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Nucleic Acids Research, 2002, Vol. 30, No. 15 e74
© 2002 Oxford University Press

SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis

Stéphanie Le Hellard*,1, Stéphane J. Ballereau1, Peter M. Visscher2, Helen S. Torrance1, Jeni Pinson1, Stewart W. Morris1, Marian L. Thomson1, Colin A. M. Semple1,3, Walter J. Muir4, Douglas H. R. Blackwood4, David J. Porteous1 and Kathryn L. Evans1

1 Medical Genetics Section, Molecular Medicine Centre, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK, 2 Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK, 3 MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK and 4 Department of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK

*To whom correspondence should be addressed. Tel: +44 131 651 1061; Fax: +44 131 651 1059; Email: s.lehellard{at}ed.ac.uk

We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of a set of heterozygotes (k); (ii) the repeatability of an assay is more important than pinpoint accuracy when estimating allele frequencies, and assays should therefore be optimised to increase the repeatability; and (iii) the size of a pool has a relatively small effect on the accuracy of allele frequency estimation. We therefore recommend that large pools are genotyped and replicated a minimum of four times. In addition, we describe statistical approaches to allow rigorous comparison of DNA pool results. Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies.


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