Inter-chromosomal variation in the pattern of human population genetic structure

<p>Abstract</p> <p>Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We exa...

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Main Author: Baye Tesfaye M
Format: Article
Language:English
Published: BMC 2011-05-01
Series:Human Genomics
Subjects:
Online Access:http://www.humgenomics.com/content/5/4/220
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author Baye Tesfaye M
author_facet Baye Tesfaye M
author_sort Baye Tesfaye M
collection DOAJ
description <p>Abstract</p> <p>Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC), cluster, discriminant, fixation index (F<sub>ST</sub>) and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (<it>OCA2</it>), hect domain and RLD 2 (<it>HERC2</it>), ectodysplasin A receptor (<it>EDAR</it>) and solute carrier family 45, member 2 (<it>SLC45A2</it>). These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (<it>IFNG</it>) and death-associated protein kinase 1 (DAPK1), which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the application of complementary statistical and functional network analysis in human genetic variation studies.</p>
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spelling doaj.art-4c55d17b920848b39ccf27df894a31f82022-12-22T01:56:24ZengBMCHuman Genomics1479-73642011-05-015422024010.1186/1479-7364-5-4-220Inter-chromosomal variation in the pattern of human population genetic structureBaye Tesfaye M<p>Abstract</p> <p>Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC), cluster, discriminant, fixation index (F<sub>ST</sub>) and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (<it>OCA2</it>), hect domain and RLD 2 (<it>HERC2</it>), ectodysplasin A receptor (<it>EDAR</it>) and solute carrier family 45, member 2 (<it>SLC45A2</it>). These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (<it>IFNG</it>) and death-associated protein kinase 1 (DAPK1), which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the application of complementary statistical and functional network analysis in human genetic variation studies.</p>http://www.humgenomics.com/content/5/4/220discriminant analysisprincipal component analysiscluster analysisfixation index<it>F<sub>ST</sub></it>population structuregene network
spellingShingle Baye Tesfaye M
Inter-chromosomal variation in the pattern of human population genetic structure
Human Genomics
discriminant analysis
principal component analysis
cluster analysis
fixation index
<it>F<sub>ST</sub></it>
population structure
gene network
title Inter-chromosomal variation in the pattern of human population genetic structure
title_full Inter-chromosomal variation in the pattern of human population genetic structure
title_fullStr Inter-chromosomal variation in the pattern of human population genetic structure
title_full_unstemmed Inter-chromosomal variation in the pattern of human population genetic structure
title_short Inter-chromosomal variation in the pattern of human population genetic structure
title_sort inter chromosomal variation in the pattern of human population genetic structure
topic discriminant analysis
principal component analysis
cluster analysis
fixation index
<it>F<sub>ST</sub></it>
population structure
gene network
url http://www.humgenomics.com/content/5/4/220
work_keys_str_mv AT bayetesfayem interchromosomalvariationinthepatternofhumanpopulationgeneticstructure