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• ICGC-LIRI-JP Release 15

  RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15

  Dataset EGAD00001000808

• Whole Exome Sequencing of healthy Spanish individuals - VCF file

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Dataset EGAD00001003101

• WGBS data for ependymomas and normal controls (fetal and adult)

  Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

  Dataset EGAD00001000966

• Cancer-Normal chronic myeloid leukaemia sequencing data for "A comparative analysis of algorithms for somatic SNV detection in cancer", Bioinformatics 29 (2013) 2223

  This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.

  Dataset EGAD00001000967

• APCDR Uganda GWAS - UG2G dataset: Whole genome low depth sequence data for 2000 Ugandans (BAMs).

  Low depth (4x) Illumina HiSeq raw sequence data for 2000 Ugandans from various ethno-linguistic group from rural South-West Uganda (related individuals included).

  Dataset EGAD00001001639

• Dataset for EGAS00001007937

  WGS, RNAseq, Methylation, variant calling analysis for a Novel paediatric case of a spinal high-grade astrocytoma with piloid features in a patient with Noonan Syndrome

  Dataset EGAD00001015412

• Single Cell Genome Sequence for DLP+ library A95629B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1051D passage 1 on DLP+ library A95629B

  Dataset EGAD00001009320

• Expression data

  This dataset contains the RPKM and raw read counts of expression for all the individuals. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005039

• Clinical phenotypes/covariates

  This dataset contains the clinical phenotypes/covariates information for all the individuals. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005040

• Bulk WES Fastq Files for 103 Samples of Cornell-NCI DLBCL Genomic Project

  Paired-read fastq files were derived from standard Illumina WES NGS sequencing for 103 DLBCL biopsy samples. This is one of three datasets associated with the multi-platform NGS sequencing efforts of the Cornell-NCI DLBCL genomic study.

  Dataset EGAD50000001747

• Analysis File for 87 Argentinean individuals

  VCF for 87 Argentinean samples. Only SNPs (no indels) that passed the Affymetrix QC. Data from Luisi et al. 2020. Plos One. Fine-Scale Genomic Analyses Of Admixed Individuals Reveal Unrecognized Genetic Ancestry Components In Argentina. Reference Allele column does NOT contain reference allele from genome assembly.

  Dataset EGAD00001006227

• RNASeq files for Mullighan TXVI dataset

  RNASeq files for paper titled "Prognostic and therapeutic significance of leukemia subtypes and minimal residual disease measurements in pediatric acute lymphoblastic leukemia treated with contemporary risk-directed trial: a cohort study"

  Dataset EGAD00001006609

• Sequencing data for oesophageal / related samples - Kazachenka et al (RNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples

  Dataset EGAD00001011076

• DNA WGS Short Read Sequence (Illumina NovaSeq) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

  DNA WGS Short Read Sequence (Illumina NovaSeq) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

  Dataset EGAD00001015399

• National Human Genome Research Institute (NHGRI) Clinical Sequencing Exploratory Research (CSER) The MedSeq Project: Integration of Whole Genome Sequencing into Clinical Medicine (HG006500)

