Table 4.
Comparison of PheMap-based PheWAS to phecodes and previous PheWAS results
| PheMap |
Phecodes |
Previous PheWAS |
||||||
|---|---|---|---|---|---|---|---|---|
| Phenotypea | Beta (95% CI)b | P Value | Cases | OR (95% CI) | P Value | Cases | OR (95% CI) | P Value |
| FTO (rs8050136, n = 56 990)c | ||||||||
| Obesity | 2.1 (1.7–2.6) | 1.0 × 10−20 | 8695 | 1.17 (1.13–1.21) | 6.0 × 10−14 | 1662 | 1.25 (1.16–1.35) | 2.1 × 10−9 |
| Diabetes mellitus | 1.5 (1.1–2.0) | 1.6 × 10−12 | 1948 | 1.04 (0.96–1.12) | 3.3 × 10−2 | – | – | – |
| Obstructive sleep apnea | 0.8 (0.6–1.1) | 1.2 × 10−8 | 6697 | 1.08 (1.04–1.13) | 2.1× 10−4 | 2335 | 1.14 (1.07–1.22) | 3.3 × 10−5 |
| Overweight | 0.9 (0.5–1.0) | 4.8 × 10−8 | 1743 | 0.99 (0.91–1.08) | 9.0× 10−1 | 3943 | 1.17 (1.11–1.24) | 1.4 × 10−8 |
| Chondrocalcinosis | 0.7 (0.4–1.0) | 9.3 × 10−8 | 286 | 0.99 (0.80–1.19) | 9.4× 10−1 | – | – | – |
| HLA-DRB1 (rs3135388, n = 56 997)d | ||||||||
| Multiple sclerosis | 2.2 (1.8–2.6) | 2.9 × 10−28 | 1505 | 2.20 (2.06–2.35) | 6.4 × 10−26 | 89 | 2.24 (1.56–3.16) | 2.8 × 10−6 |
| Type 1 diabetes | −2.0 (−2.6 to −1.4) | 4.3 × 10−12 | 2752 | 0.45 (0.30–0.61) | 2.6 × 10−23 | – | – | – |
| Other demyelinating diseases of central nervous system | 1.4 (1.0–1.9) | 1.1 × 10−9 | 738 | 1.90 (1.68–2.11) | 4.1 × 10−9 | – | – | – |
| Systemic sclerosis | 1.6 (1.0–2.2) | 9.3 × 10−8 | 357 | 1.18 (0.82–1.53) | 3.7 × 10−1 | – | – | – |
| Secondary diabetes mellitus | −1.0 (−1.4 to −0.6) | 2.4 × 10−7 | 784 | 1.24 (0.99–1.48) | 8.6 × 10−2 | – | – | – |
| TCF7L2 (rs7903146, n = 56 982) e | ||||||||
| Diabetes mellitus | 2.6 (2.3–3.0) | 5.8 × 10−28 | 1948 | 1.30 (1.22–1.38) | 5.3 × 10−10 | – | – | – |
| Type 2 diabetes | 0.9 (0.6–1.2) | 1.2 × 10−14 | 13 694 | 1.25 (1.21–1.28) | 5.6× 10−37 | – | – | – |
| Type 1 diabetes | 1.0 (0.8–1.3) | 2.8 × 10−11 | 2752 | 1.17 (1.10–1.24) | 1.2 × 10−5 | – | – | – |
| Secondary diabetes mellitus | 0.6 (0.2–0.8) | 2.0 × 10−10 | 784 | 1.21 (1.08–1.34) | 3.8 × 10−3 | – | – | – |
| Other abnormal glucose | 1.0 (0.7–1.4) | 1.1 × 10−7 | 3102 | 1.03 (0.97–1.10) | 3.3 × 10−1 | – | – | – |
Note: CI: confidence interval; PheWAS: phenome-wide association studies; OR: odds ratio; SNP: single nucleotide polymorphisms.
a
Top 5 SNP disease associations (by P value) that met the Bonferroni correction (P < 5 × 10−5).
b
Beta represents the percent increase in phenotype case probability per copy of minor allele. Betas and 95% CIs were derived from linear regression models adjusted for sex, age, date of first visit, date of last follow-up, and first 10 principle components.
c
Cronin et al, 2014.[37]
d
Denny et al, 2010.[25]
e
No prior PheWAS on rs7903146 in TCF7L2.