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• Genomic Characterization CS-MATCH-0007 Arm H

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing and RNA sequencing using pre-and post-treatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm H is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with BRAF V600K/V600E mutations are treated with Dabrafenib and Trametinib. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001888

• CSER: Exome Sequencing in Diverse Populations in Colorado and Oregon/CHARM Cancer Health Assessments Reaching Many

  The CHARM (Cancer Health Assessment Reaching Many) study, part of the Clinical Sequencing Evidence-Generating Research (CS.ER2) effort, aimed to assess the utility of clinical exome sequencing and how it affects care in diverse populations. The study population included adults at risk for hereditary cancer syndromes. The primary objective was the implementation of a hereditary cancer risk assessment program in healthy 18-49 year-olds in primary care settings within a vertically integrated health delivery system (Kaiser Permanente) and a federal qualified health center (Denver Health). The investigators aimed to assess clinical exome sequencing implementation and interpretation, as well as tailored interactions for low health literacy including a contextualized consent process, and a modified approach to results disclosure and genetic counseling. The investigators were also assessing the clinical utility (healthcare utilization and adherence to recommended care) and personal utility of primary and additional results from clinical exome sequencing, and evaluate the ethical and policy implications of considering personal utility of genomic information decisions for health care coverage.Sequencing and analysis for CHARM was conducted at the Northwest Clinical Genomics Laboratory, University of Washington, Seattle (https://nwgc.gs.washington.edu/).

  Study phs002111

• Comprehensive molecular profiling identifies novel genetic drivers and subtypes underlying medulloblastoma

  Current therapies for medulloblastoma (MB), a highly malignant childhood brain tumor, impose debilitating effects on the developing child, warranting the development of molecularly targeted treatments with reduced toxicities. Prior studies have failed to disclose the full spectrum of driver genes and molecular processes operative in MB or adequately explain heterogeneity among molecular subgroups. Herein, we detail the somatic landscape across 491 sequenced MBs and molecular heterogeneity amongst 1,256 epigenetically analyzed cases, identifying subgroup-specific mutational signatures, driver genes, and pathway alterations including previously unappreciated actionable therapeutic targets. Integrative approaches for assigning driver genes to subgroups explained >65-70% of Group 3 and Group 4, doubling previous knowledge. Novel subtypes underlying Group 3 and Group 4 were differentially enriched for specific driver events, including hotspot in-frame indels targeting KBTBD4 and ‘enhancer hijacking’ driving activation of PRDM6. Thus, application of integrative genomics to an unprecedented cohort of clinical samples derived from a single childhood cancer entity has disclosed a series of new cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for treating MB.

  Study EGAS00001001953

• Whole genome and transcriptome analysis of medullary thyroid cancer

  Medullary thyroid cancer is the neoplasm of the calcitonin-producing parafollicular cells of the thyroid gland. The hormone calcitonin acts to lower the blood calcium level, counteracting the effects of the parathyroid hormone; it can also serve as a biomarker for the presence or recurrence of medullary thyroid cancer. Surgery is the only curative treatment for this cancer. Targeted therapeutics vandetanib and cabozantinib are approved for the treatment of aggressive and metastatic tumors that are not amenable to surgery. The use of these multikinase inhibitors are supported by the observed overactivation of the RET oncoprotein in a large sub-population of medullary thyroid cancers; however, not all patients carry oncogenic alterations of this kinase. Hence, there is a need for molecular characterization of medullary tumors on the genomic scale with the aim of identifying targetable mutations. Here, we describe the genomic profiles of two medullary thyroid cancers and report the presence of a putative oncogenic BRAF fusion in one. Such alterations previously observed in other malignancies and known targets of available drugs, can benefit patients who currently have no therapy options.

