Accurate inference of local phased ancestry of modern admixed populations

Yamin Ma, Jian Zhao, Jian Syuan Wong, Li Ma, Wenzhi Li, Guoxing Fu, Wei Xu, Kui Zhang, Rick A Kittles, Yun Li, Qing Song

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis.

Original languageEnglish (US)
Article number5800
JournalScientific Reports
Volume4
DOIs
StatePublished - Jul 23 2014
Externally publishedYes

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Population
Genome
Single Nucleotide Polymorphism
Pharmacogenetics
Medical Genetics
Population Genetics
Genetic Association Studies
Proxy
Human Genome
Sample Size
Software
Technology
Datasets

ASJC Scopus subject areas

  • General

Cite this

Ma, Y., Zhao, J., Wong, J. S., Ma, L., Li, W., Fu, G., ... Song, Q. (2014). Accurate inference of local phased ancestry of modern admixed populations. Scientific Reports, 4, [5800]. https://doi.org/10.1038/srep05800

Accurate inference of local phased ancestry of modern admixed populations. / Ma, Yamin; Zhao, Jian; Wong, Jian Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A; Li, Yun; Song, Qing.

In: Scientific Reports, Vol. 4, 5800, 23.07.2014.

Research output: Contribution to journalArticle

Ma, Y, Zhao, J, Wong, JS, Ma, L, Li, W, Fu, G, Xu, W, Zhang, K, Kittles, RA, Li, Y & Song, Q 2014, 'Accurate inference of local phased ancestry of modern admixed populations', Scientific Reports, vol. 4, 5800. https://doi.org/10.1038/srep05800
Ma, Yamin ; Zhao, Jian ; Wong, Jian Syuan ; Ma, Li ; Li, Wenzhi ; Fu, Guoxing ; Xu, Wei ; Zhang, Kui ; Kittles, Rick A ; Li, Yun ; Song, Qing. / Accurate inference of local phased ancestry of modern admixed populations. In: Scientific Reports. 2014 ; Vol. 4.
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