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. 2014 Feb;38(2):97-103.
doi: 10.1002/gepi.21782. Epub 2014 Jan 9.

How to include chromosome X in your genome-wide association study

Inke R König  1 , Christina Loley, Jeanette Erdmann, Andreas Ziegler
Affiliations
Free article

How to include chromosome X in your genome-wide association study

Inke R König et al. Genet Epidemiol. 2014 Feb.
Free article

Abstract

In current genome-wide association studies (GWAS), the analysis is usually focused on autosomal variants only, and the sex chromosomes are often neglected. Recently, a number of technical hurdles have been described that add to a reluctance of including chromosome X in a GWAS, including complications in genotype calling, imputation, and selection of test statistics. To overcome this, we provide a "how to" guide for analyzing X chromosomal data within a standard GWAS. Following a general pipeline for GWAS, we highlight the steps in which the X chromosome requires specific attention, and we give tentative advice for each of these. Through this, we show that by selection of sensible algorithms and parameter settings, the inclusion of chromosome X in GWAS is manageable. Closing this gap is expected to further elucidate the genetic background of complex diseases, especially of those with sex-specific features.

Keywords: case-control association; sex chromosomes.

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