Table 3 Comparison of results with the published T2D large-scale meta-analyses. P-values and odds ratios from two independent studies [8, 9] that used imputation. Odds ratios (NA) in the NGS study [5] cannot be estimated because the allele is only present in either cases or controls. For the 2020 study, (ns) were nonsignificant but with no P-values provided. For the 2022 study, (ns) were imputed but nonsignificant with the exception of one (?) SNP that could not be imputed
From: The hazards of genotype imputation when mapping disease susceptibility variants
| Â | Â | Â | Directly observed from the NGS study [5] | 2020 Meta-analysis [8] | 2022 Meta-analysis [9] | ||||
|---|---|---|---|---|---|---|---|---|---|
SNPs | Risk | Location (bp) | χ2 | p-value | Odds ratio | p-value | Odds ratio | p-value | Odds ratio |
ACTL7B | |||||||||
 rs13285616 | A | 111556995 | 5.11 | 2.4E-02 | 2.04 | Ns |  | Ns | 0.99 |
 rs144726287 | T | 111559654 | 4.09 | 4.3E-02 | NA | Ns |  | Ns | 0.97 |
 rs60388922 | G | 111579228 | 4.37 | 3.7E-02 | 2.09 | Ns |  | ? | ? |
 rs72756001 | A | 111583976 | 4.66 | 3.1E-02 | 2.40 | Ns |  | Ns | 1.00 |
 rs10979533 | G | 111588286 | 4.13 | 4.2E-02 | 2.22 | Ns |  | Ns | 1.01 |
 rs117056494 | C | 111588683 | 4.00 | 4.6E-02 | NA | 1.1E-03 | 1.11 | Ns | 1.11 |
 rs12380226 | T | 111589552 | 4.13 | 4.2E-02 | 2.22 | Ns |  | Ns | 1.00 |
KCNK3 | |||||||||
 rs78489206 | A | 26897778 | 4.67 | 3.1E-02 | 4.73 | Ns |  | Ns | 1.00 |
 rs7588614 | G | 26898869 | 3.99 | 4.6E-02 | 3.51 | Ns |  | Ns | 1.00 |
 rs77786658 | A | 26899221 | 4.84 | 2.8E-02 | 4.85 | Ns |  | Ns | 1.00 |
 rs6707973 | G | 26901215 | 3.99 | 4.6E-02 | 3.51 | Ns |  | Ns | 1.00 |
 rs73920335 | C | 26904377 | 3.99 | 4.6E-02 | 3.51 | Ns |  | Ns | 1.00 |
 rs59435210 | G | 26905580 | 3.99 | 4.6E-02 | 3.51 | Ns |  | Ns | 1.00 |
 rs59284336 | T | 26906436 | 4.67 | 3.1E-02 | 4.73 | Ns |  | Ns | 1.00 |
 rs113076024 | A | 26909473 | 4.75 | 2.9E-02 | 4.79 | Ns |  | Ns | 1.00 |
TCF7L2 | |||||||||
 rs7081062 | A | 114740745 | 9.96 | 1.6E-03 | 2.04 | 2.8E-69 | 1.07 | 9.2E-66 | 1.07 |
 rs149954646 | G | 114741507 | 4.00 | 4.6E-02 | NA | 1.9E-24 | 1.21 | 6.5E-12 | 1.19 |
 rs145034729 | G | 114741673 | 4.00 | 4.6E-02 | NA | 2.0E-24 | 1.21 | 6.4E-12 | 1.19 |
 rs10128255 | A | 114742835 | 9.32 | 2.3E-03 | 2.00 | 3.4E-68 | 1.07 | 4.3E-66 | 1.07 |
 rs7895307 | G | 114743961 | 9.32 | 2.3E-03 | 2.00 | 6.8E-71 | 1.07 | 1.2E-67 | 1.07 |
 rs4073980 | G | 114746580 | 6.85 | 8.9E-03 | 1.73 | 3.5E-185 | 1.18 | 2.6E-213 | 1.18 |
 rs4074720 | T | 114748497 | 6.85 | 8.9E-03 | 1.73 | 4.4E-185 | 1.18 | 2.4E-214 | 1.18 |
 rs4074718 | A | 114748617 | 6.85 | 8.9E-03 | 1.73 | 2.2E-185 | 1.18 | 7.8E-215 | 1.18 |