  Study EGAS00001001473

• Defective T-cell expansion in RASGRP1 deficiency

  Inherited CTPS1- CD27- and CD70-deficiencies in humans have revealed key factors of T-lymphocyte expansion, that is a prerequisite for an efficient immunity to Epstein-Barr virus (EBV) infection. RASGRP1 is a T-lymphocyte specific nucleotide exchange factor known to activate the MAP kinases pathway. A deleterious homozygous mutation in RASGRP1 leading to the loss RASGRP1 expression was identified in two siblings who both developed a persistent EBV infection leading to Hodgkin lymphoma. RASGRP1-deficient T cells exhibited defective MAPK activation and impaired proliferation that was restored by expression of wild-type RASGRP1. Similar defects were observed in T cells from healthy individuals when RASGRP1 was downregulated. RASGRP1-deficient T cells also exhibited decreased CD27-dependent proliferation toward CD70-expressing EBV-transformed B cells, a crucial pathway required for expansion of antigen-specific T cells in anti-EBV immunity. Furthermore, RASGRP1-deficient T cells failed to upregulate CTPS1, an important enzyme required for DNA synthesis. These results show that RASGRP1 deficiency leads to susceptibility to EBV infection, and demonstrate the key role of RASGRP1 at the crossroad of pathways required for the expansion of activated T lymphocytes.

  Study EGAS00001002753

• Integrative_genome_profiling_in_AML

  AML emerges as a consequence of accumulating independent genetic aberrations that direct regulation and/or dysfunction of genes resulting in aberrant activation of signalling pathways, resistance to apoptosis and uncontrolled proliferation. Given the significant heterogeneity of AML genomes, AML patients demonstrate a highly variable response rate and poor median survival in response to current chemotherapy regimens. For the past 4 years we have conducted gene expression profiling on purified bone marrow populations equating to normal haematopoietic stem and progenitor cells from healthy subjects and patients with de novo AML in order to identify AML signatures of aberrantly expressed genes in cancer versus normal. We are now applying a series of bioinformatic methodologies combined with clinical and conventional diagnostic data to establish novel genomics strategies for improved prognostication of AML. Additionally, we use our AML signatures to unravel oncogenic signalling pathway activities in AML patients and test inhibitory drugs for these pathways inn preclinical therapeutic programmes. We consider that superimposing GEP and clinical data for our AML patient cohort with additional data on their mutational status will significantly improve the prognostic power of the study as well as unravel yet unknown mutations associated with aberrant signalling activities of oncogenic pathways.

  Study EGAS00001000858

• scRNA-seq of HSPC treated with gemcitabine and carbplatin

  The study used cryopreserved hematopoietic stem and progenitor cells (HSPCs) harvested from one patient with chronic myelogenous leukemia (CML). The cells were thawed and acclimatized for 48 hours in StemMACS HSC Expansion Media XF (Miltenyi Biotec) supplemented with StemMACS HSC Expansion Cocktail (Miltenyi Biotec) at 37°C in a humidified atmosphere containing 5% CO2. 4 samples of 2000000 HSPCs in 2 ml media each were then prepared and treated for 24 hours: carboplatin-high: 150 µg/ml carboplatin carboplatin-low: 18.75 µg/ml carboplatin gemcitabine: 25 ng/ml gemcitabine control: no drug Single-cells were subsequently extracted using the ddSEQ™ Single-Cell Isolator (Bio-Rad) and later sequenced using the SureCell™ Whole Transcriptome Analysis 3' Library Prep Kit (Illumina) on the NextSeq 500 System (Illumina) using the NextSeq 500/550 High Output Kit v2.5 150 Cycles (Illumina) all following the manufacturer's instructions. FASTQ-files were then processed following the ddSeeker (Romagnoli, D., et al., BMC Genomics 2018, doi:10.1186/s12864-018-5249-x) and Drop-seq (Macosko, E.Z., et al., Cell 2015, doi:10.1016/j.cell.2015.05.002) protocols for processing scRNA-seq data to yield the final digital gene expression for each cell.

