Introduction
Materials and methods
Materials
Subjects and controls
Selection of SNPs
Methods
Genomic DNA extraction
Synthesis of primers and probes
SNP | Upstream (5′–3′) | Downstream (3′–5′) | PCR product length (bp) |
---|---|---|---|
rs4845454 | GGGTCACAAATTCAGAAAGG | TGACCACAGCTCCAATCAAC | 82 |
rs1886734 | CCATAAGGAGCTTGCCCATC | CTGGTACACTTAAGACATGC | 98 |
rs6701216 | ACCAGCCTAGAGCCAGGGCA | CACAGGCTCCCTTTGTTAAG | 92 |
rs4085613 | ACTCCTTGAGAGCCCTTTTC | GAAAACGTCAAACTGCCTAT | 99 |
rs12023196 | AGGGCCAAAACTTCAAAGCT | CTGCTTCAGTACCCAGGGAA | 375 |
rs512208 | GGCCGCTGGTCTTAGAGACA | CAGGATCCAGGTCAGCAGCAGCCT | 378 |
rs4112788 | CCCAGTCGTAGGAGGAGCTA | TCTGCCACTATGCCAAGCTA | 497 |
Multiplex PCR
Multiplex LDR
Sequencing and genotyping
Statistical analysis
Results
Sample and SNP quality control
SNP | Allele | Number (Allele frequency %) |
χ
2
|
p
| OR (95% CI) | |
---|---|---|---|---|---|---|
Control N = 383 | Patient N = 305 | |||||
rs4845454 | C | 314 (40.99) | 283 (46.39) | 4.033 | 0.045 | 1.246 (1.005–1.544) |
rs6701216 | T | 240 (31.33) | 257 (42.13) | 17.165 | < 0.001 | 1.596 (1.278–1.992) |
rs1886734 | T | 320 (41.78) | 285 (46.72) | 3.372 | 0.066 | 1.222 (0.986–1.514) |
rs4085613 | A | 329 (42.95) | 294 (48.20) | 3.772 | 0.052 | 1.236 (0.998–1.530) |
rs12023196 | C | 255 (33.29) | 282 (46.23) | 23.894 | < 0.001 | 1.723 (1.384–2.144) |
rs512208 | T | 220 (28.72) | 276 (45.25) | 40.266 | < 0.001 | 2.051 (1.640–2.564) |
rs4112788 | T | 296 (38.64) | 295 (48.36) | 13.089 | < 0.001 | 1.487 (1.199–1.844) |
Allele frequency comparison (Table 2)
Genotype frequency comparison
SNP | Genetic model | Group | Genotype distribution | χ2 | P | OR (95% CI) |
---|---|---|---|---|---|---|
rs6701216 | Genotype | Patient | 107/139/59 | |||
CC/CT/TT | Control | 179/168/36 | ||||
Dominant | Patient | 198/107 | 9.494 | 0.002 | 1.624(1.192–2.212) | |
(TT + CT/CC) | Control | 204/179 | ||||
Recessive | Patient | 59/246 | 14.109 | 0.000 | 2.312(1.481–3.609) | |
(TT/CT + CC) | Control | 36/347 | ||||
rs4112788 | Genotype | Patient | 98/119/88 | |||
(CC/CT/TT) | Control | 148/174/61 | ||||
Dominant | Patient | 207/98 | 3.134 | 0.077 | 1.330 (0.970–1.825) | |
(TT + CT/CC) | Control | 235/148 | ||||
Recessive | Patient | 88/217 | 16.719 | 0.000 | 2.141(1.480–3.096) | |
(TT/CT + CC) | Control | 61/322 | ||||
rs12023196 | Genotype | Patient | 79/124/102 | |||
(CC/CT/TT) | Control | 42/171/170 | ||||
Dominant | Patient | 203/102 | 8.507 | 0.004 | 1.588(1.163–2.170) | |
(CC + CT/TT) | Control | 213/170 | ||||
Recessive | Patient | 79/226 | 26.131 | 0.000 | 2.838(1.883–4.278) | |
(CC/CT + TT) | Control | 42/341 | ||||
rs512208 | Genotype | Patient | 104/126/75 | |||
(GG/GT/TT) | Control | 193/160/30 | ||||
Dominant | Patient | 201/104 | 18.373 | 0.000 | 1.963(1.440–2.677) | |
(TT + GT/GG) | Control | 190/193 | ||||
Recessive | Patient | 75/230 | 36.867 | 0.000 | 3.837(2.435–6.047) | |
(TT/GT + GG) | Control | 30/353 | ||||
rs4845454 | Genotype | Patient | 100/127/78 | |||
(TT/CT/CC) | Control | 129/194/60 | ||||
Dominant | Patient | 205/100 | 0.061 | 0.805 | 1.041(0.756–1.433) | |
(CC + CT/TT) | Control | 254/129 | ||||
Recessive | Patient | 78/227 | 10.395 | 0.001 | 1.850 (1.269–2.697) | |
(CC/CT + TT) | Control | 60/323 | ||||
rs4085613 | Genotype | Patient | 98/120/87 | |||
(CC/AC/AA) | Control | 124/189/70 | ||||
Dominant | Patient | 207/98 | 0.005 | 0.946 | 1.011(0.733–1.395) | |
(AA + AC/CC) | Control | 259/124 | ||||
Recessive | Patient | 87/218 | 10.124 | 0.001 | 1.784(1.246–2.555) | |
(AA/AC + CC) | Control | 70/313 | ||||
rs1886734 | Genotype | Patient | 79/127/99 | |||
(TT/GT/GG) | Control | 63/194/126 | ||||
Dominant | Patient | 206/99 | 0.015 | 0.903 | 1.020(0.740–1.406) | |
(TT + GT/GG) | Control | 257/126 | ||||
Recessive | Patient | 79/226 | 9.262 | 0.002 | 1.776(1.224–2.576) | |
(TT/GT + GG) | Control | 63/320 |
SNP | CHR | BP | Alt Allele | Model | NMISS | OR | SE | L95 | U95 | STAT | P value | FDR_BH adjusted |
---|---|---|---|---|---|---|---|---|---|---|---|---|
rs1886734 | 1 | 152,591,142 | T | Additive | 688 | 1.21 | 0.1069 | 0.9816 | 1.492 | 1.787 | 0.074 | 0.074 |
rs4085613 | 1 | 152,550,018 | A | Additive | 688 | 1.214 | 0.1046 | 0.989 | 1.49 | 1.854 | 0.0637 | 0.074 |
rs6701216 | 1 | 152,778,526 | T | Additive | 688 | 1.58 | 0.1133 | 1.266 | 1.973 | 4.04 | 0.00005338 | 0.0001246 |
rs12023196 | 1 | 152,783,724 | C | Additive | 688 | 1.652 | 0.1088 | 1.335 | 2.044 | 4.613 | 0.000003974 | 0.00001391 |
rs4845454 | 1 | 152,592,184 | C | Additive | 688 | 1.233 | 0.1073 | 0.9996 | 1.522 | 1.956 | 0.05046 | 0.07064 |
rs512208 | 1 | 152,552,285 | T | Additive | 688 | 1.954 | 0.1128 | 1.566 | 2.437 | 5.936 | 2.915E−09 | 2.041E−08 |
rs4112788 | 1 | 152,551,276 | T | Additive | 688 | 1.424 | 0.1044 | 1.16 | 1.747 | 3.384 | 0.0007145 | 0.00125 |