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• Data Access Committee for data from EGAS00001002864

  Dac EGAC00001003487

• Data Access Committee for data from EGAS00001007832

  Dac EGAC00001003500

• Data Access Committee for data from EGAS00001007819

  Dac EGAC00001003501

• Data Access Committee for data from EGAS00001007904

  Dac EGAC00001003512

• Data Access Committee for data from EGAS00001008107

  Dac EGAC00001003568

• UCL Centre for Longitudinal Studies

  Dac EGAC00001001041

• BAP1 Project

  For our BAP1 manuscript

  Dac EGAC50000000006

• EGAD00010000608

  SNP6 data for seminoma samples

  Dataset EGAD00010000608

• PEDS-PLAN - Pediatric Precision Laboratory Advanced Neuroblastoma Therapy

  A multi-center clinical trial for newly diagnosed high-risk neuroblastoma patients. Molecular tumor boards selected one of six targeted agents based on tumor-normal whole exome sequencing and tumor RNA sequencing data.

  Study phs002303

• Genome-wide association scan in psoriasis

  To identify novel susceptibility loci for psoriasis, we undertook a genome-wide association scan of of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls.

  Study EGAS00000000108

• cfDNA sWGS BAM — Breast cancer stage II-III (HR+/HER2−)

  Plasma cfDNA sWGS for breast cancer patients (HR+/HER2−, stage II–III), blood drawn pre-operatively (no neoadjuvant), Centre Léon Bérard/MyProbe (France). Libraries: DSP and/or SSP as recorded. Sequencing by IntegraGen (2022–2024); alignment to GRCh38 with BWA-MEM; BAMs sorted/indexed; primary mapped reads only (see analysis metadata for exact filters/MAPQ). Controlled access.

  Dataset EGAD50000001877

• Bulk ATAC data

  Bulk ATAC libraries were generated for patient samples A.1, A.3, A.5, A.6, A.7, A.11, A.12, A.13 and A.15. For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010188

• Mucosal 16S sequencing data

  16S-V4 rRNA gene sequence data for intestinal biopsies from NCT02749630 trial participants. Biopsies from patients were collected at screening, day 30, and day 85 and prepared for 16SV4 rRNA gene sequencing.

  Dataset EGAD00001008843

• RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  Dataset EGAD00001008656

• single-cell RNAseq FASTq files for three muscle-invasive bladder tumors

  single-cell RNAseq FASTq files for three muscle-invasive bladder tumors

  Dataset EGAD00001008001

• Genomic and transcriptomic data of glioma specimens

  Dataset consists of 207 glioma samples of WHO grades II, III and IV. Dataset consists 182 tumor derived genomic data of ~700 cancer-related and epigenetic-related genes with matched blood samples for 48 specimens. Dataset also consists transcriptomic data for 105 specimens. In total 335 bam files were deposited.

  Dataset EGAD00001006299

• aCGH CNV detection by CNsolidate for 6,827 DDD probands

  aCGH CNV detection by CNsolidate for 6,827 DDD probands

  Dataset EGAD00001005728

• Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

  Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

  Dataset EGAD00001005519

• RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL

  RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004463

• RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL

  RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004461

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days LPS, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days LPS sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002337

• BLUEPRINT release August 2015, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

  Dataset EGAD00001001545

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days B-glucan, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days B-glucan sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002522

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days untreated, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days untreated sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002457

• BLUEPRINT release August 2016, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 2 alternatively activated macrophage sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002481

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute promyelocytic leukemia

  Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001167

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute myeloid leukemia

  Bisulfite-Seq data for 1 Acute myeloid leukemia sample(s). 18 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001162

• BLUEPRINT release January 2015, DNase-Hypersensitivity for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001161

• BLUEPRINT release January 2015, Bisulfite-Seq for Multiple myeloma

  Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001152

• BLUEPRINT release January 2015, DNase-Hypersensitivity for CD14-positive, CD16-negative classical monocyte

  DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001130

• BLUEPRINT release August 2014, DNase-Hypersensitivity for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000942

• BLUEPRINT release August 2014, Bisulfite-Seq for Multiple myeloma

  Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000934

• BLUEPRINT release August 2014, DNase-Hypersensitivity for CD14-positive, CD16-negative classical monocyte

  DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000905

• cell-free DNA Whole Genome Sequencing of 3784 samples on MGI and Illumina platform

  The dataset of Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA includes 3784 whole genome sequencing bam files on the MGI and Illumina platform. The analyzed samples include plasma samples from normal individuals and patients with cancer.

