Table 3.
Top 10 Results for identified CNV regions, sorted by Liptak p-value, for the CAMP BMI analysis
| SNP | Chr. | Position* | FBAT | Rank-based | Liptak | Liptak |
|---|---|---|---|---|---|---|
| (bp) | p-value | Wald p-value | test | p-value | ||
| rs1758827 | 10 | 56295820 | 4.931E-03 | 7.128E-05 | 4.68 | 2.902E-06 |
| rs1831078 | 9 | 25416556 | 2.411E-03 | 2.138E-04 | 4.64 | 3.547E-06 |
| rs1886314 | 13 | 67392298 | 3.583E-04 | 1.019E-02 | 4.16 | 3.133E-05 |
| rs9351261 | 6 | 65171419 | 1.999E-02 | 4.989E-04 | 3.97 | 7.118E-05 |
| rs11758713 | 6 | 67036364 | 2.593E-04 | 3.899E-02 | 3.83 | 1.285E-04 |
| rs7072438 | 10 | 59013036 | 2.775E-02 | 7.840E-04 | 3.79 | 1.495E-04 |
| rs696279 | 7 | 16700798 | 3.811E-03 | 1.133E-02 | 3.66 | 2.547E-04 |
| rs11004706 | 10 | 56813669 | 7.685E-02 | 3.564E-04 | 3.64 | 2.681E-04 |
| rs7856324 | 9 | 28366643 | 1.814E-03 | 2.145E-02 | 3.64 | 2.756E-04 |
SNP positions are from NCBI build 37.1. The FBAT p-value is the asymptotic p-value obtained from the Ionita-Laza FBAT – CNV test statistic. The Observed Wald p-value is the asymptotic p-value from a Wald test regressing the BMI phenotype on the expected parental CNV intensities. The Rank-based Wald p-value reflects the p-value based on the rank of the Wald test. The Liptak test is the value of the test statistic given in equation 2.2, which combines the FBAT p-value and the Rank-based Wald p-value. The Liptak p-value is the asymptotic p-value from this combined test statistic. Results with a Liptak p-value< 7.18×10−6 are significant at the α=0.05 level after Bonferroni correction for multiple comparisons.