Small ancestry informative marker panels for complete classification between the original four HapMap populations

Damrongrit Setsirichok; Theera Piroonratana; Anunchai Assawamakin; Touchpong Usavanarong; Chanin Limwongse; Waranyu Wongseree; Chatchawit Aporntewan; Nachol Chaiyaratana

doi:10.1504/ijdmb.2012.050249

arXiv · 1305.3754

Small ancestry informative marker panels for complete classification between the original four HapMap populations

Damrongrit Setsirichok·Theera Piroonratana·Anunchai Assawamakin·Touchpong Usavanarong·Chanin Limwongse·Waranyu Wongseree·Chatchawit Aporntewan·Nachol Chaiyaratana

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Abstract

A protocol for the identification of ancestry informative markers (AIMs) from genome-wide single nucleotide polymorphism (SNP) data is proposed. The protocol consists of three main steps: (a) identification of potential positive selection regions via Fst extremity measurement, (b) SNP screening via two-stage attribute selection and (c) classification model construction using a naive Bayes classifier. The two-stage attribute selection is composed of a newly developed round robin symmetrical uncertainty ranking technique and a wrapper embedded with a naive Bayes classifier. The protocol has been applied to the HapMap Phase II data. Two AIM panels, which consist of 10 and 16 SNPs that lead to complete classification between CEU, CHB, JPT and YRI populations, are identified. Moreover, the panels are at least four times smaller than those reported in previous studies. The results suggest that the protocol could be useful in a scenario involving a larger number of populations.

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Damrongrit Setsirichok, Theera Piroonratana, Anunchai Assawamakin, Touchpong Usavanarong, Chanin Limwongse, Waranyu Wongseree, Chatchawit Aporntewan, Nachol Chaiyaratana. 2013-05-16. Small ancestry informative marker panels for complete classification between the original four HapMap populations. https://doi.org/10.1504/ijdmb.2012.050249

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