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Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group

The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse...

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Autores principales: Yoon, Byung-Woo, Shin, Hyun-Tae, Seo, Jehyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8536051/
https://www.ncbi.nlm.nih.gov/pubmed/34680925
http://dx.doi.org/10.3390/genes12101530
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author Yoon, Byung-Woo
Shin, Hyun-Tae
Seo, Jehyun
author_facet Yoon, Byung-Woo
Shin, Hyun-Tae
Seo, Jehyun
author_sort Yoon, Byung-Woo
collection PubMed
description The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse ancestry. We collected 320 single-nucleotide polymorphisms (SNPs) associated with vitamin D concentrations from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher’s exact tests to assess the significance of the enrichment or depletion of the effect allele at a given SNP in the database. In addition, we calculated the SNP-based genetic risk score (GRS) and performed correlation analysis with vitamin D concentration that included latitude. European, American, and South Asian populations showed similar heatmap patterns, whereas African, East Asian, and Korean populations had distinct ones. The GRS calculated from allele frequencies of vitamin D concentration was highest among Europeans, followed by East Asians and Africans. In addition, the difference in vitamin D concentration was highly correlated with genetic factors rather than latitude effects.
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spelling pubmed-85360512021-10-23 Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group Yoon, Byung-Woo Shin, Hyun-Tae Seo, Jehyun Genes (Basel) Article The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse ancestry. We collected 320 single-nucleotide polymorphisms (SNPs) associated with vitamin D concentrations from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher’s exact tests to assess the significance of the enrichment or depletion of the effect allele at a given SNP in the database. In addition, we calculated the SNP-based genetic risk score (GRS) and performed correlation analysis with vitamin D concentration that included latitude. European, American, and South Asian populations showed similar heatmap patterns, whereas African, East Asian, and Korean populations had distinct ones. The GRS calculated from allele frequencies of vitamin D concentration was highest among Europeans, followed by East Asians and Africans. In addition, the difference in vitamin D concentration was highly correlated with genetic factors rather than latitude effects. MDPI 2021-09-28 /pmc/articles/PMC8536051/ /pubmed/34680925 http://dx.doi.org/10.3390/genes12101530 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yoon, Byung-Woo
Shin, Hyun-Tae
Seo, Jehyun
Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title_full Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title_fullStr Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title_full_unstemmed Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title_short Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group
title_sort risk allele frequency analysis of single-nucleotide polymorphisms for vitamin d concentrations in different ethnic group
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8536051/
https://www.ncbi.nlm.nih.gov/pubmed/34680925
http://dx.doi.org/10.3390/genes12101530
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