  Study EGAS00001004381

• Full blood mRNA sequencing of myotonic dystrophy type 1 patients after cognitive behavioural therapy

  Myotonic dystrophy type 1 (DM1) is an incurable multisystem disease caused by a CTG-repeat expansion in the DM1 protein kinase (DMPK) gene. The OPTIMISTIC clinical trial demonstrated positive and heterogenous effects of cognitive behavioral therapy (CBT) on the capacity for activity and social participations in DM1 patients. Here, we performed mRNA sequencing of full blood for 27 patients of the OPTIMISTIC cohort before and after the CBT intervention. We identified 608 genes for which their expression was significantly associated with the disease causing CTG-repeat expansion, as well as with 1176 genes significantly associated with the average clinical response towards the intervention. Remarkably, all 97 genes significantly associated with both returned to more normal levels in patients who benefited most from CBT. This trend was consistent with the difference observed between DM1 patients and controls in an earlier study of blood mRNA expression levels, singling these genes out as candidate biomarkers for therapy response. Together these results highlight the ability to find disease relevant information in full blood of DM1 patients and open new avenues to monitor therapy effects.

  Study EGAS00001005830

• Changes in alternative splicing and associated neo-antigens due to therapy

  Recent studies have identified alternative splicing (AS) as a novel source of neoantigens for immunotherapy. Surprisingly little is known about the AS milieu in recurrent glioblastoma (GBM), despite this being the venue for most clinical trials. We profiled 29 primary-recurrent paired human GBM specimens via RNA sequencing and re-analyzed RNA-sequencing data from non-malignant human brain tissues. From these data, we reconstructed the landscape of AS in GBM through recurrence and contrasted that to isoforms observed in non-malignant brain. The AS events we identified were cross-referenced with single-cell GBM atlases to determine cell-type specific splicing patterns. From this we identified novel splicing events in cell-surface proteins that are suitable targets for engineered T-cell therapies. We found recurrent-specific isoforms of mitogen-activated kinase pathway genes which are expressed exclusively by GBM stem-like cells that enhance invasiveness. These studies shed light on the effect of therapy on AS and identify novel targets for emerging immunotherapies.

  Study EGAS00001004524

• MECOM represses myeloid differentiation through CEBPA downregulation in AML

  Transcription factor MECOM, located at 3q26, is essential for hematopoietic stem cells (HSCs) in healthy individuals. Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of leukemia (AML). Aberrantly expressed MECOM is essential for the survival and immature phenotype of these leukemia cells. Direct depletion of MECOM using an endogenous auxin-inducible degron rapidly upregulates expression of myeloid differentiation factor CEBPA. MECOM depletion is also accompanied by a severe loss of CD34 expression and gain of mature myeloid cell surface marker CD15. MECOM exerts its inhibitory effect on differentiation by binding to the +42kb CEBPA enhancer, which is essential for neutrophil development. This is partially dependent on the interaction between MECOM and its essential co-repressor CTBP2, a potential target in this type of AML. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, AML patients with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA. Our study provides insight into the mechanism by which MECOM maintains the stem cell state in AML. Furthermore, CEBPA levels are an important read-out for successful targeting of MECOM in 3q26-rearranged AML.

  Study EGAS00001008005

• Immune Checkpoint Blockade for Relapsed Hematologic Malignancy Post-HSCT

  Relapse after allogeneic hematopoietic stem cell transplantation (HSCT) is characterized by poor outcomes and novel therapeutic options are urgently needed. Immune checkpoint blockade using CTLA-4 and PD-1 blocking antibodies are a potential concept for reinstating a dormant graft-versus-leukemia (Gvl) effect. This study investigated transcriptomic changes in biopsies obtained from patients who received immune checkpoint blockade for relapsed hematologic malignancy post-HSCT and elucidated transcriptional programs associated with successful reinvigoration of GvL. Differential gene expression analysis showed evidence of increased T cell infiltration in biopsies of responders to ipilimumab treatment and demonstrated shared gene programs between GvL and GvHD.

  Study phs003291

• Diversity of U1 small nuclear RNAs and Evaluation of Diagnostic Methods for their Mutations

  U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, including medulloblastoma, yet their identification has proven challenging due to their repetitive nature. To establish a robust DNA-based, and RNA-based method for detecting U1 snRNA mutations, we performed targeted DNA sequencing using our original gene panel for medulloblastoma and RNA-sequencing. As an RNA-based method, we developed a random forest classifier employing splicing patterns which were massively altered as a result of U1 snRNA mutations. By using both methods, we successfully detected U1 snRNA mutation in five DNA samples and four RNA samples.

