Shining a light on the FCGRs: deconvoluting their challenging (epi)genomic organisation and consequences in immune oncology

Despite monoclonal antibody (mAb) immunotherapy having revolutionised cancer treatment, resistance is still common. mAb immunotherapies educe their functional response by interacting with the Fc gamma receptors (FcγRs). The low-affinity locus encoding FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B contains a 98% homologous 85-kb segmental duplication and is highly polymorphic, harbouring multiple large copy number variations (CNVs) and single nucleotide polymorphisms (SNPs). In the past, this locus has been extremely challenging to study as the standard short-read sequencing technologies often fail to produce reads that can be adequately aligned or assembled. For the first time, an accurate and detailed genomic map of the FCGR locus can be generated. Working on a healthy human cohort (n=22) with different FCGR CNV states and SNPs, and B-cell lymphoma samples (n=11), Oxford Nanopore adaptive sampling and Cas9-targeting (tiling of 10 ROIs) resulted in 6.5- and 500-fold increases in FCGR sequencing, respectively. Oxford Nanopore sequencing represents an exciting opportunity to overcome the inherent difficulties with sequence homology, enabling the creation of comprehensive maps providing phased sequence, breakpoint, and methylation information. This in turn will facilitate greater understanding of FcγR regulation and how their function may be manipulated for the benefit of cancer patients.