pubmed.ncbi.nlm.nih.gov

Inferring ancestry from population genomic data and its applications - PubMed

  • ️Wed Jan 01 2014

Review

Inferring ancestry from population genomic data and its applications

Badri Padhukasahasram. Front Genet. 2014.

Abstract

Ancestry inference is a frequently encountered problem and has many applications such as forensic analyses, genetic association studies, and personal genomics. The main goal of ancestry inference is to identify an individual's population of origin based on our knowledge of natural populations. Because both self-reported ancestry in humans or the sampling location of an organism can be inaccurate for this purpose, the use of genetic markers can facilitate accurate and reliable inference of an individual's ancestral origins. At a higher level, there are two different paradigms in ancestry inference: global ancestry inference which tries to compute the genome-wide average of the population contributions and local ancestry inference which tries to identify the regional ancestry of a genomic segment. In this mini review, I describe the numerous approaches that are currently available for both kinds of ancestry inference from population genomic datasets. I first describe the general ideas underlying such inference methods and their relationship to one another. Then, I describe practical applications in which inference of ancestry has proven useful. Lastly, I discuss challenges and directions for future research work in this area.

Keywords: Bayesian inference; global ancestry; hidden Markov models; local ancestry; maximum likelihood estimation.

PubMed Disclaimer

Similar articles

Cited by

References

    1. Alexander D. H., Novembre J., Lange K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19 1655–1664 10.1101/gr.094052.109 - DOI - PMC - PubMed
    1. Balding D. J., Nichols R. A. (1994). DNA profile match probability calculations: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci. Int. 64 125–140 10.1016/0379-0738(94)90222-4 - DOI - PubMed
    1. Balding D. J., Nichols R. A. (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96 3–12 10.1007/BF01441146 - DOI - PubMed
    1. Baran Y., Pasaniuc B., Sankararaman S., Torgerson D. G., Gignoux C., Eng C., et al. (2012). Fast and accurate inference of local ancestry in Latino populations. Bioinformatics 28 1359–1367 10.1093/bioinformatics/bts144 - DOI - PMC - PubMed
    1. Becquet C., Patterson N., Stone A. C., Przeworski M., Reich D. (2007). Genetic structure of chimpanzee populations. PLoS Genet. 3:e66 10.1371/journal.pgen.0030066 - DOI - PMC - PubMed

Publication types