Table 1. Three-trait and four-trait meta-analysis of lipid traits in European studies using Hom-F based on Pillai-Bartlett trace.
| P-values of the Hom-F | |||||
|---|---|---|---|---|---|
| Basis of Both GVF and βℓ(t) | Basis of beta-smooth only | ||||
| Traits | Gene | B-spline basis | Fourier basis | B-spline basis | Fourier basis |
| LDL, TG, CHOL | APOB | 1.29 × 10−10 | 1.73 × 10−5 | 9.16 × 10−10 | 2.21 × 10−6 |
| APOE | 1.82 × 10−88 | 5.22 × 10−90 | 9.03 × 10−89 | 1.31 × 10−90 | |
| LDLR | 3.14 × 10−11 | 2.25 × 10−9 | 3.51 × 10−9 | 8.49 × 10−8 | |
| LPL | 1.74 × 10−7 | 2.33 × 10−8 | 8.71 × 10−8 | 1.01 × 10−8 | |
| PCSK9 | 7.55 × 10−6 | 4.00 × 10−7 | 0.000196 | 2.16 × 10−6 | |
| HDL, LDL, TG | APOB | 6.47 × 10−10 | 6.32 × 10−6 | 4.89 × 10−10 | 1.15 × 10−6 |
| APOE | 6.22 × 10−95 | 3.11 × 10−97 | 4.77 × 10−95 | 2.03 × 10−96 | |
| LDLR | 1.03 × 10−11 | 2.16 × 10−10 | 1.34 × 10−10 | 4.51 × 10−9 | |
| LPL | 6.31 × 10−7 | 2.98 × 10−7 | 3.64 × 10−7 | 1.69 × 10−6 | |
| PCSK9 | 1.46 × 10−7 | 3.62 × 10−8 | 4.54 × 10−5 | 1.08 × 10−6 | |
| HDL, LDL, CHOL | APOB | 1.01 × 10−9 | 1.67 × 10−5 | 5.61 × 10−10 | 2.23 × 10−6 |
| APOE | 1.62 × 10−82 | 1.25 × 10−83 | 5.03 × 10−81 | 5.94 × 10−83 | |
| LDLR | 1.33 × 10−10 | 6.82 × 10−10 | 3.07 × 10−9 | 2.24 × 10−8 | |
| LPL | 2.32 × 10−7 | 8.76 × 10−8 | 2.24 × 10−7 | 1.33 × 10−7 | |
| PCSK9 | 1.18 × 10−6 | 3.25 × 10−8 | 7.88 × 10−5 | 1.57 × 10−7 | |
| HDL, TG, CHOL | APOB | 1.11 × 10−10 | 2.93 × 10−6 | 1.66 × 10−10 | 4.11 × 10−7 |
| APOE | 4.59 × 10−88 | 1.10 × 10−88 | 2.10 × 10−87 | 1.06 × 10−86 | |
| LDLR | 4.67 × 10−12 | 1.48 × 10−10 | 7.33 × 10−11 | 3.23 × 10−9 | |
| LPL | 1.86 × 10−9 | 6.25 × 10−11 | 1.47 × 10−9 | 2.33 × 10−10 | |
| PCSK9 | 7.62 × 10−8 | 1.47 × 10−8 | 1.13 × 10−5 | 1.35 × 10−7 | |
| HDL, LDL, TG, CHOL | APOB | 2.23 × 10−10 | 1.60 × 10−6 | 1.67 × 10−10 | 1.24 × 10−7 |
| APOE | 4.76 × 10−93 | 1.64 × 10−94 | 7.29 × 10−94 | 8.08 × 10−94 | |
| LDLR | 3.17 × 10−11 | 6.89 × 10−11 | 1.13 × 10−9 | 5.15 × 10−9 | |
| LPL | 7.41 × 10−8 | 8.79 × 10−9 | 7.14 × 10−8 | 2.20 × 10−9 | |
| PCSK9 | 1.41 × 10−7 | 1.51 × 10−7 | 8.07 × 10−5 | 4.49 × 10−7 | |
Abbreviations: GVF, genetic variant function; Hom-F, homogeneous F-approximation test statistics.
The associations that attain a threshold significance of P<3.1 × 10−6 are highlighted in bold.5 The results of ‘Basis of Both GVF and βℓ(t)' were based on smoothing both GVF and genetic effect functions βℓ(t) of model (4), and the results of ‘Basis of beta-smooth only' were based on smoothing βℓ(t) only approach of model (7).