Introduction
Materials and methods
Subjects
Genomic DNA extraction and SNPs
SNPs | Chromosome | Functional consequence | Restriction endonuclease | Alleles | Primer (5′→3′) |
---|---|---|---|---|---|
rs1800795-174G/C | 7:22727026 | Intron variant, upstream variant 2KB |
SfaNI
| G/ C | F: 5′-TGACTTCAGCTTTACTCTTGT-3′ R: 5′-CTGATTGGAAACCTTATTAAG-3′ |
rs1800796-572C/G | 7:22726627 | Intron variant, nc transcript variant, upstream variant 2KB |
BSrBI
| C/ G | F: 5′-AGATTCCAAGGGTCACTTG-3′ R: 5′-AGAAGCAGAACCACTCTTC-3′ |
rs1554606 185C/A | 7:22729088 | Intron variant, upstream variant 2KB |
EcoNI
| C/ A | F: 5′-ACTCATACATCTGGCCGTTG-3′ R: 5′-CTGATGGAGTATGGTGGAGG-3′ |
rs2069849 | 7:22731537 | Downstream variant 500B, missense, synonymous codon |
BsrDI
| C/ T | F: 5′-CGTGCATGACTTCAGCTTTACT-3′ R: 5′-CAGTGACCAGATTAACAGGCTAGA-3′ |
Statistical analysis
Results
Variables | Osteoporosis cases (n = 758) | Controls (n = 766) | P values |
---|---|---|---|
Age (years) (means ± SD) | 65.5 ± 16.1 | 66.7 ± 17.0 | 0.157 |
BMI (kg/m2) (means ± SD) | 24.4 ± 5.9 | 23.3 ± 5.6 | 0.0002 |
WC (cm) (means ± SD) | 86.5 ± 16.1 | 84.2 ± 15.6 | 0.005 |
Smoke, N (%) | 62 (8.2) | 39 (5.1) | 0.015 |
Alcohol drinking, N (%) | 102 (13.5) | 60 (7.8) | 0.0004 |
Calcium supplementation, n (%) | 244 (32.2) | 223 (29.1) | 0.192 |
YSM (years) (means ± SD) | 9.52 ± 5.84 | 10.03 ± 5.65 | 0.083 |
T score | |||
Femoral neck | − 2.73 ± 0.69 | 0.02 ± 0.30 | 0.000 |
Total femoral | − 1.57 ± 1.01 | 0.03 ± 0.24 | 0.000 |
Lumbar spine | − 0.75 ± 0.91 | 0.45 ± 0.82 | 0.000 |
Lumbar BMD (g/cm2) (means ± SD) | 0.90 ± 0.14 | 1.05 ± 0.13 | 0.000 |
Femoral BMD (g/cm2) (means ± SD) | 0.82 ± 0.10 | 0.95 ± 0.11 | 0.000 |
SNPs | Genotypes and alleles | Frequencies N(%) |
OR (95% CI)
*
|
HWE test
| |
---|---|---|---|---|---|
OP patients (n = 758) | Controls (n = 766) | ||||
rs1800796-572C/G | CC | 377 (49.7) | 469 (61.2) | 1.00 | 0.346 |
CG | 300 (39.6) | 255 (33.3) | 1.39 (1.09–1.65) | ||
GG | 81 (10.7) | 42 (5.5) | 1.90 (1.29–2.54) | ||
CG + GG | 381 (50.3) | 297 (38.8) | 1.47 (1.13–1.78) | ||
C | 1054 (69.5) | 1193 (77.9) | |||
G | 462 (30.5) | 339 (22.1) | |||
rs1800795-174G/C | GG | 399 (52.6) | 440 (57.4) | 1.00 | 0.106 |
GC | 285 (37.6) | 270 (35.2) | 1.07 (0.94–1.39) | ||
CC | 74 (9.8) | 56 (7.3) | 1.12 (0.85–1.60) | ||
GC + CC | 359 (47.4) | 326 (42.6) | 1.09 (0.91–1.44) | ||
G | 1083 (71.4) | 1150 (75.1) | |||
C | 433 (28.6) | 382 (24.9) | |||
rs2069849 | CC | 384 (50.7) | 481 (62.8) | 1.00 | 0.730 |
CT | 306 (40.4) | 250 (32.6) | 1.65 (1.38–1.90) | ||
TT | 68 (9.0) | 35 (4.6) | 2.03 (1.63–2.84) | ||
CT + TT | 374 (49.3) | 285 (37.2) | 1.74 (1.46–2.05) | ||
C | 1074 (70.8) | 1212 (79.1) | |||
T | 442 (29.2) | 320 (20.9) | |||
rs1554606 (185C/A) | CC | 405 (53.4) | 447 (58.4) | 1.00 | 0.272 |
CA | 292 (38.5) | 269 (35.1) | 1.08 (0.91–1.36) | ||
AA | 61 (8.1) | 50 (6.5) | 1.04 (0.82–1.53) | ||
CA + AA | 353 (46.6) | 319 (41.6) | 1.07 (0.89–1.39) | ||
C | 1102 (72.7) | 1163 (75.9) | |||
A | 414 (27.3) | 369 (24.1) |
Locus no. | Best combination | Cross-validation consistency | Testing accuracy | P values* |
---|---|---|---|---|
Gene–alcohol drinking interaction* | ||||
2 | 1, 5 | 6/10 | 0.522 | 0.324 |
3 | 1, 3, 5 | 7/10 | 0.514 | 0.255 |
4 | 1, 2, 3, 5 | 6/10 | 0.597 | 0.212 |
5 | 1, 2, 3, 4, 5 | 7/10 | 0.523 | 0.240 |
Gene–smoking interaction** | ||||
2 | 3, 6 | 7/10 | 0.488 | 0.536 |
3 | 3, 1, 6 | 6/10 | 0.523 | 0.706 |
4 | 1, 2, 3, 6 | 5/10 | 0.536 | 0.862 |
5 | 1, 2, 3, 4, 6 | 6/10 | 0.518 | 0.377 |
Gene–obesity interaction*** | ||||
2 |
1, 7
|
10/10
|
0.641
|
0.012
|
3 | 1, 2,7 | 8/10 | 0.526 | 0.266 |
4 | 1, 2, 4, 7 | 9/10 | 0.514 | 0.545 |
5 | 1, 2, 3, 4, 7 | 5/10 | 0.634 | 0.372 |
rs1800796
| Obesity | OR (95% CI) * | P values |
---|---|---|---|
CC | No | 1.00 | – |
CG or GG | No | 1.21 (1.05–1.52) | 0.030 |
CC | Yes | 1.43 (1.10–1.85) | 0.003 |
CG or GG | Yes | 2.21 (1.52–3.49) | < 0.001 |