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Exploring the Genetic Architecture of Circulating 25-Hydroxyvitamin D

Authors

  • Linda T. Hiraki,

    Corresponding author
    1. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
    • Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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  • Jacqueline M. Major,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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  • Constance Chen,

    1. Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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  • Marilyn C. Cornelis,

    1. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
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  • David J. Hunter,

    1. Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
    2. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
    3. Channing Laboratory, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
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  • Eric B. Rimm,

    1. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
    2. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
    3. Channing Laboratory, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
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  • Kelly C. Simon,

    1. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
    2. Channing Laboratory, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
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  • Stephanie J. Weinstein,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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  • Mark P. Purdue,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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  • Kai Yu,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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  • Demetrius Albanes,

    1. Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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  • Peter Kraft

    1. Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
    2. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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Correspondence to: Linda Hiraki, Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, 655 Huntington Avenue, Bldg II, Room 200, Boston, MA 02115. E-mail: lindahiraki@mail.harvard.edu

Abstract

The primary circulating form of vitamin D is 25-hydroxy vitamin D (25(OH)D), a modifiable trait linked with a growing number of chronic diseases. In addition to environmental determinants of 25(OH)D, including dietary sources and skin ultraviolet B (UVB) exposure, twin- and family-based studies suggest that genetics contribute substantially to vitamin D variability with heritability estimates ranging from 43% to 80%. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) located in four gene regions associated with 25(OH)D. These SNPs collectively explain only a fraction of the heritability in 25(OH)D estimated by twin- and family-based studies. Using 25(OH)D concentrations and GWAS data on 5,575 subjects drawn from five cohorts, we hypothesized that genome-wide data, in the form of (1) a polygenic score comprised of hundreds or thousands of SNPs that do not individually reach GWAS significance, or (2) a linear mixed model for genome-wide complex trait analysis, would explain variance in measured circulating 25(OH)D beyond that explained by known genome-wide significant 25(OH)D-associated SNPs. GWAS identified SNPs explained 5.2% of the variation in circulating 25(OH)D in these samples and there was little evidence additional markers significantly improved predictive ability. On average, a polygenic score comprised of GWAS-identified SNPs explained a larger proportion of variation in circulating 25(OH)D than scores comprised of thousands of SNPs that were on average, nonsignificant. Employing a linear mixed model for genome-wide complex trait analysis explained little additional variability (range 0–22%). The absence of a significant polygenic effect in this relatively large sample suggests an oligogenetic architecture for 25(OH)D.

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