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• BLUEPRINT September 2016, ChIPmentation Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 2 sample(s) Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002944

• Whole-genome and transcriptome sequencing of NUT midline carcinoma

  In this study, we sequenced three NUT midline carcinoma genomes and their transcriptomes (NMC1, NMC2 and Ty-82), and two paired normal blood samples (for NMC1 and NMC2). Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X machines. Transcriptome (mRNA) sequencing was performed in HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

  Dataset EGAD00001003117

• Deep WGS of matched tumor-normal pairs for HGSOC copy-number signatures study

  This dataset includes 111 bam files from WGS sequence data aligned to human genome assembly GRCh37 (hg19) from 56 tumour and matched normal samples. Libraries were constructed with ~350-bp insert length using the TruSeq Nano DNA Library prep kit (Illumina) and sequenced on an Illumina HiSeq X Ten System in paired-end 150-bp reads mode. The average depth was 60× (range 40-101×) in tumours and 40× (range 24-73×) in matched blood samples.

  Dataset EGAD00001004189

• MGUS/SMM to MM WES

  This dataset contains raw sequencing reads for matched MGUS/SMM to MM patient samples, including normal germline controls. FASTQ files were generated on Illumina NextSeq 500 and HiSeq 4000 machines following exome capture using the Agilent Clinical Research Exome kit. DNA was extracted from CD138+CD38++ cells (representing MGUS/SMM/MM cells) and CD138-CD38- (representing normal cells) isolated from bone marrow. 10 patients are included with 3 samples each representing normal, MGUS/SMM, MM stages.

  Dataset EGAD00001004190

• Primary breast tumor heterogeneity through therapy

  We performed whole-exome sequencing on multiple regions (n=2-3) from four primary untreated breast tumors (n=1 HER2+, n=2 ER+/HER2-, n=1 triple-negative), as well as matched normal. We also performed whole-exome sequencing on one region from the pre-treatment diagnostic core biopsy and multiple regions (n=2-6) from the post-treatment surgical specimen for five HER2+ primary breast tumors, as well as matched normal; all were treated with combination chemotherapy and trastuzumab. Analysis of these specimens allows characterization of breast tumor heterogeneity and clonal evolution.

  Dataset EGAD00001004306

• The impact of the human leukaemia virus HTLV-1 on host gene expression

  PBMCs were purified from blood samples of 8 HTLV-1 infected individuals, and cryo-preserved in fetal calf serum containing 10% DMSO. DNA from each samples was extracted using Qiagen Blood & Tissue kit according to the manufacturer's protocol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001004169

• Whole Exome Sequencing of 60 tumor/normal matched liver Cancers (HCC)

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors using whole genome (WGS) and whole exome sequencing (WGS), integrated with DNA methylation and RNA sequencing (RNA-seq) data. The present series corresponds to 60 whole exome tumor/normal pairs with matched RNA-seq.

  Dataset EGAD00001004180

• DNA Methylation-based diagnostic biomarkers for ESCC in Han Chinese population

  To validate the methylation status of the four candidate tumor suppressor genes (ADHFE1, EOMES, SALL1, TFPI2) in Han Chinese ESCC patients, we recruited 103 patients and obtained the paired tumors(entitled as T) and adjacent normal tissues (entitled as N) as well. Targeted bisulfite sequencing was conducted to detect the methylation profiles of these four genes in these 103 paired tissues. Furthermore, the raw sequence data (fastq files) was aligned using the BSseeker2 and this dataset included all of the bam file after alignment.

  Dataset EGAD00001004288

• Chemotherapy accelerates genomic aging of normal blood in children treated for cancer

  Whole genome sequencing (WGS) data obtained from clonally expanded hematopoietic stem and progenitor cells (HSPCs) from pediatric cancer patients before and after therapy exposure. In addition, WGS data of cord-blood derived HSPCs clones exposed to various chemotherapeutics and radiation was obtained.

  Study EGAS00001005141

• FASTQ files

  Raw FASTQ files obtained from in situ Hi-C of 16 normal B cells (3 naive B cells, 3 germinal center B cells, 3 plasma cells, and 3 memory B cells, together with a merge file for each subpopulation), 7 chronic lymphocytic leukemias (2 unmutated IGHV and 5 mutated IGHV), and 5 mantle cell lymphomas (2 conventional and 3 leukemic non-nodal).

  Dataset EGAD00001006485