Table 2 Results from imputation under different experiments. The T2D-association statistic (χ2) for the observed and imputed SNPs using low- and high-marker densities. SNPs with ‘-’ were imputed as monomorphic. The first experiment was not feasible for TCF7L2. Significant SNPs were masked simultaneously (second experiment) or one at a time (third experiment)
From: The hazards of genotype imputation when mapping disease susceptibility variants
3 T2D loci studied with the NGS data on 92 T2D cases and 93 controls | First experiment | Second experiment | Third experiment | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Low density | High density | High density | ||||||||||
SNPs | Major/minor | Risk | MAF NGS EUR | MAF 1000GP | Observed NGS χ2 | Imputed χ2 | Info score | Imputed χ2 | Info score | Imputed χ2 | Info score | |
EUR | Global | |||||||||||
ACTL7B | ||||||||||||
 rs13285616 | A/G | A | 0.13 | 0.14 | 0.06 | 5.11 | - | 0.05 | - | 0.18 | - | 0.17 |
 rs144726287 | C/T | T | 0.01 | 0.01 | 0.00 | 4.09 | - | 0.00 | - | 0.07 | - | 0.07 |
 rs60388922 | T/G | G | 0.10 | 0.08 | 0.07 | 4.37 | - | 0.06 | 5.69 | 0.95 | 5.08 | 0.97 |
 rs72756001 | G/A | A | 0.08 | 0.09 | 0.12 | 4.66 | - | 0.72 | 4.97 | 0.98 | 4.97 | 0.98 |
 rs10979533 | G/T | G | 0.08 | 0.07 | 0.09 | 4.13 | 0.01 | 0.95 | 4.13 | 1.00 | 4.13 | 1.00 |
 rs117056494 | C/T | C | 0.01 | 0.01 | 0.00 | 4.00 | - | 0.03 | - | 0.06 | - | 0.06 |
 rs12380226 | T/C | T | 0.08 | 0.07 | 0.09 | 4.13 | 0.01 | 0.95 | 4.13 | 1.00 | 4.26 | 0.99 |
KCNK3 | ||||||||||||
 rs78489206 | G/A | A | 0.03 | 0.05 | 0.05 | 4.67 | - | 0.06 | 3.91 | 0.82 | 3.91 | 0.97 |
 rs7588614 | C/G | G | 0.04 | 0.05 | 0.12 | 3.99 | - | 0.13 | 5.60 | 0.81 | 5.60 | 1.00 |
 rs77786658 | G/A | A | 0.03 | 0.05 | 0.05 | 4.84 | - | 0.06 | 4.67 | 0.82 | 4.67 | 1.00 |
 rs6707973 | A/G | G | 0.04 | 0.05 | 0.17 | 3.99 | - | 0.27 | 3.99 | 0.85 | 3.99 | 0.99 |
 rs73920335 | T/C | C | 0.04 | 0.05 | 0.17 | 3.99 | - | 0.29 | 3.83 | 0.91 | 3.83 | 0.97 |
 rs59435210 | T/G | G | 0.04 | 0.05 | 0.17 | 3.99 | - | 0.30 | 3.24 | 0.89 | 3.24 | 0.98 |
 rs59284336 | C/T | T | 0.03 | 0.05 | 0.04 | 4.67 | - | 0.09 | 4.75 | 1.00 | 4.75 | 0.98 |
 rs113076024 | G/A | A | 0.03 | 0.05 | 0.04 | 4.75 | - | 0.09 | 4.67 | 1.00 | 4.67 | 1.00 |
TCF7L2 | ||||||||||||
 rs7081062 | A/G | A | 0.32 | 0.36 | 0.34 | 9.96 |  |  | - | 0.56 | 9.32 | 1.00 |
 rs149954646 | G/A | G | 0.01 | 0.03 | 0.01 | 4.00 |  |  | 4.00 | 0.61 | 4.00 | 1.00 |
 rs145034729 | G/A | G | 0.01 | 0.03 | 0.01 | 4.00 |  |  | 4.00 | 0.61 | 4.00 | 1.00 |
 rs10128255 | A/G | A | 0.32 | 0.36 | 0.34 | 9.32 |  |  | - | 0.56 | 9.14 | 1.00 |
 rs7895307 | G/A | G | 0.32 | 0.36 | 0.34 | 9.32 |  |  | - | 0.56 | 9.32 | 0.99 |
 rs4073980 | G/C | G | 0.46 | 0.50 | 0.44 | 6.85 |  |  | 0.04 | 0.75 | 7.50 | 0.99 |
 rs4074720 | T/C | T | 0.46 | 0.50 | 0.44 | 6.85 |  |  | 0.41 | 0.76 | 6.85 | 1.00 |
 rs4074718 | A/G | A | 0.46 | 0.50 | 0.44 | 6.85 |  |  | 0.41 | 0.77 | 6.85 | 1.00 |