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

Stéphanie Le Hellard, Stéphane J Ballereau, Peter M Visscher, Helen S Torrance, Jeni Pinson, Stewart W Morris, Marian L Thomson, Colin A M Semple, Walter J Muir, Douglas H R Blackwood, David J Porteous, Kathryn L Evans

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)e74
JournalNucleic Acids Research
Volume30
Issue number15
DOIs
Publication statusPublished - 1 Aug 2002

Keywords

  • Automation Base Sequence Biotechnology/economics/instrumentation/methods Chi-Square Distribution Chromatography, High Pressure Liquid *Databases, Nucleic Acid Gene Amplification Gene Frequency Genetic Markers Genotype Humans Information Storage and Retrieval Mass Spectrometry *Polymorphism, Single Nucleotide Reproducibility of Results Sequence Analysis, DNA/economics/instrumentation/*methods

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