There were three classes of SNPs – those that could be heterozygous in all subjects (chr1-22 and chrX/PAR1), those that were heterozygous in females (non-PAR chrX), and those that were hemizygous in males (non-PAR chrX and chrY). All SNPs that passed quality control checks were tested for association with MDD using 1 df Cochran-Armitage trend tests. For complex traits, it is widely believed that the contributions of individual SNPs to disease risk are often roughly additive (40) . The Cochran-Armitage trend test can be used to detect such effects. This test is usually recommended due to its robustness to the violation of the HWE assumption (41): P-values from females and males for non-PAR chrX were combined using Fisher's method (42).
