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
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
CONFLICTS OF INTEREST
Sungho Won has no a relevant financial interest with RexSoft, Inc..
AUTHOR CONTRIBUTIONS
Conception or design: H.J., S.H.K., J.W.Y., S.L.
Acquisition, analysis, or interpretation of data: H.J., S.H.K., J.W.Y., S.L.
Drafting the work or revising: K.S.P., S.W., N.H.C.
Final approval of the manuscript: K.S.P., S.W., N.H.C.
FUNDING
This research was supported by the BK21FOUR Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education (5120200513755) and grants from the Ministry of Health & Welfare, Republic of Korea (HI15C3131) and Seoul National University Hospital (2520160050).
Study population | Total | Case | Control | Male | Age, yr | BMI, kg/m2 | Fasting glucose, mg/dL | Mean of F/U duration | Genotyping platform |
SNP |
||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Genotypeda | Imputedb | 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 |
BMI, body mass index; F/U, follow-up; SNP, single nucleotide polymorphism; KoGES, Korea Genome and Epidemiology Study; GENIE, Gene-Environment Interaction and phenotype.
a 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,
b Number of imputed SNPs after QC: MAF <0.05, HWE <1.00×10−6, imputation quality scores <0.4.
SNP | Chr; position | A | Studya | 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, 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.
a Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
SNP | Chr; position | A | Studya | 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 |
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.
a Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
Trait | SNP | Chr; position | A | Studya | 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 |
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.
a Sample size are 6,122, 4,406, and 10,528 for KoGES, GENIE, and META analysis, respectively.
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.