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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4297192?pdf=render |
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| author | Umi Shakina Haridan Umairah Mokhtar Lee R Machado Abu Thalhah Abdul Aziz Rafidah Hanim Shueb Masliza Zaid Benedict Sim Mahiran Mustafa Nik Khairudin Nik Yusof Christopher K C Lee Suhaili Abu Bakar Sazaly AbuBakar Edward J Hollox Hoh Boon Peng |
| author_facet | Umi Shakina Haridan Umairah Mokhtar Lee R Machado Abu Thalhah Abdul Aziz Rafidah Hanim Shueb Masliza Zaid Benedict Sim Mahiran Mustafa Nik Khairudin Nik Yusof Christopher K C Lee Suhaili Abu Bakar Sazaly AbuBakar Edward J Hollox Hoh Boon Peng |
| author_sort | Umi Shakina Haridan |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-11T20:28:18Z |
| format | Article |
| id | doaj.art-e6c1aa50acd34fdf8be86f48912082ff |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T20:28:18Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-e6c1aa50acd34fdf8be86f48912082ff2022-12-22T00:51:54ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01101e011679110.1371/journal.pone.0116791A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B.Umi Shakina HaridanUmairah MokhtarLee R MachadoAbu Thalhah Abdul AzizRafidah Hanim ShuebMasliza ZaidBenedict SimMahiran MustafaNik Khairudin Nik YusofChristopher K C LeeSuhaili Abu BakarSazaly AbuBakarEdward J HolloxHoh Boon PengThe 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.http://europepmc.org/articles/PMC4297192?pdf=render |
| spellingShingle | Umi Shakina Haridan Umairah Mokhtar Lee R Machado Abu Thalhah Abdul Aziz Rafidah Hanim Shueb Masliza Zaid Benedict Sim Mahiran Mustafa Nik Khairudin Nik Yusof Christopher K C Lee Suhaili Abu Bakar Sazaly AbuBakar Edward J Hollox Hoh Boon Peng A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. PLoS ONE |
| title | A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. |
| title_full | A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. |
| title_fullStr | A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. |
| title_full_unstemmed | A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. |
| title_short | A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B. |
| title_sort | comparison of assays for accurate copy number measurement of the low affinity fc gamma receptor genes fcgr3a and fcgr3b |
| url | http://europepmc.org/articles/PMC4297192?pdf=render |
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