TABLE 2.
Associations between selected SNPs in BCMO1 and plasma carotenoid concentrations among women with genome-wide scans by subset1
| Training subset (n = 1554–1556) |
Testing subset (n = 775–778) |
|||||||||
| Biomarker and SNP | MAF (allele)2 | Imputation3 r2 | Imputation4 | Multiple partial5 R2 | β (SE)6 | P value | Imputation | Multiple partial R2 | β (SE) | P value |
| % | % | |||||||||
| β-Carotene | ||||||||||
| rs4889286 | 0.50 (T) | 0.98 | 100 | 0.061 | 0.1762 (0.022) | 8.5 × 10−16 | 29 | 0.061 | 0.1748 (0.030) | 9.0 × 10−9 |
| rs12934922 | 0.44 (T) | 0.90 | 25 | 0.1377 (0.022) | 5.9 × 10−10 | 26 | 0.1412 (0.031) | 5.9 × 10−6 | ||
| rs4448930 | 0.15 (C) | 0.74 | 100 | 0.09747 (0.034) | 3.8 × 10−3 | 28 | 0.01753 (0.042) | 0.68 | ||
| α-Carotene | ||||||||||
| rs4889293 | 0.42 (G) | 0.85 | 73 | 0.027 | 0.1183 (0.022) | 8.7 × 10−8 | 71 | 0.012 | 0.06480 (0.032) | 0.04 |
| rs4448930 | 0.15 (C) | 0.74 | 100 | 0.09750 (0.032) | 2.3 × 10−3 | 28 | −0.006095 (0.041) | 0.88 | ||
| rs4889286 | 0.50 (T) | 0.98 | 100 | 0.06581 (0.020) | 1.3 × 10−3 | 29 | 0.06844 (0.029) | 0.02 | ||
| β-Cryptoxanthin | ||||||||||
| rs4448930 | 0.15 (C) | 0.74 | 100 | 0.019 | 0.09872 (0.027) | 2.2 × 10−4 | 28 | 0.008 | 0.02774 (0.035) | 0.43 |
| rs12918164 | 0.17 (A) | 0.83 | 100 | 0.07583 (0.024) | 1.9 × 10−3 | 100 | 0.05948 (0.035) | 0.09 | ||
| rs4889293 | 0.42 (G) | 0.85 | 73 | 0.06043 (0.018) | 1.0 × 10−3 | 71 | 0.04819 (0.027) | 0.07 | ||
| Lutein/zeaxanthin | ||||||||||
| rs56389940 | 0.36 (A) | 0.94 | 100 | 0.074 | 0.1636 (0.015) | 2.6 × 10−27 | 100 | 0.097 | 0.1792 (0.021) | 2.0 × 10−17 |
| rs10048138 | 0.14 (A) | 0.92 | 73 | 0.06580 (0.020) | 1.3 × 10−3 | 71 | 0.1334 (0.030) | 1.1 × 10−5 | ||
Multivariate linear regression of each natural log–transformed plasma biomarker concentration (μg/L) on additively modeled SNPs selected by stepwise selection by using the Schwartz Bayesian information criterion and the following covariates were forced into the model: age, case-control status, cholesterol (mg/dL, or missing indicator), BMI (kg/m2), smoking (never/former, current <15 cigarettes/d, or current ≥15 cigarettes/d), menopausal status and PMH use (premenopausal; postmenopausal, no PMH; postmenopausal, PMH; or unknown), alcohol intake (g/d), total fat intake (g/d), and dietary intake of the outcome of interest (μg/d for carotenoids or IU/d for retinol). Dietary retinol intake (IU/d) was also forced into the models for β-carotene, α-carotene, and β-cryptoxanthin. Results are shown for rs4889286 and rs4448930 original imputed values in the training subset on which selection was performed. Results in the testing subset include later genotyped values when available. MAF, minor allele frequency; PMH, postmenopausal hormone; SNP, single nucleotide polymorphism; SSE, sum of squared errors.
Weighted average MAF among all women with genome-wide scans.
Minimac imputation r2 among all women with genome-wide scans.
Percentage of women with imputed data.
Multiple partial R2: SSE for the covariate-only model − SSE for the model with SNPs and covariates divided by SSE for the covariate-only model.
β-Coefficient from the final selected model described above.