Applications of Pooled DNA Samples to the Assessment of Population Affinities: Short Tandem Repeats

Document Type

Article

Authors

M. H. Crawford, Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045.
P. Banerjee, Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY.
D. A. Demarchi, Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045.
J. McComb, Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045.
G. Livshits, Department of Anatomy, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
M. Henneberg, Department of Anatomical Sciences, University of Adelaide, Adelaide, Australia.
M. J. Mosher, Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045., Department of Epidemiology, University of North Carolina, Chapel Hill, NC.
M. S. Schanfield, Department of Forensic Sciences, George Washington University, Washington, DC; and Analytical Genetic Testing, Denver, CO.
J. A. Knowles, Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY.

Abstract

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

Recommended Citation

Crawford, M. H.; Banerjee, P.; Demarchi, D. A.; McComb, J.; Livshits, G.; Henneberg, M.; Mosher, M. J.; Schanfield, M. S.; and Knowles, J. A. (2005) "Applications of Pooled DNA Samples to the Assessment of Population Affinities: Short Tandem Repeats," Human Biology: Vol. 77: Iss. 6, Article 1.
Available at: https://digitalcommons.wayne.edu/humbiol/vol77/iss6/1