Extended Data Table 1: Comparison between association results using imputed dosages and directly genotyped markers.
| SNP | Imputed Dosages (N=9,921) | Sequenom genotypes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||
| CHR | POS | RSID | REF | ALT | OR | SE | P | N | R2 | OR | SE | P |
| 1 | 11493832 | rs2922240 | C | T | 1.141 | 0.029 | 5.82E-06 | 9,864 | 0.991 | 1.141 | 0.029 | 5.72E-06 |
| 1 | 175151950 | rs3766688 | C | T | 0.870 | 0.029 | 1.93E-06 | 9,901 | 0.995 | 0.871 | 0.029 | 2.32E-06 |
| 1 | 228052027 | rs57047840 | G | A | 1.141 | 0.032 | 4.13E-05 | 9,724 | 0.974 | 1.141 | 0.032 | 3.91E-05 |
| 5 | 9161674 | rs55713588 | G | A | 1.302 | 0.052 | 3.34E-07 | 9,636 | 0.925 | 1.263 | 0.050 | 2.87E-06 |
| 6 | 4386107 | rs55800092 | T | C | 0.819 | 0.040 | 6.35E-07 | 9,881 | 0.992 | 0.817 | 0.040 | 5.52E-07 |
| 10 | 69624180 | rs12415800 | A | G | 1.167 | 0.029 | 8.44E-08 | 9,689 | 0.993 | 1.167 | 0.029 | 9.30E-08 |
| 10 | 126244970 | rs35936514 | T | C | 0.845 | 0.033 | 2.91E-07 | 9,915 | 0.993 | 0.842 | 0.033 | 1.40E-07 |
| 13 | 107659212 | rs61967003 | T | C | 1.765 | 0.116 | 9.64E-07 | 9,914 | 0.997 | 1.748 | 0.116 | 1.53E-06 |
| 14 | 66833851 | rs17827252 | G | C | 0.896 | 0.029 | 1.12E-04 | 8,562 | 0.999 | 0.897 | 0.031 | 3.94E-04 |
| 19 | 34493757 | rs11880240 | G | C | 1.281 | 0.056 | 1.08E-05 | 9,912 | 0.996 | 1.281 | 0.056 | 1.14E-05 |
| X | 24656658 | rs1921918 | A | G | 0.877 | 0.032 | 3.59E-05 | 9,899 | 0.994 | 0.880 | 0.032 | 6.39E-05 |
| X | 25011374 | rs11573525 | T | C | 1.158 | 0.033 | 9.60E-06 | 9,912 | 0.969 | 1.144 | 0.032 | 3.21E-05 |
The table reports results for association between MDD and 12 SNPs. The first five columns give the chromosome (CHR), genomic position (POS), SNP identifier (RSID), reference allele (REF) on Human Genome Reference GRCh37.p5 and alternative allele (ALT) called in CONVERGE. The next three columns show results for imputed allele dosages at 12 SNPs (odds ratio (OR) of association with MDD with respect to the alternative allele and standard error (SE); P-values of association (P)). The next two columns present the number of samples successfully genotyped using the Sequenom platform (a high sensitivity and specificity assay), and the Pearson correlation (R2) between the imputed allele dosages and the genotypes from Sequenom. The final three columns present results of association with MDD using genotypes from the Sequenom genotyping platform. Bold type indicates the genome-wide significant markers: Extended Data Table 1b gives further information on the results for these markers.