Analysis of copy number variation using quantitative interspecies competitive PCR

Nucleic Acids Research Advance Access originally published online on August 12, 2008
Nucleic Acids Research 2008 36(17):e112; doi:10.1093/nar/gkn495


Nucleic Acids Research, 2008, Vol. 36, No. 17 e112
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

--------------------------------------------------------------------------------

Methods Online


Analysis of copy number variation using quantitative interspecies competitive PCR
Nigel M. Williams1,*, Hywel Williams1, Elisa Majounie1, Nadine Norton1, Beate Glaser1, Huw R. Morris2, Michael J. Owen1 and Michael C. O’Donovan1
1Department of Psychological Medicine, Wales School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN and 2Department of Neurology, Ophthalmology and Audiological Medicine, Wales School of Medicine, Cardiff University, Cardiff, UK

*To whom correspondence should be addressed. Tel: +44(0)2920 687070; Fax: +44(0)2920 687068; Email: williamsnm@cf.ac.uk

Received May 23, 2008. Revised July 17, 2008. Accepted July 17, 2008.

Over recent years small submicroscopic DNA copy-number variants (CNVs) have been highlighted as an important source of variation in the human genome, human phenotypic diversity and disease susceptibility. Consequently, there is a pressing need for the development of methods that allow the efficient, accurate and cheap measurement of genomic copy number polymorphisms in clinical cohorts. We have developed a simple competitive PCR based method to determine DNA copy number which uses the entire genome of a single chimpanzee as a competitor thus eliminating the requirement for competitive sequences to be synthesized for each assay. This results in the requirement for only a single reference sample for all assays and dramatically increases the potential for large numbers of loci to be analysed in multiplex. In this study we establish proof of concept by accurately detecting previously characterized mutations at the PARK2 locus and then demonstrating the potential of quantitative interspecies competitive PCR (qicPCR) to accurately genotype CNVs in association studies by analysing chromosome 22q11 deletions in a sample of previously characterized patients and normal controls.