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Title: A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B
Authors: Haridan, Umi Shakina
Mokhtar, Umairah
Machado, Lee R.
Abdul Aziz, Abu Thalhah
Shueb, Rafidah Hanim
Zaid, Masliza
Sim, Benedict
Mustafa, Mahiran
Nik Yusof, Nik Khairudin
Lee, Christopher K. C.
Abu Bakar, Suhaili
AbuBakar, Sazaly
Hollox, Edward J.
Boon Peng, Hoh
First Published: 16-Jan-2015
Publisher: Public Library of Science
Citation: PLoS One, 2015, 10(1):e0116791
Abstract: 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.
DOI Link: 10.1371/journal.pone.0116791
eISSN: 1932-6203
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright: © 2015 Haridan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Appears in Collections:Published Articles, Dept. of Genetics

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