Ancestry-specific polygenic scores and SNP heritability of 25(OH)D in African- and European-ancestry populations

Hum Genet. 2019 Oct;138(10):1155-1169. doi: 10.1007/s00439-019-02049-x. Epub 2019 Jul 24.

Abstract

Vitamin D inadequacy, assessed by 25-hydroxyvitamin D [25(OH)D], affects around 50% of adults in the United States and is associated with numerous adverse health outcomes. Blood 25(OH)D concentrations are influenced by genetic factors that may determine how much vitamin D intake is required to reach optimal 25(OH)D. Despite large genome-wide association studies (GWASs), only a small portion of the genetic factors contributing to differences in 25(OH)D has been discovered. Therefore, knowledge of a fuller set of genetic factors could be useful for risk prediction of 25(OH)D inadequacy, personalized vitamin D supplementation, and prevention of downstream morbidity and mortality. Using PRSice and weights from published African- and European-ancestry GWAS summary statistics, ancestry-specific polygenic scores (PGSs) were created to capture a more complete set of genetic factors in those of European (n = 9569) or African ancestry (n = 2761) from three cohort studies. The PGS for African ancestry was derived using all input SNPs (a p value cutoff of 1.0) and had an R2 of 0.3%; for European ancestry, the optimal PGS used a p value cutoff of 3.5 × 10-4 in the target/tuning dataset and had an R2 of 1.0% in the validation cohort. Those with highest genetic risk had 25(OH)D that was 2.8-3.0 ng/mL lower than those with lowest genetic risk (p = 0.0463-3.2 × 10-13), requiring an additional 467-500 IU of vitamin D intake to maintain equivalent 25(OH)D. PGSs are a powerful predictive tool that could be leveraged for personalized vitamin D supplementation to prevent the negative downstream effects of 25(OH)D inadequacy.

MeSH terms

  • Black People / genetics*
  • Cohort Studies
  • Databases, Genetic
  • Dietary Supplements
  • Female
  • Genetics, Population*
  • Genome-Wide Association Study
  • Humans
  • Inheritance Patterns*
  • Male
  • Middle Aged
  • Multifactorial Inheritance*
  • Polymorphism, Single Nucleotide*
  • Ultraviolet Rays
  • Vitamin D / analogs & derivatives*
  • Vitamin D / blood
  • White People / genetics*

Substances

  • Vitamin D
  • 25-hydroxyvitamin D

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