A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set
The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry usin...
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| Veröffentlicht in: | European journal of human genetics : EJHG 2016-05, Vol.24 (5), p.725-731 |
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| creator | Santos, Hadassa C Horimoto, Andréa V R Tarazona-Santos, Eduardo Rodrigues-Soares, Fernanda Barreto, Mauricio L Horta, Bernardo L Lima-Costa, Maria F Gouveia, Mateus H Machado, Moara Silva, Thiago M Sanches, José M Esteban, Nubia Magalhaes, Wagner C S Rodrigues, Maíra R Kehdy, Fernanda S G Pereira, Alexandre C |
| description | The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals. |
| doi_str_mv | 10.1038/ejhg.2015.187 |
| format | Article |
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The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.</description><identifier>ISSN: 1018-4813</identifier><identifier>EISSN: 1476-5438</identifier><identifier>DOI: 10.1038/ejhg.2015.187</identifier><identifier>PMID: 26395555</identifier><language>eng</language><publisher>England: Nature Publishing Group</publisher><subject>African Continental Ancestry Group ; American Native Continental Ancestry Group ; Brazil ; Cardiology ; Data processing ; Ethnic groups ; European Continental Ancestry Group ; Gene mapping ; Genetic Markers ; Genetics ; Genome, Human ; Genomes ; Genotypes ; Genotyping ; Humans ; Pedigree ; Pigmentation ; Polymorphism, Single Nucleotide ; Population ; Population - genetics ; Principal components analysis ; Single-nucleotide polymorphism ; Skin ; Skin Pigmentation - genetics ; Studies</subject><ispartof>European journal of human genetics : EJHG, 2016-05, Vol.24 (5), p.725-731</ispartof><rights>Copyright Nature Publishing Group May 2016</rights><rights>Copyright © 2016 Macmillan Publishers Limited 2016 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c448t-780482e20a4ee6deb9f29f348fb84b74a2c90879ef870f170567b742835039303</citedby><cites>FETCH-LOGICAL-c448t-780482e20a4ee6deb9f29f348fb84b74a2c90879ef870f170567b742835039303</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930091/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930091/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26395555$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Santos, Hadassa C</creatorcontrib><creatorcontrib>Horimoto, Andréa V R</creatorcontrib><creatorcontrib>Tarazona-Santos, Eduardo</creatorcontrib><creatorcontrib>Rodrigues-Soares, Fernanda</creatorcontrib><creatorcontrib>Barreto, Mauricio L</creatorcontrib><creatorcontrib>Horta, Bernardo L</creatorcontrib><creatorcontrib>Lima-Costa, Maria F</creatorcontrib><creatorcontrib>Gouveia, Mateus H</creatorcontrib><creatorcontrib>Machado, Moara</creatorcontrib><creatorcontrib>Silva, Thiago M</creatorcontrib><creatorcontrib>Sanches, José M</creatorcontrib><creatorcontrib>Esteban, Nubia</creatorcontrib><creatorcontrib>Magalhaes, Wagner C S</creatorcontrib><creatorcontrib>Rodrigues, Maíra R</creatorcontrib><creatorcontrib>Kehdy, Fernanda S G</creatorcontrib><creatorcontrib>Pereira, Alexandre C</creatorcontrib><creatorcontrib>Brazilian EPIGEN Project Consortium</creatorcontrib><creatorcontrib>The Brazilian EPIGEN Project Consortium</creatorcontrib><title>A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set</title><title>European journal of human genetics : EJHG</title><addtitle>Eur J Hum Genet</addtitle><description>The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.</description><subject>African Continental Ancestry Group</subject><subject>American Native Continental Ancestry Group</subject><subject>Brazil</subject><subject>Cardiology</subject><subject>Data processing</subject><subject>Ethnic groups</subject><subject>European Continental Ancestry Group</subject><subject>Gene mapping</subject><subject>Genetic Markers</subject><subject>Genetics</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Humans</subject><subject>Pedigree</subject><subject>Pigmentation</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population - genetics</subject><subject>Principal components analysis</subject><subject>Single-nucleotide polymorphism</subject><subject>Skin</subject><subject>Skin Pigmentation - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>European journal of human genetics : EJHG</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Santos, Hadassa C</au><au>Horimoto, Andréa V R</au><au>Tarazona-Santos, Eduardo</au><au>Rodrigues-Soares, Fernanda</au><au>Barreto, Mauricio L</au><au>Horta, Bernardo L</au><au>Lima-Costa, Maria F</au><au>Gouveia, Mateus H</au><au>Machado, Moara</au><au>Silva, Thiago M</au><au>Sanches, José M</au><au>Esteban, Nubia</au><au>Magalhaes, Wagner C S</au><au>Rodrigues, Maíra R</au><au>Kehdy, Fernanda S G</au><au>Pereira, Alexandre C</au><aucorp>Brazilian EPIGEN Project Consortium</aucorp><aucorp>The Brazilian EPIGEN Project Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set</atitle><jtitle>European journal of human genetics : EJHG</jtitle><addtitle>Eur J Hum Genet</addtitle><date>2016-05-01</date><risdate>2016</risdate><volume>24</volume><issue>5</issue><spage>725</spage><epage>731</epage><pages>725-731</pages><issn>1018-4813</issn><eissn>1476-5438</eissn><abstract>The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.</abstract><cop>England</cop><pub>Nature Publishing Group</pub><pmid>26395555</pmid><doi>10.1038/ejhg.2015.187</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | European journal of human genetics : EJHG, 2016-05, Vol.24 (5), p.725-731 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; SpringerLink Journals - AutoHoldings |
| subjects | African Continental Ancestry Group American Native Continental Ancestry Group Brazil Cardiology Data processing Ethnic groups European Continental Ancestry Group Gene mapping Genetic Markers Genetics Genome, Human Genomes Genotypes Genotyping Humans Pedigree Pigmentation Polymorphism, Single Nucleotide Population Population - genetics Principal components analysis Single-nucleotide polymorphism Skin Skin Pigmentation - genetics Studies |
| title | A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set |
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