  Study EGAS50000000693

• Development of molecular targeted therapy for small cell lung cancer by comprehensive genome analysis

  Aims: Identifying new therapeutic targets of small cell lung cancer (SCLC), genome-wide mutation analysis has been performed. Methods: Genomic DNA was extracted from formalin-fixed or methanol-fixed tissue samples. 71 Mb of DNA fragments containing whole coding exons were concentrated using SureSelect Human All Exon V4+UTRs Kit (Agilent Technologies) followed by 100-bp paired end sequencing by HiSeq 2000 (Illumina). Participants/Materials: 51 of 1042 cases of pathologically diagnosed small seen lung cancer that were registered to National Cancer Hospital East Lung Cancer Database in 1992-2012, and which surgically resected or biopsy samples were suitable for DNA extraction for further analyses.

  Study JGAS000037

• Genomic DNA analysis for malignant mesothelioma from the patients of Japan and USA.

  Malignant mesotheliomas (MMs) are highly aggressive adult malignancies and exposure to asbestos is the major factor involved in MM pathogenesis. It is desirable for a better understanding of the molecular pathogenesis of MM will lead to more specific and effective targeted therapies. In addition it is reported that germline mutation in a specific gene (ex. BAP1) associates familial MMs, and new candidate markers to determine a subject?s predisposition to MM and for early detection need to be identified. Analysis of genomic DNA from MM tumors and reference peripheral blood from Japan and USA are ongoing to find the common genomic characters beyond race.

  Study JGAS000108

• Exome array analysis of adverse reactions to fluoropyrimidine-based therapy for gastrointestinal cancer

  Fluoropyrimidines, including 5-fluororacil (5FU) and its pro-drug Capecitabine, are the common treatment for colorectal, breast, neck and head cancers – either as monotherapy or in combination therapy. Adverse reactions (ADRs) to the treatment are common and often result in treatment discontinuation or dose reduction. Factors contributing to ADRs, including genetic variation, are poorly characterized. We performed exome array analysis to identify genetic variants that contribute to adverse reactions.Our final dataset consisted of 504 European ancestry individuals undergoing fluoropyrimidine-based therapy for gastrointestinal cancer. A subset of 254 of these were treated with Capecitabine. All individuals were genotyped on the Illumina HumanExome Array.

  Study EGAS00001002763

• Partner independent fusion gene detection by multiplexed CRISPR Cas9 enrichment and long read Nanopore sequencing (FUDGE)

  Targeted long-read nanopore sequencing. Abstract: Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. To accurately and impartially identify fusions, we developed FUDGE: FUsion Detection from Gene Enrichment. FUDGE couples target-selected and strand-specific CRISPR/Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location – to long-read Nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints - within two days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay, providing unparalleled opportunity for diagnostic pan-cancer fusion detection.

  Dataset EGAD00001006111

• Professors Colin Palmer and Ewan Pearson, from University of Dundee, are both members of the Access Group panel for the GoDARTS bioresource, which provided the data for the current study. The current Study used genotypes (EGAD00010000282) generated by the WTCCC2 (EGAS00000000121), on which both Colin and Ewan are also DAC panel members.

  Dac EGAC00001000504

• Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.

  Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.

  Dataset EGAD00001000024

• Dataset for WGS and RNA melanoma samples

  This dataset contains WGS and RNA sequencing data for 4 melanoma samples. Sequencing was performed on Illumina Novaseq 6000 and Illumina HiSeq X. The sequencing was always paired.

  Dataset EGAD50000000093

• BAM files from whole-exome sequencing of 5 agressive B-cell lymphoma tumour samples

  This dataset contains BAM files from whole-exome sequencing (WES) of 5 agressive B-cell lymphoma tumour samples for cases 2, 3, 4 and 5. For case 2, non-tumor whole-exome sequencing is also available.

  Dataset EGAD50000000803

• WGS of ecDNA neuroblastoma cell lines

  ecDNA reconstruction for MYCN-amplified neuroblastoma cell lines using shallow long-read whole-genome sequencing (MinION platform, WGS mean-coverage 5-10X).

