NDLI: Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population

Content Provider	Springer Nature : BioMed Central
Author	Andiappan, Anand Kumar Anantharaman, Ramani Nilkanth, Pallavi Parate Wang, De Yun Chew, Fook Tim
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.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/1471-2156-11-36.pdf
Ending Page	16
Page Count	16
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/1471-2156-11-36
Journal	BMC Genomic Data
Issue Number	1
Volume Number	11
Language	English
Publisher	BioMed Central
Publisher Date	2010-05-07
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Minor Allele Frequency Common SNPs Chinese Sample Linkage Disequilibrium Pattern Hapmap Population
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25

Patterns of population differentiation of candidate genes for cardiovascular disease

Power analysis for genome-wide association studies

Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

Characteristics of linkage disequilibrium in North American Holsteins

Weighted selective collapsing strategy for detecting rare and common variants in genetic association study

Volume measures for linkage disequilibrium

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25

Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population

Similar Documents

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25

Patterns of population differentiation of candidate genes for cardiovascular disease

Power analysis for genome-wide association studies

Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium

Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

Characteristics of linkage disequilibrium in North American Holsteins

Weighted selective collapsing strategy for detecting rare and common variants in genetic association study

Volume measures for linkage disequilibrium

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: Analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25

Evaluating the transferability of Hapmap SNPs to a Singapore Chinese population