Prioritization of Variants for Investigation of Genotype-Directed Nutrition in Human Superpopulations

Abstract

Dietary guidelines recommended by key health agencies are generally designed for a global population. However, ethnicity affects human disease and environment-gene interactions, including nutrient intake. Historically, isolated human populations with different genetic backgrounds have adapted to distinct environments with varying food sources. Ethnicity is relevant to the interaction of food intake with genes and disease susceptibility; yet major health agencies generally do not recommend food and nutrients codified by population genotypes and their frequencies. In this paper, we have consolidated published nutrigenetic variants and examine their frequencies in human superpopulations to prioritize these variants for future investigation of population-specific genotype-directed nutrition. The nutrients consumed by individuals interact with their genome and may alter disease risk. Herein, we searched the literature, designed a data model, and manually curated hundreds of papers. The resulting database houses 101 variants that reached significance (p < 0.05), from 35 population studies. Nutrigenetic variants associated with modified nutrient intake have the potential to reduce the risk of colorectal cancer, obesity, metabolic syndrome, type 2 diabetes, and several other diseases. Since many nutrigenetic studies have identified a major variant in some populations, we suggest that superpopulation-specific genotype-directed nutrition modifications be prioritized for future study and evaluation. Genotype-directed nutrition approaches to dietary modification have the potential to reduce disease risk in select human populations.

Computational Strategies in Nutrigenetics: Constructing a Reference Dataset of Nutrition-Associated Genetic Polymorphisms

“…Inconsistencies, errors, and biases in the original studies may be transferred to the constructed dataset. Finally, the dataset may cover only some populations and ethnicities, which could limit its applicability to diverse populations with different genetic backgrounds [30].…”

Obesity and Nutrigenetics Testing: New Insights

“…As nutritional genomics promises to transform global health and medicine, there is growing interest in the relationship between genotype and phenotype. The phenotype derives from genetic and environmental contributions [ 54 ]. Once “the” genetic variants that may predispose a trait or disease have been identified, the next challenge is to decode the genetic variation that explains heritability, in addition to the epigenetic changes [ 55 ].…”

Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents

“…A large number of studies have focused on how genetic variation might affect micronutrient metabolism, clinical and metabolomic measurements, and phenotypic expression 4 – 6 with the goal of personalizing recommendations based on genetic variation 7 . Over 2300 publications on associations between single-nucleotide polymorphisms (SNPs) in candidate genes involved in nutrient (including vitamins and minerals) metabolism or response, as well as with disease 8 , 9 have been published since 2001 10 . The majority of reports found statistical correlations but effect sizes were uniformly very small (usually < 1% of total phenotype) and reproducibility between studies is low.…”