Introduction
Methods
Study | Cohort |
N (male %) | Age (years) | AAD (year) | Diabetes duration (years) | BMI (kg/m2) | FPG (mmol/l) |
---|---|---|---|---|---|---|---|
Stage 1 (genome scan) | |||||||
HK1 | Control | 99 (36.4) | 37.3 ± 10.2 | – | – | 20.8 ± 2.0 | 4.7 ± 0.4 |
T2D patient | 99 (40.4) | 40.6 ± 8.8 | 31.8 ± 7.7 | 8.0 ± 8.3 | 30.9 ± 4.4 | – | |
HK2 | Diseased control | 659 (48.7) | 37.1 ± 17.0 | – | – | 23.3 ± 3.7 | – |
T2D patient | 388 (49.5) | 60.6 ± 10.8 | 51.1 ± 12.1 | 9.5 ± 7.0 | 25.0 ± 3.8 | – | |
SH | Control | 197 (50.8) | 66.4 ± 10.1 | – | – | 20.6 ± 1.7 | 4.8 ± 0.4 |
T2D patient | 197 (57.9) | 41.6 ± 10.4 | 34.5 ± 4.8 | 7.3 ± 8.5 | 23.8 ± 4.1 | – | |
Stage 2 (de novo replication in Chinese) | |||||||
HK1 | Adolescent control | 985 (44.2) | 15.5 ± 1.9 | – | – | 22.7 ± 5.4 | 4.9 ± 0.4 |
Adults control | 513 (47.0) | 42.0 ± 10.4 | – | – | 19.9 ± 3.5 | 4.7 ± 0.3 | |
Elderly control | 976 (51.4) | 72.3 ± 5.3 | – | – | 23.2 ± 3.2 | – | |
T2D patient | 5,366 (45.1) | 56.7 ± 13.4 | 48.8 ± 14.9 | 6.6 ± 6.9 | 24.6 ± 5.3 | – | |
SH1 | Control | 3,964 (37.6) | 51.3 ± 13.5 | – | – | 23.6 ± 3.2 | 5.0 ± 0.5 |
T2D patient | 4,035 (52.0) | 61.2 ± 12.1 | 54.2 ± 11.3 | 7.2 ± 6.9 | 24.5 ± 3.5 | – | |
HK Family 2 | Control | 368 (41.0) | 37.0 ± 13.6 | – | – | 24.0 ± 4.1 | 4.9 ± 0.4 |
T2D patient | 325 (40.6) | 48.0 ± 14.4 | 41.7 ± 13.1 | 6.3 ± 7.6 | 25.9 ± 4.4 | – | |
SH Family 2 | Control | 168 (51.2) | 62.8 ± 11.2 | – | – | 23.7 ± 3.5 | 4.8 ± 0.6 |
T2D patient | 657 (43.7) | 54.6 ± 15.6 | 50.0 ± 14.2 | 4.9 ± 7.3 | 23.9 ± 3.5 | – | |
Stage 3 (in silico replication in East Asians) | |||||||
Japanese | Control | 3,023 (54.5) | 51.9 ± 15.2 | – | – | 22.4 ± 3.7 | – |
T2D patient | 4,465 (68.0) | 65.8 ± 10.0 | 56.5 ± 11.4 | 9.4 ± 8.4 | 24.1 ± 3.8 | – | |
Korean 1 | Control | 2,943 (46.0) | 51.1 ± 8.6 | – | – | 24.1 ± 3.0 | 4.5 + 0.4 |
T2D patient | 1,042 (51.7) | 56.4 ± 8.6 | – | – | 25.5 ± 3.3 | 7.0 ± 2.6 | |
Korean 2 | Control | 1,305 (54.5) | 65.2 ± 2.6 | – | – | 23.9 ± 3.0 | 5.0 ± 0.5 |
T2D patient | 1,183 (46.5) | 58.6 ± 7.1 | – | – | 25.2 ± 3.4 | 7.4 ± 2.7 | |
Singapore Chinese 1 | Control | 1,006 (21.6) | 47.7 ± 11.1 | – | – | 22.3 ± 3.7 | 4.7 ± 0.4 |
T2D patient | 1,082 (37.2) | 65.1 ± 9.7 | 55.7 ± 12.0 | – | 25.3 ± 3.9 | – | |
Singapore Chinese 2 | Control | 939 (63.8) | 46.7 ± 10.2 | – | – | 22.8 ± 3.4 | 4.7 ± 0.5 |
T2D patient | 928 (64.9) | 63.7 ± 10.8 | 52.2 ± 14.4 | – | 25.4 ± 3.8 | – | |
Chinese | Control | 1,839 (43.7) | 54.1 ± 9.2 | – | – | 24.00 ± 3.18 | 5.04 ± 0.35 |
T2D patient | 1,873 (46.0) | 58.6 ± 8.4 | – | – | 25.00 ± 3.24 | 8.43 ± 2.90 | |
Stage 4 (in silico replication in non-East Asians) | |||||||
