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: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science
2015
|
| Online Access: | http://psasir.upm.edu.my/id/eprint/43474/ http://psasir.upm.edu.my/id/eprint/43474/1/A%20Comparison%20of%20Assays%20for%20Accurate%20Copy.PDF |
| _version_ | 1848850238294458368 |
|---|---|
| author | Haridan, Umi Shakina Mokhtar, Umairah Machado, Lee R. Abdul Aziz, Abu Thalhah Shomiad @ Shueb, Rafidah Hanim Zaid, Masliza Sim, Benedict Mustafa, Mahiran Nik Yusof, Nik Khairudin Lee, Christopher K. C. Abu Bakar, Suhaili Abu Bakar, Sazaly Hollox, Edward J. Hoh, Boon Peng |
| author_facet | Haridan, Umi Shakina Mokhtar, Umairah Machado, Lee R. Abdul Aziz, Abu Thalhah Shomiad @ Shueb, Rafidah Hanim Zaid, Masliza Sim, Benedict Mustafa, Mahiran Nik Yusof, Nik Khairudin Lee, Christopher K. C. Abu Bakar, Suhaili Abu Bakar, Sazaly Hollox, Edward J. Hoh, Boon Peng |
| author_sort | Haridan, Umi Shakina |
| building | UPM Institutional Repository |
| collection | Online Access |
| 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 | 2025-11-15T10:03:07Z |
| format | Article |
| id | upm-43474 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T10:03:07Z |
| publishDate | 2015 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-434742019-10-01T02:13:46Z http://psasir.upm.edu.my/id/eprint/43474/ 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 Shomiad @ Shueb, Rafidah Hanim Zaid, Masliza Sim, Benedict Mustafa, Mahiran Nik Yusof, Nik Khairudin Lee, Christopher K. C. Abu Bakar, Suhaili Abu Bakar, Sazaly Hollox, Edward J. Hoh, Boon Peng 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 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/43474/1/A%20Comparison%20of%20Assays%20for%20Accurate%20Copy.PDF 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 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116791 10.1371/journal.pone.0116791 |
| spellingShingle | Haridan, Umi Shakina Mokhtar, Umairah Machado, Lee R. Abdul Aziz, Abu Thalhah Shomiad @ Shueb, Rafidah Hanim Zaid, Masliza Sim, Benedict Mustafa, Mahiran Nik Yusof, Nik Khairudin Lee, Christopher K. C. Abu Bakar, Suhaili Abu Bakar, Sazaly Hollox, Edward J. Hoh, Boon Peng 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
|
| 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://psasir.upm.edu.my/id/eprint/43474/ http://psasir.upm.edu.my/id/eprint/43474/ http://psasir.upm.edu.my/id/eprint/43474/ http://psasir.upm.edu.my/id/eprint/43474/1/A%20Comparison%20of%20Assays%20for%20Accurate%20Copy.PDF |