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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Determination of beta-defensin genomic copy number in different populations: A comparison of three methods
PLoS ONE, Volume 6, No. 2, Article e16768, Year 2011
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Description
Background: There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories. Findings: In this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations. Conclusions: QPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number. © 2011 Fode et al.
Authors & Co-Authors
Fode, Peder
Denmark, Copenhagen
Statens Serum Institut
Jespersgaard, Cathrine
Denmark, Copenhagen
Statens Serum Institut
Hardwick, Robert J.
United Kingdom, Leicester
University of Leicester
Bogle, Helen
United Kingdom, Leicester
University of Leicester
United Kingdom, Newcastle
University of Newcastle Upon Tyne, Faculty of Medical Sciences
Theisen, Michael
Denmark, Copenhagen
Statens Serum Institut
Dodoo, Daniel K.
Ghana, Accra
Noguchi Memorial Institute for Medical Research
Lenicek, Martin
Czech Republic, Prague
Charles University
Vitek, Libor
Czech Republic, Prague
Charles University
Vieira, Ana
Portugal, Almada
Hospital Garcia de Orta
Freitas, Joao
Portugal, Almada
Hospital Garcia de Orta
Skyt Andersen, Paal Skytt
Denmark, Copenhagen
Statens Serum Institut
Hollox, Edward J.
United Kingdom, Leicester
University of Leicester
Statistics
Citations: 48
Authors: 12
Affiliations: 6
Identifiers
Doi:
10.1371/journal.pone.0016768
e-ISSN:
19326203
Research Areas
Genetics And Genomics
Infectious Diseases
Study Design
Cohort Study
Study Approach
Quantitative