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 Cragg & 1 others Jonathan C Strefford

    Research output: Contribution to journalArticleResearchpeer-review

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

    TY - JOUR

    T1 - Evaluation of high-throughput genomic assays for the Fc gamma receptor locus

    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

    Y1 - 2015/11/6

    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