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The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium.
Zaitlen, Noah; Huntsman, Scott; Hu, Donglei; Spear, Melissa; Eng, Celeste; Oh, Sam S; White, Marquitta J; Mak, Angel; Davis, Adam; Meade, Kelly; Brigino-Buenaventura, Emerita; LeNoir, Michael A; Bibbins-Domingo, Kirsten; Burchard, Esteban G; Halperin, Eran.
Afiliación
  • Zaitlen N; Department of Medicine, University of California, San Francisco, California 94158 noah.zaitlen@ucsf.edu heran@post.tau.ac.il.
  • Huntsman S; Department of Medicine, University of California, San Francisco, California 94158.
  • Hu D; Department of Medicine, University of California, San Francisco, California 94158.
  • Spear M; Department of Medicine, University of California, San Francisco, California 94158.
  • Eng C; Department of Medicine, University of California, San Francisco, California 94158.
  • Oh SS; Department of Medicine, University of California, San Francisco, California 94158.
  • White MJ; Department of Medicine, University of California, San Francisco, California 94158.
  • Mak A; Department of Medicine, University of California, San Francisco, California 94158.
  • Davis A; Childrens Hospital and Research Center Oakland, California 94609.
  • Meade K; Childrens Hospital and Research Center Oakland, California 94609.
  • Brigino-Buenaventura E; Department of Allergy and Immunology, Kaiser Permanente Vallejo Medical Center, California 94589.
  • LeNoir MA; Bay Area Pediatrics, Oakland, California 94601.
  • Bibbins-Domingo K; Department of Medicine, University of California, San Francisco, California 94158.
  • Burchard EG; Department of Medicine, University of California, San Francisco, California 94158.
  • Halperin E; Department of Medicine, University of California, San Francisco, California 94158 noah.zaitlen@ucsf.edu heran@post.tau.ac.il.
Genetics ; 205(1): 375-383, 2017 01.
Article en En | MEDLINE | ID: mdl-27879348
Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry-based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first direct evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Negro o Afroamericano / Desequilibrio de Ligamiento / Migración Humana / Modelos Genéticos Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Genetics Año: 2017 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Negro o Afroamericano / Desequilibrio de Ligamiento / Migración Humana / Modelos Genéticos Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Genetics Año: 2017 Tipo del documento: Article Pais de publicación: Estados Unidos