Background
Methods
Participants
Extraction of genomic DNA and genotyping
SNPs | Chromosome | Functional Consequence | Major/minor alleles | Genotyping assays or primers |
---|---|---|---|---|
EBI3 | 19:4229916 | Intron variant | G > C | GAATTTGAGTCACACTCATTCCTTT[C/G] |
rs428253 | GTTTCTTTTTGGTTTTGTTTTTTGA | |||
EBI3 | 19:4236999 | Missense variant, coding sequence variant | G > A | TGTGCGGCCCCGAGCCAGGTACTAC[A/G] |
rs4740 | TCCAAGTGGCGGCTCAGGACCTCAC | |||
IL-12A rs2243115 | 3:159988493 | Upstream transcript variant, intron variant | T > G | Forward: 5′-AGAAAAGACCTGTGAACAAAACGACT-3′ |
Reverse: 5′-AGATGGCTCACTAGATGCCAGG-3′ | ||||
IL-12A rs568408 | 3:159995680 | 3 prime UTR variant, intron variant | G > A | Forward: 5′-GAAGGATGGGACYATTACATCCATAT-3′ |
Reverse: 5′-CAGGATGGATATTTTCCCTTCT-3′ |
Statistical analysis
Results
Variables | CHD patients (n = 921) | Controls (n = 926) | p-values |
---|---|---|---|
Age (years) (means ± SD) | 60.6 ± 11.3 | 61.3 ± 12.0 | 0.197 |
Males, N (%) | 463 (50.3) | 474 (51.2) | 0.694 |
BMI (kg/m2) (means ± SD) | 24.6 ± 9.1 | 23.9 ± 9.5 | 0.106 |
CRP (mg/l) (means ± SD) | 32.2 ± 16.7 | 12.9 ± 7.5 | < 0.0001 |
Hypertension, N (%) | 389 (42.2) | 272 (29.4) | 0.000001 |
T2DM, N (%) | 170 (18.5) | 104 (11.2) | 0.000013 |
Smoking status, N (%) | 0.000012 | ||
Current | 267 (29.0) | 187 (20.2) | |
Never | 654 (71.0) | 739 (79.8) | |
Alcohol consumption, N (%) | 0.000089 | ||
Current | 319 (34.6) | 243(26.2) | |
Never | 602 (65.4) | 683 (73.8) |
SNP | Genotypes or Alleles | Frequencies N (%) | Adjusted OR (95% CI)a | p-values | |
---|---|---|---|---|---|
CHD cases (N = 921) | Controls (N = 926) | ||||
EBI3-rs428253 | |||||
GG genotype | 458 (49.7) | 594 (64.1) | 1.00 (ref) | ||
GC genotype | 369 (40.1) | 285 (30.8) | 1.87 (1.21–2.58) | < 0.001 | |
CC genotype | 94 (10.2) | 47 (5.1) | 2.06 (1.45–2.75) | < 0.001 | |
G allele | 1285 (69.8) | 1473 (79.5) | 1.00 | ||
C allele | 557 (30.2) | 379 (20.5) | 1.91 (1.28–2.64) | < 0.001 | |
P values for HWE | 0.097 | ||||
EBI3-rs4740 | |||||
GG genotype | 483 (52.4) | 543 (58.6) | 1.00 (ref) | ||
GA genotype | 359 (39.0) | 323 (34.9) | 1.41 (0.95–1.97) | 0.325 | |
AA genotype | 79 (8.6) | 60 (6.5) | 1.56 (0.87–2.26) | 0.561 | |
G allele | 1325 (71.9) | 1409 (76.1) | 1.00 | ||
A allele | 517 (28.1) | 443 (23.9) | 1.46 (0.92–2.04) | 0.487 | |
P values for HWE | 0.205 | ||||
IL-12A-rs2243115 | |||||
TT genotype | 513 (55.7) | 633 (68.4) | 1.00 (ref) | ||
TG genotype | 332 (36.1) | 257 (27.8) | 1.76 (1.32–2.18) | < 0.001 | |
GG genotype | 76 (8.3) | 36 (3.9) | 1.93 (1.23–2.65) | < 0.001 | |
T allele | 1358 (73.7) | 1523 (82.2) | 1.00 | ||
G allele | 484 (26.3) | 329 (17.8) | 1.80 (1.30–2.23) | < 0.001 | |
P values for HWE | 0.127 | ||||
IL-12A-rs568408 | |||||
GG genotype | 563 (61.1) | 641 (69.2) | 1.00 (ref) | ||
GA genotype | 312 (33.9) | 253 (27.3) | 1.31 (0.82–1.82) | 0.436 | |
AA genotype | 46 (5.0) | 32 (3.5) | 1.53 (0.74–2.33) | 0.628 | |
G allele | 1438 (78.1) | 1535 (82.9) | 1.00 | ||
A allele | 404 (21.9) | 317 (17.1) | 1.37 (0.80–1.91) | 0.541 | |
P values for HWE | 0.259 |
Locus no | Best combination | Cross-validation consistency | Testing balanced accuracy | p-valuesa |
---|---|---|---|---|
Gene–gene interactionsa | ||||
2 | 1, 3 | 7/10 | 0.607 | 0.321 |
3 | 1, 3, 2 | 6/10 | 0.532 | 0.528 |
4 | 1, 2, 4, 3 | 7/10 | 0.496 | 0.625 |
Gene–alcohol consumption interactionsb | ||||
2 | 1, 5 | 8/10 | 0.491 | 0.624 |
3 | 1, 2, 5 | 7/10 | 0.526 | 0.425 |
4 | 1, 2, 3, 5 | 5/10 | 0.518 | 0.746 |
5 | 1, 2, 3, 4, 5 | 6/10 | 0.521 | 0.857 |
Gene–smoking interactionsc | ||||
2 | 1, 6 | 10/10 | 0.632 | 0.010 |
3 | 1, 2, 6 | 7/10 | 0.532 | 0.172 |
4 | 1, 2, 3, 6 | 6/10 | 0.515 | 0.324 |
5 | 1, 2, 3, 4, 6 | 7/10 | 0.512 | 0.425 |