  Whole genome sequencing (WGS) and whole exome sequencing (WES) services are currently available to and being utilized by physicians and their patients in both research and clinical settings, and recently to anyone in the general public via direct-to-consumer companies. But the widespread availability and use of WGS and WES in the practice of clinical medicine is imminent. In the very near future, sequencing of individual genomes will be inexpensive and ubiquitous, and patients will be looking to the medical establishment for interpretations, insight and advice to improve their health. Developing standards and procedures for the use of WGS information in clinical medicine is an urgent need, but there are numerous obstacles related to integrity and storage of WGS data, interpretation and responsible clinical integration. The MedSeq Project is an exploratory trial of WGS in clinical medicine. At the conclusion of this study, we will have helped create innovative protocols and novel outcome measures that can be applied safely in future large-scale multi-site randomized clinical trials with larger numbers of physicians from broad specialties and with more economically and ethnically diverse patients. Together with our colleagues from across the nation through the U01 consortium formed as a result of this funding from the NIH, we will have invented a process of implementation and evaluation whereby the fruits of the Human Genome Project can be applied for the first time to the daily practice of medicine for the betterment of human health. The objectives of the MedSeq Project are to: Recruit, consent and enroll 2 study groups: 10 primary care physicians and 100 of their healthy middle-aged patients 10 cardiologists and 100 of their patients with cardiomyopathy. Randomize each study group to receive standard of care versus standard of care plus WGS. Monitor the entire protocol for subject safety. Only half the enrolled patients were selected for sequencing. Fifty subjects were selected from the primary care cohort and fifty were selected from the cardiomyopathy cohort. Whole genome sequencing was performed at 30x coverage in Illumina's CLIA-certified laboratory on these 100 individuals. Generate and optimize an algorithm for interpreting WGS data covering the spectrum of human genetic variation, in terms of both previously reported and novel variants likely to influence the health of patients. Create patient reports and provide an interface for communicating clinically relevant genomic information to practicing physicians. Describe physicians' and patients' attitudes toward, and preferences for, the disclosure of WGS results at the start of the study. Evaluate physicians' experiences with receiving and interpreting patients' genetic test results and how they communicate these results to their patients. Explore how patients respond to and use WGS results by administering validated scales of psychological impact, personal utility, and behavioral responses, as well as economic and health outcomes. Although we do not have a large enough sample size for statistical comparisons of outcomes, we will conduct exploratory comparisons: Exploratory Hypotheses: Patients who receive WGS results will show equivalent levels of distress compared to patients who receive family history only. Patients with higher genetic literacy and better understanding will report greater satisfaction and less decisional regret. Patients who receive WGS will (a) be more likely to change health behaviors and (b) utilize more health care resources than those who do not receive WGS.

  Study phs000958

• Center for Common Disease Genomics [CCDG] - Cardiovascular: TexGen

  Cardiovascular disease (CVD), especially coronary heart disease, heart failure and cerebrovascular disease remain the leading causes of death in men and women across all race groups in the United States. Substantial evidence exists for genetic factors underlying CVD risk, and their discovery offers an opportunity to enhance understanding of disease mechanisms, to provide specific diagnostic and prognostic indicators, and to identify novel therapeutic targets. The Centers for Common Disease Genomics (CCDG) are a large-scale genome sequencing effort undertaken as a collaboration to identify rare risk and protective alleles for common chronic diseases, with a current focus on early onset heart disease, hemorrhagic stroke, and autism. In this study, whole genome sequencing (WGS) was performed in 6,146 individuals with any personal or family history of CVD from the TexGen study who were recruited from several institutions in the Texas Medical Center located in Houston, Texas. The participants included patients who were admitted with a variety of diagnoses including acute coronary syndromes, strokes, and transient ischemic attacks, or who underwent percutaneous coronary interventions or coronary artery bypass grafting (CABG) (Virani SS et al. Am J Cardiology 107:1504-1509, 2011). Patients in the TexGen cohort with a confirmed diagnosis of acute coronary syndrome (ACS) or CABG when discharged from the hospital between 2001-2008 were eligible for a follow-up study of recurrent myocardial infarction (Virani SS et al. Circulation J 76:950-956, 2012), while those presenting with ACS beginning in 2007 were recruited for an investigation of the role of depressive symptoms in the risk of major adverse coronary events (Sanner J et al. Biol Res Nurs 20:168-176, 2018). In addition, the initial criterion for enrollment in a third TexGen sub-study undertaken between 2007 and 2013 was the occurrence of premature acute myocardial infarction in men ≤ 50 years and women ≤ 55 years in order to establish a blood sample collection resource with the intention of localizing genes that contribute to disease risk. This definition was later expanded to include individuals with a clinical history of premature coronary heart disease such as CABG or percutaneous coronary interventions.

