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Quality Control of Genotypes Using Heritability Estimates of Gene Content

Monday, August 18, 2014
Posters (The Westin Bayshore)
Natalia S. Forneris , Department of Animal Science, University of Buenos Aires, Buenos Aires, Argentina
Andres Legarra , INRA, Castanet-Tolosan, France
Zulma G. Vitezica , INRA, Castanet-Tolosan, France
Shogo Tsuruta , University of Georgia, Athens, GA
Ignacio Aguilar , INIA, Las Brujas, Uruguay
Rodolfo J.C. Cantet , CONICET, Buenos Aires, Argentina
Ignacy Misztal , University of Georgia, Athens, GA
Abstract Text: Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip

Keywords:

Quality Control

Gene Content

Heritability