  Study EGAS50000000349

• DAC for "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients."

  This is the DAC for the study "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients." of Andreas Trumpp (a.trumpp@dkfz.de), Roberto Würth (r.wuerth@dkfz.de) and Martin Sprick (Martin.Sprick@hi-stem.de).

  Dac EGAC50000000371

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• RNA-seq dataset for two NUP98-Rearranged Acute Myeloid Leukemia PDX samples

  This dataset includes RNA-seq of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.

  Dataset EGAD50000001564

• NGS-based targeted exome sequencing of osteosarcoma

  The present study aimed to identify potential genomic markers for the prediction of chemosensitivity in patients with OS using a genomic approach.

  Study JGAS000282

• Clinical and neuroimaging study on preclinical Alzheimer's disease.

  This clinical study aims to discriminate MCI individuals at risk for development of Alzheimer dementia, as well as preclinical AD without clinical manifestations.

  Study JGAS000272

• Zimbabwe Mendelian Disorders Genomics DAC

  Data Access Committee responsible for reviewing and approving access requests to human genomic data generated from individuals with suspected Mendelian disorders. The DAC ensures ethical use of genomic data in accordance with institutional, national, and international guidelines, protecting participant privacy while enabling responsible data sharing for research purposes.

  Dac EGAC50000000963

• Exome_sequencing_of_Non_syndromic_Congenital_Heart_Defects

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD

  Study EGAS00001002522

• 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

• A118869A

  Whole genome sequencing for single cells for library A118869A 1165 cells; filetype=bam

  Dataset EGAD00001007099

• A98258B

  Whole genome sequencing for single cells for library A98258B 1357 cells; filetype=bam

  Dataset EGAD00001007127

• A98285A

  Whole genome sequencing for single cells for library A98285A 1422 cells; filetype=bam

  Dataset EGAD00001007131

• Single Cell Genome Sequence for DLP+ library A98243B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1096A, patient-derived xenograft SA1052D passage 1 on DLP+ library A98243B

  Dataset EGAD00001009481

• A96183B

  Whole genome sequencing for single cells for library A96183B 1191 cells; filetype=bam

  Dataset EGAD00001007619

• A98253B

  Whole genome sequencing for single cells for library A98253B 1388 cells; filetype=bam

  Dataset EGAD00001007630

• A98289A

  Whole genome sequencing for single cells for library A98289A 1066 cells; filetype=bam

  Dataset EGAD00001007634

• A108863A

  Whole genome sequencing for single cells for library A108863A 1301 cells; filetype=bam

  Dataset EGAD00001007597

• A110618B

  Whole genome sequencing for single cells for library A110618B 1047 cells; filetype=bam

  Dataset EGAD00001007600

• A110621A

  Whole genome sequencing for single cells for library A110621A 1137 cells; filetype=bam

  Dataset EGAD00001007601

• A98172B

  Whole genome sequencing for single cells for library A98172B 941 cells; filetype=bam

  Dataset EGAD00001007641

• HV31 - Oxford Nanopore PromethION long-read sequencing

  Oxford Nanopore long-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~63×. Sequencing was performed at the Wellcome Centre for Human Genetics using the Oxford Nanopore PromethION platform.

  Dataset EGAD00001007043

• WGBS for T-Cell and B-Cell, control and tumor

  WGBS data for 75 paired fastq, spread over 31 samples (4 healthy T-cell, 7 healthy B-cell, 20 B-cell CLL tumors) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005970

• Single cell karyotype sequencing of 7 samples from colorectal cancer (CRC) patients

  Contains data for all cells sequenced for this study. Data is organized as one bam-file per sample. Individual cells can be identified through the CB tag in the bam-files.

