Please use this identifier to cite or link to this item: https://doi.org/10.1186/1471-2164-15-332
Title: Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium
Authors: Liu, X.
Saw, W.-Y.
Ali, M.
Ong, R.T.H. 
Teo, Y.-Y. 
Keywords: Genetic diversity
Haplotype phasing
Population structure
Positive selection
Issue Date: 2014
Source: Liu, X., Saw, W.-Y., Ali, M., Ong, R.T.H., Teo, Y.-Y. (2014). Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium. BMC Genomics 15 (1) : -. ScholarBank@NUS Repository. https://doi.org/10.1186/1471-2164-15-332
Abstract: Background: 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.Results: 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.Conclusions: 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. © 2014 Liu et al.; licensee BioMed Central Ltd.
Source Title: BMC Genomics
URI: http://scholarbank.nus.edu.sg/handle/10635/108922
ISSN: 14712164
DOI: 10.1186/1471-2164-15-332
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
2014-evaluating_possibility_detecting_evidence_positive-published.pdf2.86 MBAdobe PDF

OPEN

PublishedView/Download

SCOPUSTM   
Citations

5
checked on Apr 23, 2018

WEB OF SCIENCETM
Citations

5
checked on Apr 23, 2018

Page view(s)

23
checked on Mar 12, 2018

Download(s)

3
checked on Mar 12, 2018

Google ScholarTM

Check

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.