Testing association for markers on the X chromosome.
Test statistics for association between markers on autosomal chromosomes and a disease have been extensively studied. No research has been reported on performance of such test statistics for association on the X chromosome. With 100,000 or more single-nucleotide polymorphisms (SNPs) available for genome-wide association studies, thousands of them come from the X chromosome. The X chromosome contains rich information about population history and linkage disequilibrium. To identify X-linked marker susceptibility to a disease, it is important to study properties of various statistics that can be used to test for association on the X chromosome. In this article, we compare performance of several approaches for testing association on the X chromosome, and examine how departure from Hardy-Weinberg equilibrium would affect type I error and power of these association tests using X-linked SNPs. The results are applied to the X chromosome of Klein et al. [2005], a genome-wide association study with 100K SNPs for age-related macular degeneration. We found that a SNP (rs10521496) covered by DIAPH2, known to cause premature ovarian failure (POF) in females, is associated with age-related macular degeneration.
Zheng
Gang
G
Office of Biostatistics Research, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-7938, USA. zhengg@nhlbi.nih.gov
Joo
Jungnam
J
Zhang
Chun
C
Geller
Nancy L
NL
D041321:Chromosomes, Human, X; D005260:Female; D040181:Genetic Diseases, X-Linked; D008040:Genetic Linkage; D005819:Genetic Markers; D006801:Humans; D008268:Macular Degeneration / Q000235:genetics; D008297:Male; D020641:Polymorphism, Single Nucleotide; D016649:Primary Ovarian Insufficiency / Q000235:genetics; D013223:Statistics as Topic
D005819:Genetic Markers