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Genetic differences among ethnic groups

BACKGROUND: Many differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale g...

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Autores principales: Huang, Tao, Shu, Yang, Cai, Yu-Dong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687076/
https://www.ncbi.nlm.nih.gov/pubmed/26690364
http://dx.doi.org/10.1186/s12864-015-2328-0
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author Huang, Tao
Shu, Yang
Cai, Yu-Dong
author_facet Huang, Tao
Shu, Yang
Cai, Yu-Dong
author_sort Huang, Tao
collection PubMed
description BACKGROUND: Many differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale genotype data from Caucasian, African and Asian population samples have been available. The project found that these populations were located in different areas of the PCA (Principal Component Analysis) plot. However, as an unsupervised method, PCA does not measure the differences in each single nucleotide polymorphism (SNP) among populations. RESULTS: We applied an advanced mutual information-based feature selection method to detect associations between SNP status and ethnic groups using the latest HapMap Phase 3 release version 3, which included more sub-populations. A total of 299 SNPs were identified, and they can accurately predicted the ethnicity of all HapMap populations. The 10-fold cross validation accuracy of the SMO (sequential minimal optimization) model on training dataset was 0.901, and the accuracy on independent test dataset was 0.895. CONCLUSIONS: In-depth functional analysis of these SNPs and their nearby genes revealed the genetic bases of skin and eye color differences among populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2328-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-46870762015-12-23 Genetic differences among ethnic groups Huang, Tao Shu, Yang Cai, Yu-Dong BMC Genomics Research Article BACKGROUND: Many differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale genotype data from Caucasian, African and Asian population samples have been available. The project found that these populations were located in different areas of the PCA (Principal Component Analysis) plot. However, as an unsupervised method, PCA does not measure the differences in each single nucleotide polymorphism (SNP) among populations. RESULTS: We applied an advanced mutual information-based feature selection method to detect associations between SNP status and ethnic groups using the latest HapMap Phase 3 release version 3, which included more sub-populations. A total of 299 SNPs were identified, and they can accurately predicted the ethnicity of all HapMap populations. The 10-fold cross validation accuracy of the SMO (sequential minimal optimization) model on training dataset was 0.901, and the accuracy on independent test dataset was 0.895. CONCLUSIONS: In-depth functional analysis of these SNPs and their nearby genes revealed the genetic bases of skin and eye color differences among populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2328-0) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-21 /pmc/articles/PMC4687076/ /pubmed/26690364 http://dx.doi.org/10.1186/s12864-015-2328-0 Text en © Huang et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Huang, Tao
Shu, Yang
Cai, Yu-Dong
Genetic differences among ethnic groups
title Genetic differences among ethnic groups
title_full Genetic differences among ethnic groups
title_fullStr Genetic differences among ethnic groups
title_full_unstemmed Genetic differences among ethnic groups
title_short Genetic differences among ethnic groups
title_sort genetic differences among ethnic groups
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687076/
https://www.ncbi.nlm.nih.gov/pubmed/26690364
http://dx.doi.org/10.1186/s12864-015-2328-0
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