SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis.
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.
Medical Genetics Section, Molecular Medicine Centre, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. s.lehellard@ed.ac.uk
Stéphanie
S
Le Hellard
Stéphane J
SJ
Ballereau
Peter M
PM
Visscher
Helen S
HS
Torrance
Jeni
J
Pinson
Stewart W
SW
Morris
Marian L
ML
Thomson
Colin A M
CA
Semple
Walter J
WJ
Muir
Douglas H R
DH
Blackwood
David J
DJ
Porteous
Kathryn L
KL
Evans
D001331:Automation; D001483:Base Sequence; D001709:Biotechnology / Q000191:economics / Q000295:instrumentation / Q000379:methods; D016009:Chi-Square Distribution; D002851:Chromatography, High Pressure Liquid; D030561:Databases, Nucleic Acid; D005784:Gene Amplification; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000191:economics / Q000295:instrumentation / Q000379:methods*
D005819:Genetic Markers