TY - JOUR
T1 - Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats
AU - Armour, John A.L.
AU - Palla, Raquel
AU - Zeeuwen, Patrick L.J.M.
AU - Heijer, Martin Den
AU - Schalkwijk, Joost
AU - Hollox, Edward J.
N1 - Funding Information: Diana Olthuis and Gys de Jongh are acknowledged for technical assistance, and Evelien Hoenselaar and Gaby Schobers for technical assistance with the MLPA assays. We thank Mark Jobling for access to HapMap DNA samples, Matt Hurles for helpful discussions, and Jess Tyson and Tamsin Majerus for helpful comments on the manuscript. This work was supported by a grant to JS from the Netherlands Organization for Scientific Research (NWO-Genomics 050-10-102), and a Wellcome Trust Bioarchaeology Postdoctoral Fellowship to EJH (no.071024). Funding to pay the Open Access publication charges for this article was provided by the Wellcome Trust.
PY - 2007/2
Y1 - 2007/2
N2 - Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.
AB - Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.
UR - http://www.scopus.com/inward/record.url?scp=33847390726&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/nar/gkl1089
DO - https://doi.org/10.1093/nar/gkl1089
M3 - Article
C2 - 17175532
SN - 0305-1048
VL - 35
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 3
M1 - e19
ER -