Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data.
We explored five sex-specific quality control filters in North American Rheumatoid Arthritis Consortium's Illumina 550 k datasets. Three X chromosome and three autosomal single-nucleotide polymorphisms flagged by sex quality control filters were missed by filters of call rate at 95% and Hardy-Weinberg equilibrium at 10-6. We applied a subset of these sex-specific quality control filters to eight chromosomes in the Framingham Heart Study samples genotyped by Affymetrix 500 k SNP arrays, and identified another two single-nucleotide polymorphisms that failed to be picked up by the above global filters.
Ling
Hua
H
Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA. hling1@jhmi.edu.
Hetrick
Kurt
K
Bailey-Wilson
Joan E
JE
Pugh
Elizabeth W
EW