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

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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

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