  Study phs003010

• Effectiveness and Safety of Intermittent Antimicrobial Therapy for the Treatment of New Onset Pseudomonas Aeruginosa Airway Infection in Young Patients With Cystic Fibrosis (EPIC-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To investigate the efficacy and safety of 4 antipseudomonal treatments in children with cystic fibrosis (CF) with recently acquired Pseudomonas aeruginosa (PA) infection.Background: CF is an inherited disease that causes mucus to build up in the lungs and digestive tract, which can cause lung infections and digestive problems. It is the most common type of chronic lung disease in children and young adults and may result in early death. There is no cure for this disease. The primary cause of death in individuals with CF is progressive obstructive pulmonary disease associated with chronic Pseudomonas aeruginosa (PA) infection. PA infection can occur early in life and can become highly resistant to antibiotics. Once an individual has been diagnosed with chronic PA infection, it is almost impossible to manage effectively. The need exists for an effective treatment to control and eliminate PA infection. Past research has shown that if PA infection is treated early, there is a greater likelihood that it may be eliminated completely.Participants: There were 304 participants.Design: Participants were randomized to 1 of 4 antibiotic regimens for 18 months (six 12-week quarters) between December 2004 and June 2009. Participants randomized to cycled therapy received tobramycin inhalation solution (300 mg twice a day) for 28 days, with oral ciprofloxacin (15-20 mg/kg twice a day) or oral placebo for 14 days every quarter, while participants randomized to culture-based therapy received the same treatments only during quarters with positive P aeruginosa cultures. The primary end points were time to pulmonary exacerbation requiring intravenous antibiotics and proportion of PA - positive cultures.Conclusions: No difference in the rate of exacerbation or prevalence of PA positivity was detected between cycled and culture-based therapies. Adding ciprofloxacin produced no benefits (Arch Pediatr Adolesc Med 2011; 165(9):847-856).

  Study phs004067

• Automated machine-learning approach for next generation profiling of sequence alterations, mutation burden, microsatellite instability, and structural variants in human cancers

  Sequence and structural alterations together with tumor mutation burden (TMB) and microsatellite instability (MSI) have been identified as biomarkers for the determination of response to targeted and immune checkpoint inhibitor therapies. However, widespread clinical adoption of these biomarkers has historically been limited due to barriers such as evidence of clinical utility and reimbursement. We have developed 2.2 Mb targeted NGS system and an automated machine-learning analysis approach (PGDx elio™ tissue complete, ETC) that has been FDA cleared for examination of 500+ cancer-related genes and 68 mononucleotide repeats for identification of sequence and structural alterations, TMB, and MSI in solid cancers in a clinical setting. We designed and trained this approach using sequence data from 4,174 cancers and >124,000 in silico alterations and evaluated the methodology in >2,550 tumor or non-cancerous normal samples. Independent analyses of ETC sequence changes in 440 formalin fixed paraffin embedded (FFPE) tumor or cell line samples using MSK-IMPACT™, FoundationOne®, and ddPCR revealed a positive percent agreement (PPA) >97% with high sensitivity as low as 3% mutant allele fraction. We observed high concordance between panel-wide and whole-exome TMB for 307 pan-cancer FFPE tumors (Pearson r=0.95, p < 0.0001) using samples with ≥20% tumor cellularity. Comparison of the mutation context and repeat-based MSI approach in ETC with a multiplex MSI PCR assay in 223 samples revealed a PPA of 99% and negative predictive agreement (NPA) >99%. We confirmed the accuracy and precision of TMB and MSI measurements across three independent laboratories (CV of <5% and average PPA >99%, respectively). Finally, evaluation of amplifications and translocations against DNA and RNA-based approaches exhibited >98% NPA and PPA of 86% and 82% respectively. These results demonstrate high analytical performance for determination of sequence and structural changes, TMB, and MSI using a targeted NGS panel and provide a scalable and facile approach for evaluating these biomarkers in a clinical laboratory.

  Study EGAS00001005556

• University of Washington Developmental Single Cell Atlas

  We set out to generate a human cell atlas of both gene expression and chromatin accessibility using tissues obtained during development. In this study, we applied an assay for single cell profiling of gene expression based on three-level combinatorial indexing (sci-RNA-seq3) to 121 fetal tissue samples representing 15 organs, altogether profiling transcription in over 4 million single cells. In parallel, we devised an improved assay for single cell profiling of chromatin accessibility also based on three-level combinatorial indexing (sci-ATAC-seq3). We applied this method to 53 fetal tissue samples representing 15 organs, altogether profiling on the order of one million single cells. From these data, we identify and characterize diverse human cell types and annotate them with respect to marker genes, expression and regulatory modules. These data comprise a rich resource for the exploration of human biology.

