Table 3.
Association of KCNE1 top SNPs with BDI scores at baseline and year 1 in the full sample and the Non-Hispanic White subsample.
| SNP* | Chr | Position (Build 137) | Nearest Gene | Alleles** | MAF | N | Time | Effect | Unadjusted BDI | Adjusted BDI | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Beta | SE | p-value | Beta | SE | p-value | ||||||||||
| OVERALL SAMPLE | rs1543654 | 21 | 35799050 | KCNE1 | T/C | 35.03 | 2118 | Baseline | Average | 0.35 | 0.16 | 0.0257 | 0.33 | 0.17 | 0.0578 |
| Year 1 | ILI | −0.12 | 0.21 | 0.5487 | −0.19 | 0.22 | 0.3863 | ||||||||
| DSE | −1.05 | 0.21 | 6.9E-07 | −1.02 | 0.22 | 1.9E-06 | |||||||||
| Average | −0.59 | 0.15 | 0.0001 | −0.61 | 0.15 | 0.0001 | |||||||||
| ILI-DSE Diff | 0.92 | 0.3 | 0.0019 | 0.83 | 0.31 | 0.0069 | |||||||||
| rs9975215 | 21 | 35814953 | KCNE1 | G/C | 31.42 | 2118 | Baseline | Average | 0.22 | 0.16 | 0.1808 | 0.22 | 0.18 | 0.2164 | |
| Year 1 | ILI | 0.06 | 0.21 | 0.7923 | 0.08 | 0.23 | 0.7313 | ||||||||
| DSE | −1.05 | 0.22 | 1.5E-06 | −1.07 | 0.23 | 2.1E-06 | |||||||||
| Average | −0.50 | 0.15 | 0.0012 | −0.50 | 0.16 | 0.0019 | |||||||||
| ILI-DSE Diff | 1.11 | 0.31 | 0.0003 | 1.15 | 0.32 | 0.0003 | |||||||||
| NON-HISPANIC WHITE SAMPLE | rs1543654 | 21 | 35799050 | KCNE1 | T/C | 37.42 | 1614 | Baseline | Average | 0.33 | 0.17 | 0.0467 | 0.34 | 0.18 | 0.068 |
| Year 1 | ILI | 0.13 | 0.22 | 0.5468 | 0.09 | 0.23 | 0.7119 | ||||||||
| DSE | −1.10 | 0.23 | 1.1E-06 | −1.08 | 0.24 | 5.3E-06 | |||||||||
| Average | −0.48 | 0.16 | 0.0022 | −0.49 | 0.17 | 0.0028 | |||||||||
| ILI-DSE Diff | 1.23 | 0.32 | 0.0001 | 1.16 | 0.33 | 0.0004 | |||||||||
| rs9975215 | 21 | 35814953 | KCNE1 | G/C | 30.89 | 1614 | Baseline | Average | 0.26 | 0.18 | 0.1485 | 0.28 | 0.2 | 0.152 | |
| Year 1 | ILI | 0.26 | 0.23 | 0.2676 | 0.30 | 0.25 | 0.2205 | ||||||||
| DSE | −1.26 | 0.24 | 1.7E-07 | −1.29 | 0.26 | 4.5E-07 | |||||||||
| Average | −0.50 | 0.17 | 0.0027 | −0.49 | 0.18 | 0.0057 | |||||||||
| ILI-DSE Diff | 1.52 | 0.34 | 5.7E-06 | 1.59 | 0.36 | 7.6E-06 | |||||||||
LD between the pair: D′=0.87, R2 =0.80 based on the full sample and D′=0.97, R2 =0.84 based on the NHW sample.
Major/minor alleles
Three-way interaction models of individual SNP markers (0, 1 or 2 copies of the minor allele; additive model) with measurement time (baseline vs. year 1) and study arm (ILI vs. DSE) were estimated using Generalized Estimating Equation procedures. Beta coefficients reflect the effect of one additional copy of the corresponding minor allele on a) depression levels across ILI and DSE at baseline; b) year 1 depression levels in ILI; c) year 1 depression levels in DSE; d) year 1 depression levels combined across treatment arms; and e) ILI vs. DSE differences in depression levels, or SNP * time * treatment interactions. Longitudinal regression models adjusted all of these genetic effects for age at interview, gender, genetic ancestry, and clinic site.