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

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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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

dc.contributor.author	Fardo, David W.
dc.contributor.author	Ionita-Laza, Iuliana
dc.contributor.author	Dermitzakis, Emmanouil T.
dc.contributor.author	Lange, Christoph
dc.date.accessioned	2012-02-12T04:55:32Z
dc.date.issued	2009
dc.identifier.citation	Fardo, David W., Iuliana Ionita-Laza, and Christoph Lange. 2009. 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. PLoS Genetics 5(7): e1000572.	en_US
dc.identifier.issn	1553-7390	en_US
dc.identifier.uri	http://nrs.harvard.edu/urn-3:HUL.InstRepos:8156570
dc.description.abstract	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.	en_US
dc.language.iso	en_US	en_US
dc.publisher	Public Library of Science	en_US
dc.relation.isversionof	doi://10.1371/journal.pgen.1000572	en_US
dc.relation.hasversion	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706974/pdf/	en_US
dash.license	LAA
dc.subject	genetics and genomics	en_US
dc.subject	complex traits	en_US
dc.subject	mathematics	en_US
dc.subject	statistics	en_US
dc.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	en_US
dc.type	Journal Article	en_US
dc.description.version	Version of Record	en_US
dc.relation.journal	PLoS Genetics	en_US
dash.depositing.author	Lange, Christoph
dc.date.available	2012-02-12T04:55:32Z
dash.affiliation.other	HMS^Medicine-Brigham and Women's Hospital	en_US
dash.affiliation.other	SPH^Biostatistics	en_US