Please use this identifier to cite or link to this item: https://scholarbank.nus.edu.sg/handle/10635/100614
Title: Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population
Authors: Andiappan, A.K.
Anantharaman, R. 
Nilkanth, P.P.
Wang, D.Y.
Chew, F.T. 
Issue Date: 7-May-2010
Citation: Andiappan, A.K., Anantharaman, R., Nilkanth, P.P., Wang, D.Y., Chew, F.T. (2010-05-07). Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population. BMC Genetics 11 : -. ScholarBank@NUS Repository.
Abstract: Background: The International Hapmap project serves as a valuable resource for human genome variation data, however its applicability to other populations has yet to be exhaustively investigated. In this paper, we use high density genotyping chips and resequencing strategies to compare the Singapore Chinese population with the Hapmap populations. First we compared 1028 and 114 unrelated Singapore Chinese samples genotyped using the Illumina Human Hapmap 550 k chip and Affymetrix 500 k array respectively against the 270 samples from Hapmap. Secondly, data from 20 candidate genes on 5q31-33 resequenced for an asthma candidate gene based study was also used for the analysis.Results: A total of 237 SNPs were identified through resequencing of which only 95 SNPs (40%) were in Hapmap; however an additional 56 SNPs (24%) were not genotyped directly but had a proxy SNP in the Hapmap. At the genome-wide level, Singapore Chinese were highly correlated with Hapmap Han Chinese with correlation of 0.954 and 0.947 for the Illumina and Affymetrix platforms respectively with deviant SNPs randomly distributed within and across all chromosomes.Conclusions: The high correlation between our population and Hapmap Han Chinese reaffirms the applicability of Hapmap based genome-wide chips for GWA studies. There is a clear population signature for the Singapore Chinese samples and they predominantly resemble the southern Han Chinese population; however when new migrants particularly those with northern Han Chinese background were included, population stratification issues may arise. Future studies needs to address population stratification within the sample collection while designing and interpreting GWAS in the Chinese population. © 2010 Andiappan et al; licensee BioMed Central Ltd.
Source Title: BMC Genetics
URI: http://scholarbank.nus.edu.sg/handle/10635/100614
ISSN: 14712156
Appears in Collections:Staff Publications
Elements

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
2010-evaluating_transferability_hapmap-published.pdf5.88 MBAdobe PDF

OPEN

PublishedView/Download

SCOPUSTM   
Citations

13
checked on Mar 5, 2018

WEB OF SCIENCETM
Citations

12
checked on Dec 31, 2018

Page view(s)

87
checked on Sep 7, 2019

Download(s)

18
checked on Sep 7, 2019

Google ScholarTM

Check


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