Price et al. 2009
Tue Jul 07 2009
Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease
mapping to learning about history. Most methods require the use of unlinked markers; but, using all markers from genome-
wide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite
accuracy. We describe a method, HAPMIX, which employs an explicit population genetic model to perform such local
ancestry inference based on fine-scale variation data. We show that HAPMIX outperforms other methods, and we explore its
utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate the method
empirically by applying it to populations that have experienced recent and ancient admixture: 935 African Americans from
the United States and 29 Mozabites from North Africa. HAPMIX will be of particular utility for mapping disease genes in
recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association
signals to be combined, enabling more powerful tests of association than with either signal alone.
Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease
mapping to learning about history. Most methods require the use of unlinked markers; but, using all markers from genome-
wide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite
accuracy. We describe a method, HAPMIX, which employs an explicit population genetic model to perform such local
ancestry inference based on fine-scale variation data. We show that HAPMIX outperforms other methods, and we explore its
utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate the method
empirically by applying it to populations that have experienced recent and ancient admixture: 935 African Americans from
the United States and 29 Mozabites from North Africa. HAPMIX will be of particular utility for mapping disease genes in
recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association
signals to be combined, enabling more powerful tests of association than with either signal alone.