TY - JOUR T1 - XWAS: A toolset for genetic data analysis and association studies of the X chromosome JF - bioRxiv DO - 10.1101/009795 SP - 009795 AU - Diana Chang AU - Feng Gao AU - Alon Keinan Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/10/30/009795.abstract N2 - Background The X chromosome plays an important role in complex human traits and diseases, especially those with sexually dimorphic characteristics. Special attention needs to be given to analysis of X, since unlike the non-sex chromosomes, males only carry one copy of the chromosome that they inherit from their mother, while in females, one of the two copies is transcriptionally silenced via X-inactivation. The different mode of inheritance leads to several analytical complications that have resulted in the majority of genome-wide association studies (GWAS) not considering the X chromosome or otherwise mishandling it by applying the same tools designed for non-sex chromosomes. Hence, there is a need for tools deploying association methods and quality control procedures that are specifically designed for the X chromosome and that account for its uniqueness.Results We present XWAS (chromosome X-Wide Analysis toolSet) – a toolset specially designed for analysis of the X chromosome in association studies, both on the level of single markers and the level of entire genes. It further offers other X-specific analysis tools, including quality control procedures for X-linked data. We applied the analysis pipeline offered by this toolset to 16 GWAS datasets of immune-related disorders. We discovered several new associations on the X chromosome that have not been previously reported, one of which shows evidence of a pleiotropic affect across several diseases.Conclusion The XWAS toolset facilitates proper analysis of X-linked data from different types of association studies. This toolset, together with its use to discover genes underlying autoimmune disease risk, will provide the tools and incentive for others to incorporate X into GWAS, thereby enabling discoveries of novel X-linked loci implicated in many diseases and in their sexual dimorphism. ER -