Table 2.
Association analysis results for the top SNPs from the GWAS discovery + in silico replication analysis, selected for additional de novo replication
| Stages | rs61277444a CHR 4 | rs7562121 CHR 2 | rs1989248 CHR 7 | rs72809865 CHR 10 | ||
|---|---|---|---|---|---|---|
| Geneb: in PTPN13 | Geneb: in AFF3 | Geneb: 23kb to CNTNAP2 | Geneb: 350kb to NRG3 | |||
| Pheno:c,dESRD Versus Non-ESRD | Pheno:dESRD Versus No DKD | Pheno:c,dESRD Versus Non-ESRD | Pheno:dCKD+DKD | Pheno:cESRD Versus No DKD | Pheno:cCombined DKD | |
| Stage 1 | ||||||
| N | 813/3995 | 813/2394 | 813/3995 | 1117/2018 | 813/2394 | 2563/2593 |
| EAF | 0.09 | 0.09 | 0.23 | 0.28 | 0.28 | 0.16 |
| OR | 1.55 | 1.58 | 1.46 | 1.28 | 1.40 | 1.30 |
| 95% CI | 1.26 to 1.91 | 1.26 to 1.97 | 1.28 to 1.66 | 1.12 to 1.47 | 1.21 to 1.62 | 1.16 to 1.46 |
| P | 4.3×10−6 | 8.7×10−6 | 8.9×10−8 | 1.8×10−4 | 4.0×10−6 | 5.0×10−6 |
| Stage 2 | ||||||
| N | 964/4806 | 964/3187 | 964/4806 | 1104/1981 | 964/3187 | 2659/3842 |
| P | 2×10−3 | 3×10−3 | 0.04 | 1×10−3 | 0.02 | 0.05 |
| Stage 3 | ||||||
| N | 94/993 | 94/627 | 67/822 | 367/516 | ||
| P | 0.19 | 0.14 | 0.59 | 0.54 | ||
| All | ||||||
| N | 1871/9794 | 1871/6208 | 1844/9623 | 2221/3999 | 1777/5581 | 5589/6951 |
| N total | 11,665 | 8079 | 11,467 | 6220 | 7358 | 12,540 |
| OR | 1.41 | 1.42 | 1.27 | 1.26 | 1.29 | 1.17 |
| 95% CI | 1.21 to 1.65 | 1.20 to 1.67 | 1.17 to 1.39 | 1.15 to 1.38 | 1.17 to 1.43 | 1.09 to 1.26 |
| P | 1.9×10−6 | 6.0×10−6 | 3.5×10−7 | 6.0×10−7 | 1.8×10−6 | 7.4×10−6 |
The association in FinnDiane was moderately attenuated from OR=1.49 (95% CI, 1.19 to 1.86; P=4.5×10−4; ESRD versus non-ESRD) and OR=1.50 (95% CI, 1.18 to 1.91; P=1×10−3; ESRD versus no DKD) with the imputed data to OR=1.36 (95% CI, 1.11 to 1.66; P=3.0×10−3; ESRD versus non-ESRD) and OR=1.40 (95% CI, 1.11 to 1.75; P=3.9×10−3; ESRD versus no DKD) using directly genotyped data. CHR, chromosome; Pheno, phenotypic comparison; N, number of cases/controls; EAF, effect allele frequency; 95% CI, 95% confidence interval.
Because of moderate imputation quality at the discovery stage, rs61277444 was directly genotyped in 2913/3415 FinnDiane subjects.
The closest gene/genes.
Selection criteria for de novo replication: P value <10−6 for discovery + stage two meta-analysis.
Selection criteria for de novo replication: P value <0.05 in the in silico replication for the phenotype selected for replication.