  Dataset EGAD00001006438

• A98256A

  Whole genome sequencing for single cells for library A98256A 1372 cells; filetype=bam

  Dataset EGAD00001007124

• A95646B

  Whole genome sequencing for single cells for library A95646B 507 cells; filetype=bam

  Dataset EGAD00001007306

• A98168A

  Whole genome sequencing for single cells for library A98168A 1294 cells; filetype=bam

  Dataset EGAD00001007624

• Glioblastoma stem cell lines WGS data

  WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available. For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample

  Dataset EGAD00001006488

• A110673B

  Whole genome sequencing for single cells for library A110673B 1153 cells; filetype=bam

  Dataset EGAD00001007603

• A118830A

  Whole genome sequencing for single cells for library A118830A 912 cells; filetype=bam

  Dataset EGAD00001007604

• A95697B

  Whole genome sequencing for single cells for library A95697B 1233 cells; filetype=bam

  Dataset EGAD00001007610

• Single Cell Genome Sequence for DLP+ library A118808A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1096B passage 1 on DLP+ library A118808A

  Dataset EGAD00001009440

• A96175C

  Whole genome sequencing for single cells for library A96175C 1473 samples; filetype=bam

  Dataset EGAD00001008243

• A96186C

  Whole genome sequencing for single cells for library A96186C 525 samples; filetype=bam

  Dataset EGAD00001008250

• A96130B

  Whole genome sequencing for single cells for library A96130B 1267 cells; filetype=bam

  Dataset EGAD00001007114

• 10x Genomics Single Cell Gene Expression for SA1054

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTERT-22 L9 83.86

  Dataset EGAD00001009113

• 10x Genomics Single Cell Gene Expression for SA1096BX1XB02037

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1096 passage 1

  Dataset EGAD00001009137

• 10x Genomics Single Cell Gene Expression for OV2295(R2)

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma cell line OV2295(R2)

  Dataset EGAD00001009144

• Single Cell Genome Sequence for DLP+ library A96180A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 6 on DLP+ library A96180A

  Dataset EGAD00001009463

• 10x Genomics Single Cell Gene Expression for SA1035X6XB03211

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 6

  Dataset EGAD00001009150

• 10x Genomics Single Cell Gene Expression for TOV2295(R)

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma cell line TOV2295(R)

  Dataset EGAD00001009158

• Transcriptomic profiles of neuroblastoma PDXs and primary tumors

  This dataset contains bam files for RNA-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft) and 3 pairs of neuroblastoma tumors at diagnosis and at relapse.

  Dataset EGAD00001003393

• A96183C

  Whole genome sequencing for single cells for library A96183C 1036 samples; filetype=bam

  Dataset EGAD00001008247

• A96115B

  Whole genome sequencing for single cells for library A96115B 1201 cells; filetype=bam

  Dataset EGAD00001007112

• Illumina genome sequencing data for HICF2 craniosynostosis families (Genome Medicine)

  BAM files for two families recruited to the HICF2 genome sequencing project due to craniosynostosis. One family is a singleton and the other is an affected mother-daughter duo.

  Dataset EGAD00001011373

• A98253A

  Whole genome sequencing for single cells for library A98253A 1250 cells; filetype=bam

  Dataset EGAD00001007629

• Single Cell Genome Sequence for DLP+ library A96113A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage on DLP+ library A96113A

  Dataset EGAD00001009453

• Single Cell Genome Sequence for DLP+ library A96130A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA609 passage 8 on DLP+ library A96130A

  Dataset EGAD00001009454

• Single Cell Genome Sequence for DLP+ library A96154A

  Single Cell Genome Sequence for triple negative breast cancer patient SA1135, patient SA1162SA on DLP+ library A96154A

  Dataset EGAD00001009456

• Single Cell Genome Sequence for DLP+ library A96175A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 7 on DLP+ library A96175A

  Dataset EGAD00001009461

• A96120A

  Whole genome sequencing for single cells for library A96120A 1143 cells; filetype=bam

  Dataset EGAD00001007640

• Single Cell Genome Sequence for DLP+ library A95652B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage 1 on DLP+ library A95652B

  Dataset EGAD00001009327

• A95623B

  Whole genome sequencing for single cells for library A95623B 1363 cells; filetype=bam

  Dataset EGAD00001007608

• A96155C

  Whole genome sequencing for single cells for library A96155C 1316 cells; filetype=bam

