The database of Genotypes and Phenotypes (dbGaP)
The database of Genotypes and Phenotypes (dbGaP) is a database that was developed by the United States' National Center for Biotechnology Information to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in humans.[1] [2][3][4][5]
It is a mixture of public data, controlled access data (usually requiring ethics approval for access) and analysis of data.
The dbGaP archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. The individual level data hosted at the dbGaP is distributed through a controlled access system. The types of data distributed through the dbGaP include:
- phenotype data
- association (GWAS) data
- summary level analysis data
- SRA (Short Read Archive) data
- reference alignment (BAM) data
- VCF (Variant Call Format) data
- expression data
- imputed genotype data
- image data[6]
The individual-level data submitted to the dbGaP is required to be de-identified. No names or identifiable information is attached to the data. The genetic fingerprint however is embedded in individual's genotype data, which is not de-identifiable[6].
Starting from June, 2016, all TCGA data, including the phenotype and sequencing data, are hosted at the Genomics Data Commons website[6]
After dbGaP stopped accepting some very large data files, another portal, National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS), was established to accept them.[7][8]
References[edit]
- ↑ "Home - dbGaP - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-07-29.
- ↑ "Home - dbGaP - NCBI". 2017-11-20. Retrieved 2017-11-20.
- ↑ Tryka, Kimberly A.; Hao, Luning; Sturcke, Anne; Jin, Yumi; Kimura, Masato; Wang, Zhen Y.; Ziyabari, Lora; Lee, Moira; Feolo, Michael (2013-08-15). The Database of Genotypes and Phenotypes (dbGaP) and PheGenI. National Center for Biotechnology Information (US). Search this book on
- ↑ Mailman, Matthew D.; Feolo, Michael; Jin, Yumi; Kimura, Masato; Tryka, Kimberly; Bagoutdinov, Rinat; Hao, Luning; Kiang, Anne; Paschall, Justin (2007). "The NCBI dbGaP database of genotypes and phenotypes". Nature genetics. 39 (10): 1181–1186. doi:10.1038/ng1007-1181. ISSN 1061-4036. PMC 2031016. PMID 17898773.
- ↑ {{Cite news|url=https://medicalxpress.com/news/2014-08-nih-issues-policy-genomic.html%7Ctitle=NIH issues finalized policy on genomic data sharing|access-date=2018-07-29}|work=Medical Xpress |date=August 27, 2014}
- ↑ 6.0 6.1 6.2 Information, National Center for Biotechnology; Pike, U. S. National Library of Medicine 8600 Rockville; MD, Bethesda; Usa, 20894 (2009). Individual-level Data: General Questions. National Center for Biotechnology Information (US). Search this book on
- ↑ Slabodkin, Greg (July 24, 2018). "Portal to make largest Alzheimer's genetic database available to researchers". Health Data Management. Retrieved 2018-07-29.
- ↑ "Largest genetic database on Alzheimer's disease now re-open for business". Medical Press. July 23, 2018. Retrieved 2018-07-29.
External links[edit]
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