期刊
AMERICAN JOURNAL OF HUMAN GENETICS
卷 79, 期 1, 页码 1-12出版社
CELL PRESS
DOI: 10.1086/504302
关键词
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资金
- NHGRI NIH HHS [HG003054, R01 HG003054] Funding Source: Medline
- NIGMS NIH HHS [GM073059, R01 GM073059] Funding Source: Medline
A chromosome in an individual of recently admixed ancestry resembles a mosaic of chromosomal segments, or ancestry blocks, each derived from a particular ancestral population. We consider the problem of inferring ancestry along the chromosomes in an admixed individual and thereby delineating the ancestry blocks. Using a simple population model, we infer gene-flow history in each individual. Compared with existing methods, which are based on a hidden Markov model, the Markov-hidden Markov model ( MHMM) we propose has the advantage of accounting for the background linkage disequilibrium ( LD) that exists in ancestral populations. When there are more than two ancestral groups, we allow each ancestral population to admix at a different time in history. We use simulations to illustrate the accuracy of the inferred ancestry as well as the importance of modeling the background LD; not accounting for background LD between markers may mislead us to false inferences about mixed ancestry in an indigenous population. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single- nucleotide polymorphism panel. One application of our method is to perform admixture mapping without genotyping special ancestry-informative-marker panels.
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