Comparison of four GWA studies
| FHS | Mexican American | Pima C/C | Pima family | Amish | |
|---|---|---|---|---|---|
| n | 1,087 | 281 case/280 control | 300 case/334 control | 172 sibships | 124 case/295 control |
| Type | Population, family-based | Case/control | Case/control | Family | Case/control |
| Ethnicity | Non-Hispanic white | Mexican American | American Indian | American Indian | Non-Hispanic white |
| Male/female | 527/560 | ||||
| Case | 108/173 | 114/186 | 48/92 | 41/83 | |
| Control | 69/211 | 160/174 | 57/64 | 153/142 | |
| Mean age (years) | 51.5 ± 9.8 | ||||
| Case | 57.7 ± 10.8 | 19.2 ± 4.5 | 41.0 ± 8.3 | 51.3 ± 10.5 | |
| Control | — | 55.5 ± 9.8 | 27.8 ± 7.9 | 64.4 ± 12.9 | |
| Mean BMI (kg/m2) | 27.5 ± 5.2 | ||||
| Case | 31.5 ± 6.2 | 38.9 ± 8.4 | 38.9 ± 9.3 | 29.3 ± 5.8 | |
| Control | — | 35.4 ± 8.0 | 36.9 ± 8.9 | 27.4 ± 4.7 | |
| Quantitative glycemic traits analyzed | FPG, tFPG, A1C, FI, HOMA-IR, Gutt ISI 0_120 | FASTG, glucose AUC, insulin AUC, HOMA-IR, insulin secretion index | |||
| Notes | 91 cases of incident diabetes | Controlled for admixture | Age of onset <25 years | Sibships overlap with C/C | Cases have (+) FH; active lifestyle |
| SNPs analyzed | 66,543 | 88,702 | 80,044 | 80,044 | 82,485 |
| SNPs failed | 39,205 MAF <10%; 4,064 HWE P < 0.001; 10,438 call rate <90% | 19,032 MAF <5%; 1,562 HWE P < 0.001; 4,818 call rate <85% | 28,215 MAF <1%; 2,429 HWE P < 0.001; 5,122 call rate <85% and/or error rate >3% in duplicate samples | 28,215 MAF <1%; 2,429 HWE P < 0.001; 5,122 call rate <85% and/or error rate >3% in duplicate samples | 26,816 MAF <5%; 2,573 HWE P < 0.001; 1,866 call rate <90% |
| P value thresholds | Strategy 1: P < 0.01 in all three glucose traits (FPG, tFPG, and A1C) or in all 3 insulin traits (FI, HOMA-IR, and Gutt) or two glucose and two insulin traits or incident type 2 diabetes; Strategy 2: P < 0.001 | Primary analysis: P < 0.01 for type 2 diabetes; In silico replication: P < 0.05 | In silico replication:P < 0.007 in combined within-family and case-control analysis (weighted to give priority to within-family test); Additional genotyping: P < 0.001 in combined within-family and case-control analysis as above | In silico replication: P < 0.007 in combined within-family and case-control analysis (weighted to give priority to within-family test); Additional genotyping: P < 0.001 in combined within-family and case- control analysis as above | Primary analysis: P < 0.01 for type 2 diabetes; Internal replication: type 2 diabetes P < 0.01 and one glucose trait (FASTG or GAUC) or one insulin trait (ISI, IAUC, or HOMA-IR) P < 0.01 |
| Replication cohort | 1,465 unrelated FHS participants (non-overlapping) | 760 overlapping individuals for SNP verification | Non-overlapping Pima Indians: 1,207 case/1,627 control | Non-overlapping Pima Indians: 1,207 case/1,627 control | 427 nondiabetic Amish participants (295 control from primary type 2 analysis) |
| In silico replication | T2D 100K Consortium + DGI 500K | T2D 100K Consortium + DGI 500K | T2D 100K Consortium + DGI 500K | T2D 100K Consortium + DGI 500K | T2D 100K Consortium + DGI 500K |
T2D, type 2 Diabetes.