Singapore Malaysian | Control | 1,240 (52.0) | 56.9 ± 11.4 | – | – | 25.1 ± 4.8 | – |
T2D patient | 794 (51.0) | 62.3 ± 9.90 | 54.4 ± 11.2 | – | 27.8 ± 4.9 | – | |
Singapore Indians | Control | 1,169 (48.4) | 55.7 ± 9.7 | – | – | 25.3 ± 4.4 | – |
T2D patient | 977 (54.4) | 60.7 ± 9.9 | 51.4 ± 10.6 | – | 27.1 ± 5.1 | – | |
DIAGRAM+ | Control | 38,987 (–) | – | – | – | – | – |
T2D patient | 8,130 (–) | – | – | – | – | – |
Results
Hong Kong replication 1 (5,366 T2D vs 2,474 controls) | Shanghai replication 1 (4,035 T2D vs 3,964 controls) | Combined | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SNP | Chromosome | Nearest gene(s) | Position (B36) | Minor/major allele | Case MAF | Control MAF | OR (95% CI) |
p
additive
| Case MAF | Control MAF | OR (95% CI) |
p
additive
| OR (95% CI) |
p
meta (uncorrected) |
p
het
|
I
2
|
rs10229583 | 7 |
PAX4
| 127034139 | A/G | 0.847 | 0.83 | 1.14 (1.03, 1.23) | 0.0077 | 0.846 | 0.825 | 1.16 (1.08, 1.27) | 3.7 × 10−4
| 1.15 (1.08, 1.22) | 1.0 × 10−5
| 0.6406 | 0.000 |
rs2721960 | 8 |
TRPS1
| 116725904 | T/C | 0.657 | 0.644 | 1.05 (0.98, 1.14) | 0.1566 | 0.655 | 0.638 | 1.08 (1.01, 1.15) | 0.0277 | 1.06 (1.02, 1.12) | 0.0095 | 0.7067 | 0.000 |
rs2737250 | 8 |
TRPS1
| 116731048 | G/A | 0.631 | 0.62 | 1.05 (0.98, 1.12) | 0.1807 | 0.641 | 0.621 | 1.09 (1.02, 1.16) | 0.0090 | 1.08 (1.02, 1.12) | 0.0045 | 0.4582 | 0.000 |
rs3858158 | 10 |
COL13A1
| 71310056 | C/T | 0.516 | 0.521 | 0.98 (0.92, 1.05) | 0.6000 | 0.569 | 0.561 | 1.03 (0.97, 1.10) | 0.3211 | 1.01 (0.96, 1.05) | 0.7408 | 0.3026 | 0.506 |
rs2395272 | 10 |
COL13A1
| 71310261 | A/G | 0.531 | 0.534 | 0.99 (0.93, 1.06) | 0.7680 | 0.594 | 0.584 | 1.04 (0.97, 1.11) | 0.2312 | 1.02 (0.97, 1.06) | 0.4589 | 0.3027 | 0.364 |
rs57703465 | 10 |
COL13A1
| 71311074 | T/C | 0.654 | 0.662 | 0.96 (0.89, 1.04) | 0.3463 | 0.667 | 0.656 | 1.05 (0.98, 1.12) | 0.1502 | 1.01 (0.96, 1.06) | 0.6467 | 0.0976 | 0.765 |
rs11065441 | 12 |
P2RX7
| 120045354 | C/T | 0.728 | 0.724 | 1.02 (0.94, 1.11) | 0.6224 | 0.728 | 0.733 | 0.97 (0.91, 1.04) | 0.4312 | 0.99 (0.94, 1.05) | 0.7756 | 0.3748 | 0.000 |
rs684201 | 12 |
P2RX7
| 120054726 | A/G | 0.73 | 0.726 | 1.02 (0.94, 1.10) | 0.5916 | 0.735 | 0.739 | 0.98 (0.91, 1.05) | 0.5609 | 1.00 (0.94, 1.05) | 0.9462 | 0.4332 | 0.000 |
rs11065450 | 12 |
P2RX7
| 120064040 | A/C | 0.682 | 0.688 | 0.97 (0.90, 1.05) | 0.4995 | 0.702 | 0.707 | 0.98 (0.92, 1.05) | 0.5520 | 0.98 (0.93, 1.03) | 0.3699 | 0.9111 | 0.000 |
rs208290 | 12 |
P2RX7
| 120078439 | T/C | 0.612 | 0.609 | 1.01 (0.94, 1.09) | 0.7086 | 0.643 | 0.645 | 0.99 (0.93, 1.06) | 0.7950 | 1.00 (0.95, 1.05) | 0.9605 | 0.6472 | 0.000 |
rs10849851 | 12 |
P2RX7
