Along with the presence/absence of the Y-chromosome, males and females also differ in the number of X-chromosomes present. Until recently, very little information was generated about the X-chromosome’s relationship to complex human disease because most studies omitted it from analysis, or did the analysis incorrectly [8]. Past reasons for this omission include lack of coverage on genotyping chips, different number of genes on the X-chromosome versus the autosomes, and lack of statistical power to detect associations. With the advances in genotyping technology, though, microarrays now include thousands of markers on the X-chromosome compared to the arrays of old that include only a few. This increase in amount and quality of X-chromosomal data is beginning to uncover associations between X-linked genes and conditions like autoimmune disease [9], autism [10, 11], impaired cognitive function [12], and even alcoholism [13]. Further, genes on the X-chromosome are more likely to have sex-specific expression compared to genes on the autosomes [14, 15], which results from X-inactivation in females. However, the copy of the X-chromosome that is inactivated differs within each cell and some genes (~15%)