  Study phs002003

• Genomic Analysis of Low Grade B-Cell Lymphoma

  We included tumors from 64 newly diagnosed or untreated Low Grade B-Cell Lymphoma (LGBCL) patients, consisting of SMZL (n = 48), NMZL (n = 6), EMZL (n = 2), LPL (n = 5), and B-NOS (n = 3) in this study. Samples were selected from cases consented to the Molecular Epidemiology Resource (MER) of the University of Iowa and Mayo Clinic Lymphoma Specialized Program of Research Excellence (SPORE). RNA or DNA were extracted from 64 frozen LGBCLs tumors (with available matched germline DNA for N=61. For RNA sequencing, library preparation was done using the Illumina TruSeq RNA Exome Kit and sequenced with 100 nucleotide paired-end reads using the HiSeq 4000. For WES, library preparation was done using the Agilent SureSelect XT kit and sequenced with 100 nucleotide paired-end reads using the Illumina HiSeq 4000.

  Study phs002552

• HuBMAP: KULMAP - Human Kidney, Urinary Tract, and Lung Mapping Center

  The major goal of the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) is to generate multi-omic and spatially resolved molecular anatomical maps of the human bladder, ureter and kidneys (BUKMAP) and the lung airways and parenchyma (LAPMAP) at a single cell resolution. This entails sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner. These profiles will then inform on highly multiplexed RNA in situ imaging for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space. The combination of sequencing single dissociated cells and multiplexed in situ mapping will allow the construction of detailed spatial maps for these large organs.

  Study phs002249

• Genome-Wide Analysis of Splenic Marginal Zone Lymphoma

  Splenic Marginal Zone Lymphoma (SMZL) is a B-cell malignancy of unknown pathogenesis and thus orphan of targeted therapies. By integrating whole-exome sequencing and copy-number analysis of 8 paired tumor-normal DNAs from patients with SMZL, we show that the typical SMZL exome carries ~30 genetic alterations. Targeted resequencing of selected candidates in an extended panel of 40-117 samples revealed activating mutations of NOTCH2, a gene required for marginal-zone (MZ) development, as the most frequent and SMZL-specific lesion, accounting for approximately 20% of cases. Additional altered genes suggest that deregulation of signaling pathways normally involved in MZ development (NOTCH, NF-kappa B, and B-cell receptor) represents a critical event in SMZL pathogenesis. These findings have direct implications for the treatment of SMZL patients since drugs are available which can target NOTCH as well as other pathways deregulated in this disease.

  Study phs000502

• Host Response to Respiratory Infections

  In this study, we describe a strategy to identify undiagnosed respiratory viral infections through screening nasopharyngeal (NP) swabs for the chemokine CXCL10, which is highly induced in the nasopharynx as part of the host antiviral response. Using this strategy, we conducted two screens: first, we screened NP swabs collected at Yale New Haven Hospital (YNHH) in January 2017 from patients with undiagnosed respiratory viral infections and identified patients infected with seasonal coronaviruses and the relatively uncommon influenza C virus. Second, we screened samples from the beginning of March 2020 in the weeks before YNHH tested for SARS-CoV-2 and identified four patients that had undiagnosed SARS-CoV-2 infections. Sequences uploaded as part of this study include samples with rhinovirus, human coronavirus NL63, and 8 samples as part of the January 2017 screen for undiagnosed respiratory viral infections.

  Study phs002442

• Nature and Contribution of Noncoding, Regulatory Mutations in Neurodevelopmental Disorders

  This dbGaP study contains variant call files generated from whole-genome sequencing data of families with autism. The variant callers include FreeBayes, GATK, Platypus, and Strelka2. A family-level VCF file, from each caller, is provided for each family in the study. The families included in this study are from the Simons Simplex Collection (SSC), the Study of Autism Genetics Exploration (SAGE), and The Autism Simplex Collection (TASC); sequencing was performed at the New York Genome Center, as part of the Centers for Common Disease Genomics (CCDG) Consortium. The analysis to generate the variant callsets was supported by a K99 Pathway to Independence grant to Dr. Tychele Turner (1K99MH117165-01). *Access to phenotype data at the individual level for Simons Simplex Collection (SSC) subjects can be requested from SFARI Base: https://www.sfari.org/resource/sfari-base/.

  Study phs001874

• Genomic Characterization CS-MATCH-0007 Arm B

  The CS-MATCH-0007 protocol is part of a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and post-treatment tumor biopsy specimens from 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 specific genomic alterations found in their cancers. Arm B is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with HER2- activating mutations are treated with Afatinib. This subprotocol is one of the treatment arms included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood.

  Study phs002028