title: Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus.
abstract: 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.
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Chantal E
authors.initials: CE
authors.lastname: Hargreaves
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.|Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
authors.forename: Chisako
authors.initials: C
authors.lastname: Iriyama
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Matthew J J
authors.initials: MJ
authors.lastname: Rose-Zerilli
authors.affiliation: Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX, Amsterdam, The Netherlands.
authors.forename: Sietse Q
authors.initials: SQ
authors.lastname: Nagelkerke
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Khiyam
authors.initials: K
authors.lastname: Hussain
authors.affiliation: Molecular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom.
authors.forename: Rosalind
authors.initials: R
authors.lastname: Ganderton
authors.affiliation: Molecular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Genetics, University of Leicester, Leicester, LE1 7RH, United Kingdom.|School of Health, University of Northampton, Northampton, NN2 7AL, United Kingdom.
authors.forename: Lee R
authors.initials: LR
authors.lastname: Machado
authors.affiliation: Department of Genetics, University of Leicester, Leicester, LE1 7RH, United Kingdom.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Hollox
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Parker
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Kate V
authors.initials: KV
authors.lastname: Latham
authors.affiliation: Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX, Amsterdam, The Netherlands.|Department of Pediatric Hematology, Immunology and Infectious Disease, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.
authors.forename: Taco W
authors.initials: TW
authors.lastname: Kuijpers
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Kathleen N
authors.initials: KN
authors.lastname: Potter
authors.affiliation: Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Coupland
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Davies
authors.affiliation: Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Stackpole
authors.affiliation: Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom.
authors.forename: Melanie
authors.initials: M
authors.lastname: Oates
authors.affiliation: Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, United Kingdom.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Pettitt
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Glennie
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Cragg
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Strefford
mesh_terms: D000911:Antibodies, Monoclonal / Q000627:therapeutic use; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D056915:DNA Copy Number Variations; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000276:immunology; D060885:Multiplex Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D017452:Receptors, IgG / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D000911:Antibodies, Monoclonal; C445323:FCGR2A protein, human; C499173:FCGR2B protein, human; C496124:FCGR3A protein, human; D017452:Receptors, IgG; D004247:DNA