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词条 Draft:The database of Genotypes and Phenotypes (dbGaP)
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{{AFC submission|d|essay|ns=118|u=Jacknunn|decliner=K.e.coffman|declinets=20181024215012|ts=20180729212447}} {{AFC submission|d|nn|u=Jacknunn|ns=118|decliner=Ernestchuajiasheng|declinets=20171230090928|small=yes|ts=20171120025936}} {{AFC comment|1=Since much of this content appears verbatim on a gov website, a Wiki page does not appear to be necessary. K.e.coffman (talk) 21:50, 24 October 2018 (UTC)}}{{AFC comment|1=Note, reference 5 (" issues finalized policy on genomic data sharing") is incorrectly formatted, and the URL 404's. I'm assuming https://www.nih.gov/news-events/news-releases/nih-issues-finalized-policy-genomic-data-sharing would be a good substitute, but please verify that. -- RoySmith (talk) 16:47, 1 August 2018 (UTC)}}{{AFC comment|1=Per Copyrights#Works by the United States Federal Government, taking text from the NCBI website is probably not a copyright violation. Still, earwig shows some additional duplication from other sources (which may, in turn, all just be traceable back to NCBI). Even if this isn't strictly a copyvio, best practice would be to rewrite this as original text. -- RoySmith (talk) 16:37, 1 August 2018 (UTC)}}{{AFC comment|1=To the reviewer, be advised that 75% of the content appears directly taken from: https://www.ncbi.nlm.nih.gov/books/NBK117240/

I'm unsure if it strictly meets the requirements for a full CSD, but if removed there wouldn't appear to be any suitable content left.

To the creator, please paraphrase your information when you source it, we don't have permission to directly copy information Nosebagbear (talk) 21:47, 31 July 2018 (UTC)}}


{{Refimprove|date=July 2018}}

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

1. ^{{Cite web|url=https://www.ncbi.nlm.nih.gov/gap|title=Home - dbGaP - NCBI|website=www.ncbi.nlm.nih.gov|language=en|access-date=2018-07-29}}
2. ^{{Cite web|url=https://web.archive.org/web/20171120025343/https://www.ncbi.nlm.nih.gov/gap|title=Home - dbGaP - NCBI|date=2017-11-20|access-date=2017-11-20}}
3. ^{{Cite book|url=https://www.ncbi.nlm.nih.gov/books/NBK154410/|title=The Database of Genotypes and Phenotypes (dbGaP) and PheGenI|last=Tryka|first=Kimberly A.|last2=Hao|first2=Luning|last3=Sturcke|first3=Anne|last4=Jin|first4=Yumi|last5=Kimura|first5=Masato|last6=Wang|first6=Zhen Y.|last7=Ziyabari|first7=Lora|last8=Lee|first8=Moira|last9=Feolo|first9=Michael|date=2013-08-15|publisher=National Center for Biotechnology Information (US)|language=en}}
4. ^{{Cite journal|last=Mailman|first=Matthew D.|last2=Feolo|first2=Michael|last3=Jin|first3=Yumi|last4=Kimura|first4=Masato|last5=Tryka|first5=Kimberly|last6=Bagoutdinov|first6=Rinat|last7=Hao|first7=Luning|last8=Kiang|first8=Anne|last9=Paschall|first9=Justin|date=2007|title=The NCBI dbGaP database of genotypes and phenotypes|url=|journal=Nature genetics|volume=39|issue=10|pages=1181–1186|doi=10.1038/ng1007-1181|issn=1061-4036|pmc=2031016|pmid=17898773|via=}}
5. ^{{Cite news|url=https://medicalxpress.com/news/2014-08-nih-issues-policy-genomic.html|title=NIH issues finalized policy on genomic data sharing|access-date=2018-07-29}|work=Medical Xpress |date=August 27, 2014}
6. ^1 2 {{Cite book|url=https://www.ncbi.nlm.nih.gov/books/NBK117240/|title=Individual-level Data: General Questions|last=Information|first=National Center for Biotechnology|last2=Pike|first2=U. S. National Library of Medicine 8600 Rockville|last3=MD|first3=Bethesda|last4=Usa|first4=20894|date=2009|publisher=National Center for Biotechnology Information (US)}}
7. ^{{Cite news|url=https://www.healthdatamanagement.com/news/portal-to-make-largest-alzheimers-genetic-database-available-to-researchers|title=Portal to make largest Alzheimer's genetic database available to researchers|work=Health Data Management|first=Greg |last=Slabodkin|date=July 24, 2018|access-date=2018-07-29|language=en}}
8. ^{{Cite news|url=https://medicalxpress.com/news/2018-07-largest-genetic-database-alzheimer-disease.html|title=Largest genetic database on Alzheimer's disease now re-open for business|work=Medical Press |date=July 23, 2018| access-date=2018-07-29}}

External links

  • {{Official website|https://www.ncbi.nlm.nih.gov/gap}}
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