  Dataset EGAD00001007617

• Single Cell Genome Sequence for DLP+ library A96205B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage 1 on DLP+ library A96205B

  Dataset EGAD00001009471

• A108732A

  Whole genome sequencing for single cells for library A108732A 1139 cells; filetype=bam

  Dataset EGAD00001007592

• A110618A

  Whole genome sequencing for single cells for library A110618A 1184 cells; filetype=bam

  Dataset EGAD00001007599

• A110673A

  Whole genome sequencing for single cells for library A110673A 1089 cells; filetype=bam

  Dataset EGAD00001007602

• Exome and Targeted sequencing of GZL

  Tumor and matching normal exomes for 28 GZL cases (n=56) and targeted capture sequencing for 42 GZL cases with 3 matching normals and 2 pooled normals (n=47)

  Dataset EGAD00001006328

• Single Cell Genome Sequence for DLP+ library A95717B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050D passage 1 on DLP+ library A95717B

  Dataset EGAD00001009489

• PPIL4 is essential for brain angiogenesis and implicated in intracranial aneurysms in humans

  Patients in IA cohort with PPIL4 mutations (Please see Supplementary Table 3 for clinical characteristics of the patients)

  Dataset EGAD00001008106

• BLUEPRINT September 2016, ATAC-seq for bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002710

• 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

• 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

• A96149B

  Whole genome sequencing for single cells for library A96149B 1792 samples; filetype=bam

  Dataset EGAD00001008235

• Single Cell Genome Sequence for DLP+ library A96161A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96161A

  Dataset EGAD00001009457

• Data for the genome‐wide association study of cutaneous leishmaniasis in Brazil

  DNAs were genotyped on Illumina Infinium HumanCoreExome Beadchips (Illumina Inc., San Diego, CA, USA) with probes for 551,004 single nucleotide variants (SNVs): 282,373 informative across ancestries; 268,631 exome-focused. Human genome build 37 (hg19) was used.

  Dataset EGAD00001006681

• 10x Genomics Single Cell Gene Expression for SA1055

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTERT-22 L9 112.109

  Dataset EGAD00001009111

• 10x Genomics Single Cell Gene Expression for SA1053FX1XB01611

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1053 passage 1

  Dataset EGAD00001009128

• 10x Genomics Single Cell Gene Expression for SA1051DX1XB01482

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1051 passage 1

  Dataset EGAD00001009133

• 10x Genomics Single Cell Gene Expression for SA1096CX1XB02039

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1096 passage 1

  Dataset EGAD00001009136

• 10x Genomics Single Cell Gene Expression for SA1035X5XB03021

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 5

  Dataset EGAD00001009153

• A96118A

  Whole genome sequencing for single cells for library A96118A 1193 cells; filetype=bam

  Dataset EGAD00001007113

• Whole exome sequencing of human and mouse sarcoma samples for personalized therapy

  Whole exome sequencing of human and mouse sarcoma samples for creation of personalized therapy options. Tissues were sequenced directly; no interventions or alterations were made to the tissue samples

  Dataset EGAD00001004885

• Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Dataset EGAD00001000806

• V4 panel bait design test (2018-03-07)

  Targeted gene screen of FFPEs, cell lines and primary CRC tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07.

  Dataset EGAD00001004001

• GENCORD2_GENOTYPES

  204 individuals were genotyped with the Illumina 2.5M Omni chip. Filtered genotypes were imputed into the 1000 genomes project European panel SNPs. Beagle R2 is indicated in VCF files for further filtering. See Materials and Methods in publication for details.

  Dataset EGAD00001000428

• Single Cell Genome Sequence for DLP+ library A118816A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1180C passage 1 on DLP+ library A118816A

  Dataset EGAD00001009444

• Single Cell Genome Sequence for DLP+ library A96194A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1053B passage 1 on DLP+ library A96194A

  Dataset EGAD00001009468

• Single Cell Genome Sequence for DLP+ library A96194B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1053E passage 1 on DLP+ library A96194B

  Dataset EGAD00001009469