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A comparison of assays for accurate copy number measurement of the low-affinity fc gamma receptor genes FCGR3A and FCGR3B


Haridan, Umi Shakina and Mokhtar, Umairah and Machado, Lee R. and Abdul Aziz, Abu Thalhah and Shomiad @ Shueb, Rafidah Hanim and Zaid, Masliza and Sim, Benedict and Mustafa, Mahiran and Nik Yusof, Nik Khairudin and Lee, Christopher K. C. and Abu Bakar, Suhaili and Abu Bakar, Sazaly and Hollox, Edward J. and Hoh, Boon Peng (2015) A comparison of assays for accurate copy number measurement of the low-affinity fc gamma receptor genes FCGR3A and FCGR3B. PLOS ONE, 10 (1). art. no. e0116791. pp. 1-13. ISSN 1932-6203


The FCGR3 locus encoding the low affinity activating receptor FcγRIII, plays a vital role in immunity triggered by cellular effector and regulatory functions. Copy number of the genes FCGR3A and FCGR3B has previously been reported to affect susceptibility to several autoimmune diseases and chronic inflammatory conditions. However, such genetic association studies often yield inconsistent results; hence require assays that are robust with low error rate. We investigated the accuracy and efficiency in estimating FCGR3 CNV by comparing Sequenom MassARRAY and paralogue ratio test-restriction enzyme digest variant ratio (PRT-REDVR). In addition, since many genetic association studies of FCGR3B CNV were carried out using real-time quantitative PCR, we have also included the evaluation of that method's performance in estimating the multi-allelic CNV of FCGR3B. The qPCR assay exhibited a considerably broader distribution of signal intensity, potentially introducing error in estimation of copy number and higher false positive rates. Both Sequenom and PRT-REDVR showed lesser systematic bias, but Sequenom skewed towards copy number normal (CN = 2). The discrepancy between Sequenom and PRT-REDVR might be attributed either to batch effects noise in individual measurements. Our study suggests that PRT-REDVR is more robust and accurate in genotyping the CNV of FCGR3, but highlights the needs of multiple independent assays for extensive validation when performing a genetic association study with multi-allelic CNVs.

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Additional Metadata

Item Type: Article
Divisions: Faculty of Medicine and Health Science
DOI Number: https://doi.org/10.1371/journal.pone.0116791
Publisher: Public Library of Science
Keywords: FCGR3A; FCGR3B; Gamma; Genes
Depositing User: Mohd Hafiz Che Mahasan
Date Deposited: 24 Jun 2016 07:49
Last Modified: 01 Oct 2019 02:13
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.1371/journal.pone.0116791
URI: http://psasir.upm.edu.my/id/eprint/43474
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