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dc.creatorBoudeau, Samantha
dc.creatorRamakodi, Meganathan P.
dc.creatorZhou, Yan
dc.creatorLiu, Jeffrey
dc.creatorRagin, Camille
dc.creatorKulathinal, Rob J.
dc.date.accessioned2023-09-13T16:51:22Z
dc.date.available2023-09-13T16:51:22Z
dc.date.issued2023-02-23
dc.identifier.citationBoudeau S, Ramakodi MP, Zhou Y, Liu JC, Ragin C and Kulathinal RJ (2023) Extensive set of African ancestry-informative markers (AIMs) to study ancestry and population health. Front. Genet. 14:1061781. doi: 10.3389/fgene.2023.1061781
dc.identifier.issn1664-8021
dc.identifier.urihttp://hdl.handle.net/20.500.12613/9037
dc.description.abstractIntroduction: Human populations are often highly structured due to differences in genetic ancestry among groups, posing difficulties in associating genes with diseases. Ancestry-informative markers (AIMs) aid in the detection of population stratification and provide an alternative approach to map population-specific alleles to disease. Here, we identify and characterize a novel set of African AIMs that separate populations of African ancestry from other global populations including those of European ancestry. Methods: Using data from the 1000 Genomes Project, highly informative SNP markers from five African subpopulations were selected based on estimates of informativeness (In) and compared against the European population to generate a final set of 46,737 African ancestry-informative markers (AIMs). The AIMs identified were validated using an independent set and functionally annotated using tools like SIFT, PolyPhen. They were also investigated for representation of commonly used SNP arrays. Results: This set of African AIMs effectively separates populations of African ancestry from other global populations and further identifies substructure between populations of African ancestry. When a subset of these AIMs was studied in an independent dataset, they differentiated people who self-identify as African American or Black from those who identify their ancestry as primarily European. Most of the AIMs were found to be in their intergenic and intronic regions with only 0.6% in the coding regions of the genome. Most of the commonly used SNP array investigated contained less than 10% of the AIMs. Discussion: While several functional annotations of both coding and non-coding African AIMs are supported by the literature and linked these high-frequency African alleles to diseases in African populations, more effort is needed to map genes to diseases in these genetically diverse subpopulations. The relative dearth of these African AIMs on current genotyping platforms (the array with the highest fraction, llumina’s Omni 5, harbors less than a quarter of AIMs), further demonstrates a greater need to better represent historically understudied populations.
dc.format.extent12 pages
dc.languageEnglish
dc.language.isoeng
dc.relation.ispartofOpen Access Publishing Fund
dc.relation.haspartFrontiers in Genetics, Vol. 14
dc.relation.isreferencedbyFrontiers Media
dc.rightsAttribution CC BY
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAfrican ancestry
dc.subjectAims
dc.subjectPopulation structure
dc.subject1000 genomes project
dc.subjectAncestry and health
dc.titleExtensive set of African ancestry-informative markers (AIMs) to study ancestry and population health
dc.typeText
dc.type.genreJournal article
dc.contributor.groupFox Chase Cancer Center
dc.description.departmentBiology
dc.description.departmentOtolaryngology
dc.relation.doihttps://doi.org/10.3389/fgene.2023.1061781
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.description.schoolcollegeTemple University. College of Science and Technology
dc.description.schoolcollegeLewis Katz School of Medicine
dc.description.sponsorTemple University Libraries Open Access Publishing Fund, 2022-2023 (Philadelphia, Pa.)
dc.creator.orcidLiu|0000-0001-8377-0905
dc.creator.orcidRagin|0000-0003-0816-4942
dc.temple.creatorBoudeau, Samantha
dc.temple.creatorRamakodi, Meganathan P.
dc.temple.creatorZhou, Yan
dc.temple.creatorLiu, Jeffrey C.
dc.temple.creatorRagin, Camille
dc.temple.creatorKulathinal, Rob J.
refterms.dateFOA2023-09-13T16:51:22Z


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