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Open Access Open Badges Research article

Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium

Xuanyao Liu12, Woei-Yuh Saw3, Mohammad Ali3, Rick Twee-Hee Ong1 and Yik-Ying Teo12345*

Author Affiliations

1 Saw Swee Hock School of Public Health, National University of Singapore, MD3 16 Medical Drive, Singapore 117597, Singapore

2 NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456, Singapore

3 Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore

4 Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore

5 Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore

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BMC Genomics 2014, 15:332  doi:10.1186/1471-2164-15-332

Published: 2 May 2014



The HUGO Pan-Asian SNP Consortium (PASNP) has generated a genetic resource of almost 55,000 autosomal single nucleotide polymorphisms (SNPs) across more than 1,800 individuals from 73 urban and indigenous populations in Asia. This has offered valuable insights into the correlation between the genetic ancestry of these populations with major linguistic systems and geography. Here, we attempt to understand whether adaptation to local climate, diet and environment partly explains the genetic variation present in these populations by investigating the genomic signatures of positive selection.


To evaluate the impact to the selection analyses due to the considerably lower SNP density as compared to other population genetics resources such as the International HapMap Project (HapMap) or the Singapore Genome Variation Project, we evaluated the extent of haplotype phasing switch errors and the consistency of selection signals from three haplotype-based approaches (iHS, XP-EHH, haploPS) when the HapMap data is thinned to a similar density as PASNP. We subsequently applied haploPS to detect and characterize positive selection in the PASNP populations, identifying 59 genomics regions that were selected in at least one PASNP populations. A cluster analysis on the basis of these 59 signals showed that indigenous populations such as the Negrito from Malaysia and Philippines, the China Hmong, and the Taiwan Ami and Atayal shared more of these signals. We also reported evidence of a positive selection signal encompassing the beta globin gene in the Taiwan Ami and Atayal that was distinct from the signal in the HapMap Africans, suggesting the possibility of convergent evolution at this locus due to malarial selection.


We established that the lower SNP content of the PASNP data conferred weaker ability to detect signatures of positive selection, but the availability of the new approach haploPS retained modest power. Out of all the populations in PASNP, we identified only 59 signals, suggesting a strong need for high-density population-level genotyping data or sequencing data in order to achieve a comprehensive survey of positive selection in Asian populations.

Haplotype phasing; Positive selection; Population structure; Genetic diversity