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

AUTOR(ES)

Le Hellard, Stéphanie

FONTE

Oxford University Press

RESUMO

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.

Documentos Relacionados

• Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system
• Genome complexity reduction for SNP genotyping analysis
• A rapid semi-automated microtiter plate method for analysis and sequencing by PCR from bacterial stocks.
• Sites of cleavage by restriction enzymes in viral DNAs: comparison of observed and expected frequencies
• Molecular comparison of delta beta-thalassemia and hereditary persistence of fetal hemoglobin DNAs: evidence of a regulatory area?