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Activity Number:
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470
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Type:
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Contributed
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Date/Time:
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Wednesday, August 5, 2009 : 10:30 AM to 12:20 PM
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Sponsor:
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Section on Statistics in Epidemiology
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| Abstract - #303476 |
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Title:
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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
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Author(s):
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David Fardo*+ and Iuliana Ionita-Laza and Christophe Lange
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Companies:
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University of Kentucky and Harvard School of Public Health and Harvard University
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Address:
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Dept. of Biostatistics, College of Public Health, Lexington, KY, 40506,
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Keywords:
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genome-wide association studies ; family-based association ; genetic epidemiology ; quality control
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Abstract:
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Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based GWAS. We propose a transmission test based on this feature that can be used for QC filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powered to identify probands with unreliable genotyping quality that cannot be detected with standard QC 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 GWAS to identify subjects with insufficient genotyping quality that were not identified by standard QC filtering.
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