  Dataset EGAD00001009335

• DAC for achalasia risk consortium (arc)

  Dac EGAC00001000394

• DAC for aflatoxin project Qidong patient samples

  Dac EGAC00001000679

• DAC for seminoma genomic data

  Dac EGAC00001000231

• DAC for study WES of pituitary tumors

  Dac EGAC00001000443

• Data Access Committee for Hui Lab

  Dac EGAC00001000454

• INRP - Italian Network for Research on Psychoses

  Dac EGAC00001000576

• DAC for MOMA, Short QT Exome data

  Dac EGAC00001000730

• DAC for Dissecting Tumor Microenvironment with Tumorgrafts

  Dac EGAC00001000809

• Data Access Committee for data from EGAS00001002840

  Dac EGAC00001000834

• DAC for human single nuclei RNAseq of Epilepsy

  Dac EGAC00001000860

• Laboratory for Neurobiology (VIB-KU Leuven)

  Dac EGAC00001001282

• DAC for HSTCL study. National Cancer Centre Singapore.

  Dac EGAC00001001302

• DAC for MEITL study. National Cancer Centre Singapore.

  Dac EGAC00001001323

• DAC for Phylogenetic reconstruction of breast cancer

  Dac EGAC00001001572

• Center for Technology Licensing at Cornell University

  Dac EGAC00001001587

• Data Access Commitee for single-cell analysis

  Dac EGAC00001001600

• DAC for Stuttgart Breast Cancer Cohort

  Dac EGAC00001001693

• Data Access Committee for data from EGAS00001004619

  Dac EGAC00001001712

• DAC for 16 year brca case report

  Dac EGAC00001001714

• Data Access Committee for data from EGAS00001004666

  Dac EGAC00001001756

• Data Access Committee for data from EGAS00001004455

  Dac EGAC00001001798

• Genentech DAC for IMmotion151

  Dac EGAC00001001813

• Single cell multi-omics (scNOVA) group for AML

  Dac EGAC00001001866

• Data Access Committee for IPF Collaboration

  Dac EGAC00001001878

• Center for Medical Genetics Data Access Commitee

  Dac EGAC00001001892

• DAC for cell free DNA TAPS study

  Dac EGAC00001001903

• Data access committee for lung cancer

  Dac EGAC00001001942

• DAC for single cell RNAseq in FL project

  Dac EGAC00001002114

• DAC-for-UniExome-EGA-upload-2021

  Dac EGAC00001002168

• DAC for Germline biallelic mutation

  Dac EGAC00001002423

• DAC for Identification of Germline Monoallelic Mutations

  Dac EGAC00001002461

• DAC for studying human normal breast cells

  Dac EGAC00001002481

• DAC for studying human normal breast cells

  Dac EGAC00001002498

• DAC for Castleman. National Cancer Centre Singapore.

  Dac EGAC00001003328

• PDiamond. DAC

  DAC for pdiamond project

  Dac EGAC50000000377

• DAC - Institute for Pharmacology and Toxicology

  Dac EGAC00001003385

• DAC for ALSPAC whole exome sequencing data

  Dac EGAC00001003496

• DAC for NMIBC study - UCLouvain

  Dac EGAC50000000789

• Data Access Committee for data from EGAS00001004454

  Dac EGAC00001002077

• LUMC Department Pediatrics, Laboratory for Pediatric Immunology

  Dac EGAC50000000822

• Data Access Committee for data from EGAS00001006662

  Dac EGAC00001003009

• Data Access Committee for data from EGAS00001005944

  Dac EGAC00001002583

• Tumor educated platelets for BrCA

  Study EGAS00001006821

• RNASeq for BMI GL study

  Study EGAS00001004127

• EGAD00010000606

  SNP6 data for matched normal samples

  Dataset EGAD00010000606

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (28 tumor/control pairs)

  Dataset EGAD00001003207

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (12 tumor/control pairs)

  Dataset EGAD00001003208

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (cell_line)

  Dataset EGAD00001003210

• sWGS of core biopsies from localized breast cancer patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

  Dataset EGAD00001008397

• Integrated Metabolic Profiling and Gene Expression Analysis Reveals Therapeutic Modalities in Breast Cancer

