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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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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. |
format | Online Article Text |
id | pubmed-4687076 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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