1Institute of Health and Environment, Seoul National University, Seoul, Korea
2Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
3Department of Internal Medicine, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
4Department of Bioconvergence & Engineering, Dankook University, Yongin, Korea
5Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
6Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
7Department of Public Health Sciences, Seoul National University, Seoul, Korea
8RexSoft Inc., Seoul, Korea
9Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
Copyright © 2023 Korean Diabetes Association
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Study population | Total | Case | Control | Male | Age, yr | BMI, kg/m2 | Fasting glucose, mg/dL | Mean of F/U duration | Genotyping platform | SNP |
||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Genotyped |
Imputed |
Meta | ||||||||||
KoGES | 6,122 | 790 (13) | 5,332 (87) | 2,847 (46) | 51.5±8.7 | 24.4±3.0 | 84.1±8.5 | 11 years (5.5 times) | Affymetrix SNP Array 5.0 | 399,013 | 3,758,649 | 2,713,317 |
GENIE | 4,406 | 237 (5) | 4,169 (95) | 2,604 (59) | 45.7±8.6 | 23.1±2.9 | 93.9±9.9 | 6 years(5.7 times) | Affymetrix KOR_v1.0 | 344,632 | 3,692,736 |
SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
---|---|---|---|---|---|---|---|---|
rs78529720 | 2; 169777297 | T/C | KoGES | 1.008 | 0.155 | 7.11×10−11 | G6PC2, ABCB11 (intergenic) | |
GENIE | 1.036 | 0.209 | 0.347 | 7.34×10−7 | ||||
META | 1.017 | 0.124 | 2.90×10−16 | |||||
rs895636 | 2; 45188353 | C/T | KoGES | 0.574 | 0.151 | 1.43×10−4 | SIX3, SIX2 (intergenic) | |
GENIE | 0.831 | 0.198 | 0.375 | 2.75×10−5 | ||||
META | 0.668 | 0.120 | 2.00×10−8 | |||||
rs2971670 | 7; 44226101 | C/T | KoGES | 1.346 | 0.187 | 6.17×10−13 | GCK (intronic) | |
GENIE | 1.400 | 0.250 | 0.185 | 2.18×10−8 | ||||
META | 1.365 | 0.149 | 8.34×10−20 | |||||
rs12222793 | 11; 92667047 | A/G | KoGES | 0.827 | 0.144 | 1.14×10−8 | FAT3, MTNR1B (intergenic) | |
GENIE | 0.561 | 0.192 | 0.515 | 3.49×10−3 | ||||
META | 0.731 | 0.115 | 4.30×10−10 |
SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
---|---|---|---|---|---|---|---|---|
rs10947494 | 6; 34263743 | A/G | KoGES | 0.213 | 0.046 | 4.53×10−6 | NUDT3, RPS10-NUDT3 (intronic) | |
GENIE | 0.120 | 0.068 | 0.203 | 7.96×10−2 | ||||
META | 0.183 | 0.038 | 3.64×10−6 | |||||
rs11187850 | 10; 96068480 | A/G | KoGES | 0.152 | 0.042 | 3.49×10−4 | PLCE1 (intronic) | |
GENIE | 0.266 | 0.063 | 0.253 | 2.45×10−5 | ||||
META | 0.187 | 0.034 | 4.85×10−8 | |||||
rs2414772 | 15; 62654213 | G/A | KoGES | –0.163 | 0.039 | 3.26×10−5 | MIR6085, MGC15885 (intergenic) | |
GENIE | –0.134 | 0.058 | 0.676 | 2.14×10−2 | ||||
META | –0.153 | 0.032 | 6.30×10−6 | |||||
rs16959641 | 16; 58054099 | C/G | KoGES | 0.222 | 0.068 | 1.09×10−3 | USB1 (exonic) | |
GENIE | 0.366 | 0.107 | 0.077 | 6.00×10−4 | ||||
META | 0.263 | 0.057 | 2.46×10−6 |
Trait | SNP | Chr; position | A | Study |
Effect | SE | wAF | P value | ANNOVAR |
---|---|---|---|---|---|---|---|---|---|
T2DM | rs2296172 | 1; 39835817 | A/G | KoGES | 0.145 | 0.051 | 5.08×10−3 | MACF1 (exonic) | |
GENIE | 0.097 | 0.079 | 0.144 | 2.21×10−1 | |||||
META | 0.130 | 0.042 | 3.42×10−3 | ||||||
rs243021 | 2; 60584819 | G/A | KoGES | 0.073 | 0.038 | 5.81×10−2 | LOC101927285, MIR4432H (intergenic) | ||
GENIE | 0.060 | 0.057 | 0.667 | 2.94×10−1 | |||||
META | 0.069 | 0.031 | 3.37×10−2 | ||||||
rs864745 | 7; 28180556 | T/C | KoGES | 0.070 | 0.040 | 8.51×10−2 | JAZF1 (intronic) | ||
GENIE | 0.062 | 0.061 | 0.272 | 3.11×10−1 | |||||
META | 0.067 | 0.033 | 4.90×10−2 | ||||||
rs10965250 | 9; 22133284 | G/A | KoGES | –0.094 | 0.036 | 9.85×10−3 | CDKN2B-AS1, DMRTA1 (intergenic) | ||
GENIE | –0.086 | 0.055 | 0.436 | 1.19×10−1 | |||||
META | –0.091 | 0.030 | 2.93×10−3 | ||||||
rs9552911 | 13; 23864657 | G/A | KoGES | –0.084 | 0.044 | 5.66×10−2 | SGCG (intronic) | ||
GENIE | –0.053 | 0.066 | 0.225 | 4.25×10−1 | |||||
META | –0.074 | 0.036 | 4.89×10−2 | ||||||
FPG | rs6943153 | 7; 50791579 | T/C | KoGES | –0.056 | 0.041 | 1.80×10−1 | GRB10 (intronic) | |
GENIE | –0.105 | 0.062 | 0.737 | 9.07×10−2 | |||||
META | –0.070 | 0.034 | 3.44×10−2 | ||||||
rs10811661 | 9; 22134094 | T/C | KoGES | –0.090 | 0.036 | 1.23×10−2 | CDKN2B-AS1, DMRTA1 (intergenic) | ||
GENIE | –0.076 | 0.055 | 0.438 | 1.67×10−1 | |||||
META | –0.085 | 0.030 | 5.10×10−3 | ||||||
rs2293941 | 13; 28491198 | G/A | KoGES | 0.084 | 0.037 | 2.41×10−2 | PDX1-AS1 (ncRNA_intronic) | ||
GENIE | 0.039 | 0.055 | 0.466 | 4.73×10−1 | |||||
META | 0.069 | 0.030 | 2.90×10−2 |
BMI, body mass index; F/U, follow-up; SNP, single nucleotide polymorphism; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype. Number of genotyped SNPs after quality control (QC): missingness per SNP <95%, minor allele frequency (MAF) <0.05, Hardy-Weinberg equilibrium (HWE) <1.00×10−6, and sex inconsistency, Number of imputed SNPs after QC: MAF <0.05, HWE <1.00×10−6, imputation quality scores <0.4.
SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
FPG, fasting plasma glucose; T2DM, type 2 diabetes mellitus; SNP, single nucleotide polymorphism; Chr, chromosome; A, reference/alternative allele; SE, standard error; wAF, weighted alternative allele frequency; ANNOVAR, ANNOtate VARiation; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype; META, meta-analysis. Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.