Hum Hered 2003;55:37–45

Number of SNPS Loci Needed to Detect Population Structure

Turakulov R. · Easteal S.
John Curtin School of Medical Research, Human Genetics Group and Centre for Bioinformatics Science, Australian National University, Canberra, Australia
email Corresponding Author

 goto top of outline Key Words

  • Population studies
  • Population structure
  • Population stratification
  • SNP
  • Genetic polymorphisms
  • Sample size

 goto top of outline Abstract

The study of the association of polymorphic genetic markers with common diseases is one of the most powerful tools in modern genetics. Interest in single nucleotide polymorphisms (SNPs) has steadily grown over the last decade. SNPs are currently the most developed markers in the human genome because they have a number of advantages over other marker types. One of the critical problems responsible for ‘spurious’ association findings in case-control studies is population stratification. There are many statistical approaches developed for detecting population heterogeneity. However the power to detect population structure by known methods is highly dependent on the number of loci utilised. We performed an analysis of SNPs data available in the public domain from The Single Nucleotide Consortia Ltd. (TSCL). Three populations, Afro-American, Asian and Caucasian, were compared. Estimation of the minimum number of SNPs loci necessary for detection of the population structure was performed. Two clustering approaches, distance-based and model-based, were compared. The model-based approach was superior when compared with the distance-based method. We found more than 65 random SNPs loci are required for identifying distinct geographically separated populations. Increasing the number of markers to over 100 raises the probability of correct assignment of a particular individual to an origin group to over 90%, even with conventional clustering methods.

Copyright © 2003 S. Karger AG, Basel

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 goto top of outline Author Contacts

Rust Turakulov
John Curtin School of Medical Research
Human Genetics Group and Centre for Bioinformatics Science
Australian National University, GPO Box 334, Canberra, ACT 2601 (Australia)

 goto top of outline Article Information

Received: January 2, 2003
Accepted after revision: May 5, 2003
Number of Print Pages : 9
Number of Figures : 3, Number of Tables : 0, Number of References : 31

 goto top of outline Publication Details

Human Heredity (International Journal of Human and Medical Genetics)
Founded 1950 as Acta Genetica et Statistica Medica by Gunnar Dahlberg; Continued by M. Hauge (1965–1983)

Vol. 55, No. 1, Year 2003 (Cover Date: Released August 2003)

Journal Editor: J. Ott, New York, N.Y.
ISSN: 0001–5652 (print), 1423–0062 (Online)

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