Development of Admixture Mapping Panels for African Americans from Commercial High-Density SNP Arrays

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dc.contributor.author Chen, Guanjie en_US
dc.contributor.author Shriner, Daniel en_US
dc.contributor.author Zhou, Jie en_US
dc.contributor.author Doumatey, Ayo en_US
dc.contributor.author Huang, Hanxia en_US
dc.contributor.author Gerry, Norman P en_US
dc.contributor.author Herbert, Alan en_US
dc.contributor.author Christman, Michael F en_US
dc.contributor.author Chen, Yuanxiu en_US
dc.contributor.author Dunston, Georgia M en_US
dc.contributor.author Faruque, Mezbah U en_US
dc.contributor.author Rotimi, Charles N en_US
dc.contributor.author Adeyemo, Adebowale en_US
dc.date.accessioned 2011-12-30T00:07:00Z
dc.date.available 2011-12-30T00:07:00Z
dc.date.copyright 2010 en_US
dc.date.issued 2010-7-5 en_US
dc.identifier.citation Chen, Guanjie, Daniel Shriner, Jie Zhou, Ayo Doumatey, Hanxia Huang, Norman P Gerry, Alan Herbert, Michael F Christman, Yuanxiu Chen, Georgia M Dunston, Mezbah U Faruque, Charles N Rotimi, Adebowale Adeyemo. "Development of admixture mapping panels for African Americans from commercial high-density SNP arrays." BMC Genomics 11:417. (2010) en_US
dc.identifier.issn 1471-2164 en_US
dc.identifier.uri http://hdl.handle.net/2144/2679
dc.description.abstract BACKGROUND: Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs) for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. RESULTS: We developed two panels of AIMs (~2,000 markers each) based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. CONCLUSIONS" Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1) no de novo genotyping needs to be done, thereby saving costs, and (2) markers can be filtered for various quality measures and replacement markers (to minimize gaps) can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1) the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2) clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from SNP chip genotype data provides a fresh opportunity to conduct admixture mapping for disease genes in admixed populations when genome-wide association data exist or are planned. en_US
dc.description.sponsorship National Institute of General Medicine Sciences and Minority Biomedical Research Support and Spinal Cord Opportunities for Rehabilitation Endowment (S06GM008016, S06GM008016-380111); National Center for Research Resources (2M01RR010284); Intramural Research Program of the Center for the Research on Genomics and Global Health; National Human Genome Research Institute; National Institute of Diabetes and Digestive and Kidney Diseases; Center for Information Technology; Office of the Director at the National Institutes of Health (Z01HG200362) en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2010 Chen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution 2.0 License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title Development of Admixture Mapping Panels for African Americans from Commercial High-Density SNP Arrays en_US
dc.type article en_US
dc.identifier.doi 10.1186/1471-2164-11-417 en_US
dc.identifier.pubmedid 20602785 en_US
dc.identifier.pmcid 2996945 en_US

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