Analysis of Copy Number Variation Using the Paralogue Ratio Test (PRT).
Copy number variation (CNV), where a segment of DNA differs in copy number between different individuals, is an extensive and often underappreciated source of genetic variation within species. However, reliably determining copy number of a particular DNA sequence for a large number of samples can be challenging. Here, I describe and review the paralogue ratio test (PRT) in detail. PRT was developed to robustly type the CNV of the beta-defensin locus using small amounts of genomic DNA in a high-throughput manner, and has been applied successfully at many other loci. I discuss the strategies for designing successful PRT assays using both manual and bioinformatics methods, how to optimize experimental conditions, and approaches for analyzing the data. I discuss strengths and weaknesses of the approach, and how to troubleshoot results, as well as the range of problems to which PRT can be a potential solution.
Department of Genetics, University of Leicester, Adrian Bldg., University Road, Leicester, LE1 7RH, UK. ejh33@le.ac.uk.
Edward J
EJ
Hollox
D004247:DNA / Q000235:genetics*; D056915:DNA Copy Number Variations; D017931:DNA Primers; D019075:Electrophoresis, Capillary / Q000379:methods; D006801:Humans; D016133:Polymerase Chain Reaction
D017931:DNA Primers; D004247:DNA
Beta-defensin; CNV; Copy number variation; Deletion; Duplication; Genotyping; High-throughput; PCR; PRT