Evaluation of high-throughput genomic assays for the Fc gamma receptor locus

Chantal E Hargreaves, Chisako Iriyama, Matthew J J Rose-Zerilli, Sietse Q Nagelkerke, Khiyam Hussain, Rosalind Ganderton, Charlotte Lee, Lee Machado, Edward J Hollox, Helen Parker, Kate V Latham, Taco W Kuijpers, Kathleen N Potter, Sarah E Coupland, Andrew Davies, Micheal Stackpole, Melanie Oates, Andrew R Pettitt, Martin J Glennie, Mark S CraggJonathan C Strefford

Research output: Contribution to JournalArticle

Abstract

Cancer immunotherapy has been revolutionised by the use of monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR 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 FcγR 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 FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.
Original languageEnglish
JournalPLoS ONE
Volume10
Issue number11
DOIs
Publication statusPublished - 6 Nov 2015

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IgG Receptors
Single Nucleotide Polymorphism
Multiplex Polymerase Chain Reaction
Paraffin
Formaldehyde
Monoclonal Antibodies
Sequence Homology
Immunotherapy
Antibody Formation
Blood Cells
Therapeutics
Genotype
Clinical Trials
Genes
Neoplasms

Cite this

Hargreaves, C. E., Iriyama, C., Rose-Zerilli, M. J. J., Nagelkerke, S. Q., Hussain, K., Ganderton, R., ... Strefford, J. C. (2015). Evaluation of high-throughput genomic assays for the Fc gamma receptor locus. PLoS ONE, 10(11). https://doi.org/10.1371/journal.pone.0142379
Hargreaves, Chantal E ; Iriyama, Chisako ; Rose-Zerilli, Matthew J J ; Nagelkerke, Sietse Q ; Hussain, Khiyam ; Ganderton, Rosalind ; Lee, Charlotte ; Machado, Lee ; Hollox, Edward J ; Parker, Helen ; Latham, Kate V ; Kuijpers, Taco W ; Potter, Kathleen N ; Coupland, Sarah E ; Davies, Andrew ; Stackpole, Micheal ; Oates, Melanie ; Pettitt, Andrew R ; Glennie, Martin J ; Cragg, Mark S ; Strefford, Jonathan C. / Evaluation of high-throughput genomic assays for the Fc gamma receptor locus. In: PLoS ONE. 2015 ; Vol. 10, No. 11.
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Hargreaves, CE, Iriyama, C, Rose-Zerilli, MJJ, Nagelkerke, SQ, Hussain, K, Ganderton, R, Lee, C, Machado, L, Hollox, EJ, Parker, H, Latham, KV, Kuijpers, TW, Potter, KN, Coupland, SE, Davies, A, Stackpole, M, Oates, M, Pettitt, AR, Glennie, MJ, Cragg, MS & Strefford, JC 2015, 'Evaluation of high-throughput genomic assays for the Fc gamma receptor locus', PLoS ONE, vol. 10, no. 11. https://doi.org/10.1371/journal.pone.0142379

Evaluation of high-throughput genomic assays for the Fc gamma receptor locus. / Hargreaves, Chantal E; Iriyama, Chisako; Rose-Zerilli, Matthew J J; Nagelkerke, Sietse Q; Hussain, Khiyam; Ganderton, Rosalind; Lee, Charlotte; Machado, Lee; Hollox, Edward J; Parker, Helen; Latham, Kate V; Kuijpers, Taco W; Potter, Kathleen N; Coupland, Sarah E; Davies, Andrew; Stackpole, Micheal; Oates, Melanie; Pettitt, Andrew R; Glennie, Martin J; Cragg, Mark S; Strefford, Jonathan C.

In: PLoS ONE, Vol. 10, No. 11, 06.11.2015.

Research output: Contribution to JournalArticle

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AU - Hargreaves, Chantal E

AU - Iriyama, Chisako

AU - Rose-Zerilli, Matthew J J

AU - Nagelkerke, Sietse Q

AU - Hussain, Khiyam

AU - Ganderton, Rosalind

AU - Lee, Charlotte

AU - Machado, Lee

AU - Hollox, Edward J

AU - Parker, Helen

AU - Latham, Kate V

AU - Kuijpers, Taco W

AU - Potter, Kathleen N

AU - Coupland, Sarah E

AU - Davies, Andrew

AU - Stackpole, Micheal

AU - Oates, Melanie

AU - Pettitt, Andrew R

AU - Glennie, Martin J

AU - Cragg, Mark S

AU - Strefford, Jonathan C

PY - 2015/11/6

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N2 - Cancer immunotherapy has been revolutionised by the use of monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR 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 FcγR 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 FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.

AB - Cancer immunotherapy has been revolutionised by the use of monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR 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 FcγR 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 FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.

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Hargreaves CE, Iriyama C, Rose-Zerilli MJJ, Nagelkerke SQ, Hussain K, Ganderton R et al. Evaluation of high-throughput genomic assays for the Fc gamma receptor locus. PLoS ONE. 2015 Nov 6;10(11). https://doi.org/10.1371/journal.pone.0142379