Evaluation of high-throughput genomic assays for the Fc Gamma Receptor Locus
Evaluation of high-throughput genomic assays for the Fc Gamma Receptor Locus
Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (Fc?Rs). The low-affinity Fc?R genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the Fc?R locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the Fc?R locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of Fc?R genetics in predicting response to antibody therapeutics.
1-13
Hargreaves, Chantal
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Iriyama, C.
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Rose-Zerilli, Matthew
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Nagelkerke, S.Q.
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Hussain, Khiyam
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Ganderton, R.
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Lee, C.
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Kuijpers, T.W.
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Potter, Nora
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Coupland, S.
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Davies, Andrew
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Stackpole, M.
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Oates, M.
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Pettitt, A.R.
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Glennie, Martin
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Cragg, Mark
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Strefford, Jon
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6 November 2015
Hargreaves, Chantal
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Iriyama, C.
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Rose-Zerilli, Matthew
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Nagelkerke, S.Q.
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Hussain, Khiyam
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Ganderton, R.
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Lee, C.
774e8767-13f8-4725-bc9f-c1200ccd78ab
Kuijpers, T.W.
65c3b687-fc1f-4e61-bfcd-bdcf64c8396d
Potter, Nora
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Coupland, S.
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Davies, Andrew
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Stackpole, M.
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Oates, M.
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Pettitt, A.R.
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Glennie, Martin
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Cragg, Mark
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Strefford, Jon
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Hargreaves, Chantal, Iriyama, C., Rose-Zerilli, Matthew, Nagelkerke, S.Q., Hussain, Khiyam, Ganderton, R., Lee, C., Kuijpers, T.W., Potter, Nora, Coupland, S., Davies, Andrew, Stackpole, M., Oates, M., Pettitt, A.R., Glennie, Martin, Cragg, Mark and Strefford, Jon
(2015)
Evaluation of high-throughput genomic assays for the Fc Gamma Receptor Locus.
PLoS ONE, 10 (11), , [e0142379].
(doi:10.1371/journal.pone.0142379).
(PMID:26545243)
Abstract
Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (Fc?Rs). The low-affinity Fc?R genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the Fc?R locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the Fc?R locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of Fc?R genetics in predicting response to antibody therapeutics.
Text
2015 Hargreaves Strefford FCGR PLoS One
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More information
Accepted/In Press date: 21 October 2015
Published date: 6 November 2015
Organisations:
Cancer Sciences
Identifiers
Local EPrints ID: 384401
URI: http://eprints.soton.ac.uk/id/eprint/384401
ISSN: 1932-6203
PURE UUID: 2bfb5fb2-6775-4bf5-ab52-01baa530fe6a
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Date deposited: 04 Jan 2016 14:07
Last modified: 15 Mar 2024 03:36
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Contributors
Author:
Chantal Hargreaves
Author:
C. Iriyama
Author:
S.Q. Nagelkerke
Author:
Khiyam Hussain
Author:
R. Ganderton
Author:
C. Lee
Author:
T.W. Kuijpers
Author:
S. Coupland
Author:
M. Stackpole
Author:
M. Oates
Author:
A.R. Pettitt
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