Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus

• Published in: PloS one Vol. 10; no. 11; p. e0142379
• Main Authors: Hargreaves, Chantal E, Iriyama, Chisako, Rose-Zerilli, Matthew J J, Nagelkerke, Sietse Q, Hussain, Khiyam, Ganderton, Rosalind, Lee, Charlotte, Machado, Lee R, Hollox, Edward J, Parker, Helen, Latham, Kate V, Kuijpers, Taco W, Potter, Kathleen N, Coupland, Sarah E, Davies, Andrew, Stackpole, Michael, Oates, Melanie, Pettitt, Andrew R, Glennie, Martin J, Cragg, Mark S, Strefford, Jonathan C
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.11.2015; Public Library of Science (PLoS)
• Subjects: Analysis; Antibodies, Monoclonal - therapeutic use; Assaying; Authorship; Autoimmune diseases; Blood; Cancer; Cancer immunotherapy; Chromosome 1; Clinical trials; Complexity; Copy number; Data processing; Deoxyribonucleic acid; Disease; DNA; DNA - genetics; DNA - isolation & purification; DNA Copy Number Variations; Fc receptors; Genes; Genetics; Genomic analysis; Genomics; Genotypes; Genotyping; Health aspects; Hematology; High-Throughput Nucleotide Sequencing - methods; Homology; Hospitals; Humans; Immunology; Immunotherapy; Laboratories; Leukocytes (mononuclear); Leukocytes, Mononuclear - immunology; Life assessment; Loci; Lupus; Medical research; Medicine; Monoclonal antibodies; Multiplex Polymerase Chain Reaction; Multiplexing; Mutation; Paraffin; Peripheral blood mononuclear cells; Polymorphism, Single Nucleotide; Receptor mechanisms; Receptors; Receptors, IgG - genetics; Sequence Analysis, DNA - methods; Single nucleotide polymorphisms; Single-nucleotide polymorphism; United States; United Kingdom > UK; Netherlands
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0142379

Cancer immunotherapy has been revolutionised by the use 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.