencing data 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.

  Aligned whole genome bisulfite sequencing data for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001435

• CCA ChIP-seq data (63 CCA, 8 normal, 19 cell-line)

  Fastq files for H3K27ac ChIP-seq (with matched input-DNA control) for 63 CCAs, 8 normal bile duct tissues, 16 CCA cell-lines (including replicates), and 3 normal cholangiocyte cell-lines (including replicates). Library prep was performed with the NEBNext ChIP-seq library preparation kit. Each library (including matching input DNA) was sequenced to an average depth of 20 to 30 million raw reads on Illumina HiSeq4000 sequencer, with paired-end sequencing (except for 3 normal bile tissues done with single-end sequencing).

  Dataset EGAD00001012103

• Dataset-linking-WGS-and-WES-files-from-EGAS00001004276-via-README-for-new-study-EGAS00001005327

  This dataset contains 538 Tumor and Control WGS and WES files for samples already submitted and published in study EGAS00001004276

  Dataset EGAD00001007817

• NFE2 and PF4 as Translational Biomarkers for BET Inhibition-Induced Thrombocytopenia in Preclinical and Clinical Studies

  Blood samples from patients treated with BMS-986158 were investigated for association with thrombocytopenia following BET inhibition. Hypotheses of translational biomarkers for early prediction of thrombocytopenia associated with BET inhibition were explored.

  Study EGAS50000001162

• WTCCC2 Bacteraemia Susceptibility (BS) samples

  A WTCCC2 project genome-wide association study for bacteraemia susceptibility in 4924 individuals from Kenya, genotyped on the Affymetrix 6.0 array.

  Study EGAS00001001756

• Dataset for "CutNRun" sequencing of 12 samples of patients with colorectal cancer

  This dataset contains 12 "CutNRun" sequencing samples of patients with colorectal cancer. The sequencing was performed on Illumina NextSeq 550 using Cell Signaling TechnologyDNA Library Prep _Kit for Illumina Systems. The sequencing was always paired.

  Dataset EGAD00001015694

• Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Dataset EGAD00001003435

• Reference exome data for a Northern Brazilian population

  Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from the State of Rio Grande do Nord in Brazil. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil.

  Dataset EGAD00001006407

• Genome and transcriptome sequencing of cancer of unknown primary tumours

  Genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA by whole genome sequencing of tissue and cfDNA biopsies, as well as targeted genome sequencing using two panels, including Comprehensive cancer panel (CCP) and TruSight Oncology 500 (TSO500). This study also includes profiling of tumour RNA by whole transcriptome sequencing.

  Study EGAS50000000452

• The data access committee for Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  Dac EGAC50000000588

• WGS and WXS files for Dyer ATRX study

  WGS and WXS files for Dyer ATRX study

  Dataset EGAD00001003389

• Cancer sequencing for somatic variant calling

  This dataset includes WES and RNAseq for 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy tissues, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems.

  Study EGAS00001007101

• cfMeDIP data for 72 VPC samples for validation

  We analyzed the cell free DNA methylomes using 72 plasma samples from patients with mCRPC prostate cancer in the VPC project for validation. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology. Files from multiple lanes exists per sample.

  Dataset EGAD00001008737

• UCSF Pediatric Bithalamic Glioma Genome Project

  Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001005499