Journal
GENETIC EPIDEMIOLOGY
Volume 38, Issue 2, Pages 97-103Publisher
WILEY
DOI: 10.1002/gepi.21782
Keywords
case-control association; sex chromosomes
Funding
- German Science Foundation [KO 2250/4-1]
- German Federal Ministry of Education and Research (BMBF) [01GS0417, 01GS0832, 01KU0908A, 01KU0908B]
- EU [LSHM-CT-2006-037593, 201413, HEALTH-2011-278913]
- binational BMBF/ANR [01KU0908A]
- Universitat zu Lubeck
- German Science Foundation Excellence Cluster Inflammation at Interfaces
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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.
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