  In this study, we performed metabolite profiling and RNA-sequencing on human breast cancer tumors and normal breast tissue samples, including triple negative breast cancer (TNBC), estrogen receptor positive breast cancer (ER+) and paired normal samples, and patient-derived xenografts (PDX) samples. Here, we report two distinctive groups defined by metabolites; a TNBC-HIGH group that shows high levels of pyrimidine pathway metabolites and biosynthetic enzymes, and an ER-HIGH group that shows high levels of fatty acid and arginine biosynthesis intermediates. We identify different metabolic enrichment profiles between cell lines grown in vitro vs. in vivo; cell lines grown in vivo recapitulate patient tumors metabolic profiles. Further, we identify a subset of genes that strongly correlates with the TNBC-HIGH metabolic profile using integrated metabolic and gene expression profiling, which strongly predicts patient prognosis when tested on larger human datasets. As a proof-of-principle, when we target TNBC-HIGH metabolic dysregulation with a pyrimidine biosynthesis inhibitor (Brequinar), and/or a glutaminase inhibitor (CB-839), we observe therapeutic efficacy and decreased tumor growth in representative TNBC cell lines, murine p53-null mammary tumors, and in vivo patient-derived xenografts (PDXs) upon multi-agent drug treatment. This study highlights potential new therapeutic opportunities in breast cancers guided by a genomic biomarker, which could prove impactful for breast cancers that rapidly proliferate.

  Study phs002396

• INSPIRE - Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response in Metastatic Solid Tumors

  Whole exome and RNA sequencing source data for: Clouthier, D.L., Lien, S.C., Yang, S.Y.C. et al. An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE). j. immunotherapy cancer 7, 72 (2019). https://doi.org/10.1186/s40425-019-0541-0 Bratman S*, Yang SYC*, Iafolla MAJ, Liu Z, Hansen AR, Bedard P, Lheureux S, Spreafico A, Razak AA, Shchegrova S, Louie M, Billings P, Zimmerman B, Sethi H, Aleshi A, Torti D, Marsh K, Eagles J, Cirlan I, Hanna Y, Clouthier D, Lien SC, Ohashi PS, Xu W, Siu LL, Pugh TJ. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nature Cancer. 2020:1:873-881. https://doi.org/10.1038/s43018- 020-0096-5. Yang SYC, Lien SC, Wang BX, Clouthier DL, Hanna Y, Cirlan I, Zhu K, Bruce JP, El Ghamrasni S, Iafallo MAJ, Oliva M, Hansen AR, Spreafico A, Bedard PL, Lheureux S, Razak A, Speers V, Berman HK, Aleshin A, Haibe-Kains B, Brooks DG, McGaha TL, Butler MO, Bratman SV, Ohashi PS, Siu LL, and Pugh TJ. Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. Nature Comm 2021:12, 5137. https://doi.org/10.1038/s41467-021-25432-7

  Study EGAS00001003280

• DAC for human liver NPC single cell project

  Dac EGAC00001003207

• Data Access Commitee for skin scRNA-seq

  Dac EGAC00001003129

• DAC for study PTP and Vel Exome Sequencing

  Dac EGAC00001000013

• DAC for Cell Line Data Test of TraIT

  Dac EGAC00001000436

• DAC for Department of Haematology, Aalborg University Hospital

  Dac EGAC00001000543

• DAC for Sardinia Leukocytes polyA RNAseq 624 project

  Dac EGAC00001000561

• Data Access Committee for Institut Curie Data

  Dac EGAC00001000623

• Data Access Committee for Institut Curie

  Dac EGAC00001000670

• Data Access Commitee for gastric cancer ascites

  Dac EGAC00001001026

• DAC for study EGAS00001003438: Clonal Heterogeneity in Glioblastoma

  Dac EGAC00001001118

• DAC for MCO colorectal cancer genomics at UNSW

  Dac EGAC00001001122

• DAC for Genomic characterization of metastatic breast cancers

  Dac EGAC00001001129

• DAC for GAMuT Project - Peter MacCallum Cancer Centre

  Dac EGAC00001001154

• DAC for GAMuT Project - Peter MacCallum Cancer Centre

  Dac EGAC00001001278

• DAC for Genomics of MDS Freiburg Germany

  Dac EGAC00001001294