Extended Data Table 3 Single-marker association results of top CONVERGE hits in the PGC study of MDD

From: Sparse whole-genome sequencing identifies two loci for major depressive disorder

  1. The table compares results from 12 SNPs genotyped in the CONVERGE cohort with either the same SNPs, or best available proxies within a 500 kb window, as reported by the Major Depressive Disorder Working Group of the PGC. The first five columns give the SNP identifier (RSID), chromosome (CHR), genomic position (POS), reference allele (REF) on Human Genome Reference GRCh37.p5, and alternative allele (ALT) called in CONVERGE. The next four columns show the alternative allele frequency (FREQ) and results of association testing with MDD at the 12 SNPs in CONVERGE: odds ratio (OR) of association with MDD with respect to the alternative allele and standard error (SE) in the odds ratio were obtained from a logistic regression model with PCs as covariates; P values of association (P) were obtained from a linear mixed model with a genetic relatedness matrix containing all samples. The next three columns show the SNP identifier (RSID) of best available proxy of each SNP reported in PGC-MDD, the linkage disequilibrium correlation (LD r 2) expressed as the r 2 value between the SNP in PGC-MDD and SNP in CONVERGE, and the alternative allele frequency (FREQ) at the SNP in PGC-MDD. The last three columns show the information scores (INFO), odds ratios (OR) and P values of association with MDD in PGC-MDD from a logistic regression model. Bold type indicates the genome-wide significant markers.