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Testing association for markers on the X chromosome

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. Genet. Epidemiol. 2007. Published 2007 Wiley‐Liss, Inc. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Genetic Epidemiology Wiley

Testing association for markers on the X chromosome

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References (25)

Publisher
Wiley
Copyright
Copyright © 2007 Wiley‐Liss, Inc., A Wiley Company
ISSN
0741-0395
eISSN
1098-2272
DOI
10.1002/gepi.20244
pmid
17549761
Publisher site
See Article on Publisher Site

Abstract

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. Genet. Epidemiol. 2007. Published 2007 Wiley‐Liss, Inc.

Journal

Genetic EpidemiologyWiley

Published: Dec 1, 2007

Keywords: age‐related macular degeneration; genome‐wide association; Hardy‐Weinberg equilibrium; trend test; X‐linked markers

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