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dbGaP specifications

Information


Unique identifier OMICS_00263
Name dbGaP
Alternative names database of Genotypes and Phenotypes, dbGaP Data Browser
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Michael Feolo
  • person_outline Stephen Sherry
  • person_outline Erin Ramos

Publications for database of Genotypes and Phenotypes

dbGaP citations

 (272)
library_books

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

2018
Nat Commun
PMCID: 5940825
PMID: 29739930
DOI: 10.1038/s41467-018-03621-1

[…] Genotype files were obtained from dbGaP, and updated to release 35 of the probe annotations published by Affymetrix via PLINK. Probes were filtered out that had a minor allele frequency of <0.01, were missing in >10% of subjects, or d […]

library_books

Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized

2018
BMC Cancer
PMCID: 5922022
PMID: 29703166
DOI: 10.1186/s12885-018-4373-y

[…] https://cancergenome.nih.gov/], []. Normalized read counts were log2-adjusted before further analysis. For the Prensner cohort [], RNA-Seq raw reads in fastq-format were downloaded with approval from dbGap (project #5870) with accession phs000443.v1.p1. Raw reads were mapped to the hg19 transcriptome using TopHat2 [], and featureCounts [] were used to assign the reads mapping to each gene. Normali […]

library_books

Analysis of predicted loss of function variants in UK Biobank identifies variants protective for disease

2018
Nat Commun
PMCID: 5915445
PMID: 29691411
DOI: 10.1038/s41467-018-03911-8

[…] ing exome sequencing or whole genome sequencing, as previously described–. Studies included in the MIGen consortium were: (1) the Italian Atherosclerosis Thrombosis and Vascular Biology (ATVB) study (dbGaP Study Accession phs000814.v1.p1); (2) the Exome Sequencing Project Early-Onset Myocardial Infarction (ESP-EOMI) study(9); (3) a nested case-control cohort from the Jackson Heart Study (JHS); (4) […]

library_books

Epigenome Wide Association Study of Soluble Tumor Necrosis Factor Receptor 2 Levels in the Framingham Heart Study

2018
Front Pharmacol
PMCID: 5928448
PMID: 29740313
DOI: 10.3389/fphar.2018.00207

[…] (minor allele frequency > 5% in European participants from the 1000 Genomes Project) at the CpG site, or within 10 bp of the single base extension (n = 42,251). The methylation data are available at dbGaP under the accession number phs000724.v2.p9. […]

library_books

Systemic surfaceome profiling identifies target antigens for immune based therapy in subtypes of advanced prostate cancer

2018
Proc Natl Acad Sci U S A
PMCID: 5949005
PMID: 29686080
DOI: 10.1073/pnas.1802354115

[…] FASTQ files from the Beltran 2016 RNA-Seq dataset were downloaded from dbGaP (study accession no. phs000909.v1.p1) and analyzed with the Toil RNA-Seq Pipeline. The TCGA and NIH GTEx Toil RNAseq Recompute datasets were downloaded from the University of California, Santa C […]

library_books

Identification of missing variants by combining multiple analytic pipelines

2018
BMC Bioinformatics
PMCID: 5902939
PMID: 29661148
DOI: 10.1186/s12859-018-2151-0

[…] We downloaded Sequence Read Archive (SRA) files of 10,933 ADSP individuals (5787 Alzheimer’s Disease (AD) cases and 5146 controls) from dbGap and converted to FASTQ files using the SRA Toolkit [].The FASTQ files were processed using the Mayo Clinic GenomeGPS DNA Analysis Pipeline (v3.0.2) (formerly named as TREAT) []: reads were align […]

Citations

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dbGaP institution(s)
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of Science Policy, Office of the Director, National Institutes of Health, Bethesda, MD, USA; National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, USA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
dbGaP funding source(s)
Supported by Intramural Research Program of the National Library of Medicine at the National Institutes of Health (NIH).

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