How to Include Chromosome X in Your Genome-Wide Association Study

Inke R. König*, Christina Loley, Jeanette Erdmann, Andreas Ziegler

*Corresponding author for this work
14 Citations (Scopus)


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.

Original languageEnglish
JournalGenetic Epidemiology
Issue number2
Pages (from-to)97-103
Number of pages7
Publication statusPublished - 01.02.2014


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