Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools

Hoogendoorn, Bastiaan ORCID: https://orcid.org/0000-0001-9753-169X, Norton, Nadine ORCID: https://orcid.org/0000-0002-3848-4288, Kirov, George ORCID: https://orcid.org/0000-0002-3427-3950, Williams, Nigel Melville ORCID: https://orcid.org/0000-0003-1177-6931, Hamshere, Marian Lindsay ORCID: https://orcid.org/0000-0002-8990-0958, Spurlock, Gillian, Austin, Jehannine, Stephens, Mark, Buckland, Paul Robert, Owen, Michael John ORCID: https://orcid.org/0000-0003-4798-0862 and O'Donovan, Michael Conlon ORCID: https://orcid.org/0000-0001-7073-2379 2000. Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Human Genetics 107 (5) , pp. 488-493. 10.1007/s004390000397

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Abstract

At present, the cost of genotyping single nucleotide polymorphisms (SNPs) in large numbers of subjects poses a formidable problem for molecular genetic approaches to complex diseases. We have tested the possibility of using primer extension and denaturing high performance liquid chromatography to estimate allele frequencies of SNPs in pooled DNA samples. Our data show that this method should allow the accurate estimation of absolute allele frequencies in pooled samples of DNA and also of the difference in allele frequency between different pooled DNA samples. This technique therefore offers an efficient and cheap method for genotyping SNPs in large case-control and family-based association samples.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG) Neuroscience and Mental Health Research Institute (NMHRI)
Subjects:	R Medicine > R Medicine (General)
Publisher:	Springer
ISSN:	0340-6717
Last Modified:	12 Dec 2022 08:53
URI:	https://orca.cardiff.ac.uk/id/eprint/57904

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