| 120081027 | G/A | 0.727 | 0.72 | 1.03 (0.95, 1.12) | 0.4079 | 0.737 | 0.741 | 0.98 (0.91, 1.05) | 0.5237 | 1.00 (0.95, 1.05) | 0.9308 | 0.3002 | 0.068 |
N
| Risk allele frequencies | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Stage | Cohort | Adjustment | T2D | Control | T2D | Control | OR (95% CI) |
p
additive (uncorrected GC) |
p
het
|
I
2
|
1. Discovery | Hong Kong GWAS 1 | Sex and age | 99 | 99 | 0.879 | 0.818 | 1.48 (0.85, 2.59) | 0.1645 | ||
Hong Kong GWAS 2 | Sex and age | 388 | 659 | 0.857 | 0.820 | 1.56 (1.14, 2.13) | 0.0055 | |||
Shanghai GWAS | None | 197 | 197 | 0.873 | 0.777 | 1.92 (1.32, 2.79) | 5.0 × 10−4
| |||
Meta-analysis of GWAS | 684 | 955 | 1.66 (1.33, 2.07) | 7.7 × 10−6
| 0.6455 | 0.000 | ||||
2. De novo replications in Hong Kong and Shanghai | Hong Kong replication 1 | None | 5,366 | 2,474 | 0.847 | 0.831 | 1.13 (1.03, 1.24) | 7.7 × 10−3
| ||
Shanghai replication 1 | None | 4,035 | 3,964 | 0.846 | 0.825 | 1.17 (1.07, 1.27) | 3.7 × 10−4
| |||
Hong Kong family replication 2 | Sex and age | 325 | 368 | 0.872 | 0.856 | 1.22 (0.85, 1.74) | 0.2817 | |||
Shanghai family replication 2 | Sex and age | 657 | 168 | 0.824 | 0.813 | 1.09 (0.80, 1.49) | 0.5757 | |||
Replication in Chinese | 10,383 | 6,974 | 1.15 (1.08, 1.22) | 1.0 × 10−5
| 0.6406 | 0.000 | ||||
Meta-analysis of Chinese | 11,067 | 7,929 | 1.18 (1.11, 1.25) | 2.6 × 10−8
| 0.0839 | 0.596 | ||||
3. In silico replications in East Asians | Japanese replication | None | 4,465 | 3,023 | 0.892 | 0.881 | 1.11 (1.01, 1.23) | 0.0379 | ||
Korean replication 1 | None | 1,042 | 2,943 | 0.894 | 0.878 | 1.17 (0.99, 1.38) | 0.0577 | |||
Korean replication 2 | None | 1,183 | 1,305 | 0.841 | 0.844 | 0.98 (0.84, 1.15) | 0.8101 | |||
Singapore Chinese replication 1 | None | 1,082 | 1,006 | 0.832 | 0.819 | 1.07 (0.95, 1.20) | 0.2728 | |||
Singapore Chinese replication 2 | None | 928 | 939 | 0.833 | 0.816 | |||||
Chinese replication | First 2 PCs | 1,873 | 1,839 | 0.8396 | 0.8167 | 1.17 (1.04, 1.32) | 0.01091 | |||
Replication in other East Asian | 10,573 | 11,055 | 1.10 (1.04, 1.17) | 6.0 × 10−4
| 0.6767 | 0.000 | ||||
Meta-analysis of East Asian | 21,640 | 18,984 | 1.14 (1.09, 1.19) | 2.3 × 10−10
| 0.5939 | 0.000 | ||||
4. In silico replications in South Asians and Europeans | Singapore Malaysian replication | None | 794 | 1,204 | 0.798 | 0.804 | 0.97 (0.83, 1.14) | 0.7185 | ||
Singapore Indian replication | None | 977 | 1,169 | 0.647 | 0.682 | 0.86 (0.76, 0.98) | 0.0276 | |||
DIAGRAM | None | 8,130 | 38,987 | – | – | 1.06 (1.02, 1.12) | 8.6 × 10−3
| |||
Replication in non-East Asian | 9,901 | 41,360 | 1.03 (0.99, 1.08) | 0.1156 | 0.0042 | 0.878 |