Table 3.
MUC5B Promoter Variant (rs35705950) Genotypes and Minor Allele Frequencies across the Collections
| All PF* | Familial PF | Sporadic IPF | All PF QV Carriers | In-House Control Subjects | 1KGP EUR | |
|---|---|---|---|---|---|---|
| Number of samples genotyped | 258 | 33 | 183 | 31 | 342 | 503 |
| G/G, n (%) | 115 (44.6) | 12 (36.4) | 79 (43.2) | 16 (51.6) | 272 (79.5) | 397 (78.9) |
| G/T, n (%) | 123 (47.7) | 18 (54.5) | 88 (48.1) | 15 (48.4) | 65 (19.0) | 104 (20.7) |
| T/T, n (%) | 20 (7.7) | 3 (9.1) | 16 (8.7) | 0 (0) | 5 (1.5) | 2 (0.4) |
| MAF (T allele), % | 31.59 | 36.36 | 32.79 | 24.19 | 10.96 | 10.74 |
| HWE exact test†P value | 0.11 | 0.46 | 0.25 | 0.15 | 0.58 | 0.10 |
| Allelic Fisher’s exact test P value (OR; 95% CI) compared with in-house control subjects | 8.8 × 10−19 (3.7; 2.7–5.1) | 3.8 × 10−7 (4.6; 2.5–8.3) | 3.1 × 10−17 (4.0; 2.8–5.6) | 0.007 (2.6; 1.3–5.0) | N/A | 0.87 (1.0; 0.7–1.4) |
| Cochran-Armitage test P value for trend compared with in-house control subjects | 1.3 × 10−18 | 1.0 × 10−8 | 1.7 × 10−17 | 0.002 | N/A | 0.88 |
Definition of abbreviations: CI = confidence interval; HWE = Hardy-Weinberg equilibrium; IPF = idiopathic pulmonary fibrosis; 1KGP EUR = 1000 Genomes Project European samples; MAF = minor allele frequency; N/A = not applicable; OR = odds ratio; PF = pulmonary fibrosis; QV = qualifying variant.
All allelic and trend tests were performed by comparison with a set of 342 in-house rs35705950 genotyped European control subjects. “All PF” column reports results derived from the full set of European case subjects with pulmonary fibrosis successfully genotyped for rs35705950. “Familial PF” column reports results for the subset of case subjects with a self-reported family history of pulmonary fibrosis. “Sporadic IPF” presents results for a homogeneous pulmonary fibrosis cohort with confirmed no reported family history of pulmonary fibrosis and clinically confirmed to have IPF on the basis of American Thoracic Society/European Respiratory Society/Japanese Respiratory Society/Latin American Thoracic Association guidelines. “All PF QV carriers” column reports results for the set of 31 case subjects with pulmonary fibrosis with a qualifying variant in one of the three study-wide significant genes. “In-House Control Subjects” column displays a sampling of 342 European control subjects genotyped using the same assay employed for the case genotyping. 1KGP EUR column gives the genotyping results derived from the 1000 Genomes Project (phase 3 European samples).
No significance (allelic or additive model) was observed when we compared the 31 PF QV carriers with the remaining 227 PF QV noncarriers (P > 0.1).
Adopting the recursion equations in function HWExact of R package HardyWeinberg.