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A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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 i...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297192/ https://www.ncbi.nlm.nih.gov/pubmed/25594501 http://dx.doi.org/10.1371/journal.pone.0116791 |
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author | 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 |
author_facet | 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 |
author_sort | Haridan, Umi Shakina |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4297192 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42971922015-01-26 A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B 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 PLoS One Research Article 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. Public Library of Science 2015-01-16 /pmc/articles/PMC4297192/ /pubmed/25594501 http://dx.doi.org/10.1371/journal.pone.0116791 Text en © 2015 Haridan et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited. |
spellingShingle | Research Article 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 A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B |
title | A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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title_full | A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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title_fullStr | A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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title_full_unstemmed | A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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title_short | A Comparison of Assays for Accurate Copy Number Measurement of the Low-Affinity Fc Gamma Receptor Genes FCGR3A and FCGR3B
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title_sort | comparison of assays for accurate copy number measurement of the low-affinity fc gamma receptor genes fcgr3a and fcgr3b |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297192/ https://www.ncbi.nlm.nih.gov/pubmed/25594501 http://dx.doi.org/10.1371/journal.pone.0116791 |
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