On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.

Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genoty...

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Autores principales:	David W Fardo, Iuliana Ionita-Laza, Christoph Lange
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/573f11d809654d29bf7d770e1f48517f
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spelling	oai:doaj.org-article:573f11d809654d29bf7d770e1f48517f2021-11-25T05:53:15ZOn quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.1553-73901553-740410.1371/journal.pgen.1000572https://doaj.org/article/573f11d809654d29bf7d770e1f48517f2009-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19629167/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of the genotyped SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powerful to identify probands with an unreliable genotyping quality that cannot be detected with standard quality control filters. This feature of the test is further exemplified by an application to the third release of the HapMap data. The test is ideally suited as the final layer of quality control filters in the cleaning process of genome-wide association studies. It identifies probands with insufficient genotyping quality that were not removed by standard quality control filtering.David W FardoIuliana Ionita-LazaChristoph LangePublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 5, Iss 7, p e1000572 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 David W Fardo Iuliana Ionita-Laza Christoph Lange On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
description	Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of the genotyped SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powerful to identify probands with an unreliable genotyping quality that cannot be detected with standard quality control filters. This feature of the test is further exemplified by an application to the third release of the HapMap data. The test is ideally suited as the final layer of quality control filters in the cleaning process of genome-wide association studies. It identifies probands with insufficient genotyping quality that were not removed by standard quality control filtering.
format	article
author	David W Fardo Iuliana Ionita-Laza Christoph Lange
author_facet	David W Fardo Iuliana Ionita-Laza Christoph Lange
author_sort	David W Fardo
title	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
title_short	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
title_full	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
title_fullStr	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
title_full_unstemmed	On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.
title_sort	on quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the hapmap data.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/573f11d809654d29bf7d770e1f48517f
work_keys_str_mv	AT davidwfardo onqualitycontrolmeasuresingenomewideassociationstudiesatesttoassessthegenotypingqualityofindividualprobandsinfamilybasedassociationstudiesandanapplicationtothehapmapdata AT iulianaionitalaza onqualitycontrolmeasuresingenomewideassociationstudiesatesttoassessthegenotypingqualityofindividualprobandsinfamilybasedassociationstudiesandanapplicationtothehapmapdata AT christophlange onqualitycontrolmeasuresingenomewideassociationstudiesatesttoassessthegenotypingqualityofindividualprobandsinfamilybasedassociationstudiesandanapplicationtothehapmapdata
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On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data.

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