Comprehensive somatic copy number analysis using the aqueous humor liquid biopsy for retinoblastoma

Abstract

Purpose : The aqueous humor (AH) liquid biopsy has been established as an enriched source of tumor-derived cell-free DNA (cfDNA) for retinoblastoma (RB). Use of this AH liquid biopsy allows for genomic analysis of eyes throughout treatment and at enucleation. Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q; in this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and their associated clinical features.

Methods : Patients diagnosed with RB between 12/2014-10/2020 from whom AH was obtained via clear corneal paracentesis were included. Shallow whole-genome sequencing of AH cfDNA was performed to assess for SCNAs. Mann-Whitney U and Fisher’s exact tests were used to examine the relationship between SCNAs and clinical findings.

Results : 68 eyes of 64 patients were included. 33 eyes were enucleated (16 primarily; 17 secondarily after chemotherapy) and 35 were salvaged. The most common non-highly recurrent RB SCNAs were 12p loss (8 eyes; 11.8%), 16p loss (8 eyes; 11.8%), 5p gain (7 eyes; 10.3%), 17q gain (6 eyes; 8.8%), 18q gain (6 eyes; 8.8%), 17p loss (5 eyes; 7.4%), 20q gain (5 eyes; 7.4%), and 22p gain (5 eyes; 7.4%). The prevalence of specific non-highly recurrent SCNAs differed between primarily and secondarily enucleated eyes (Fig 1). Focal MYCN amplification was present in 3 eyes, and all were enucleated (2 primarily, 1 secondarily). Of secondarily enucleated eyes, 6 eyes had AH sampled during conservative management and immediately following enucleation; 4 eyes demonstrated new SCNAs at secondary enucleation that were not present in earlier AH samples. Eyes with sphere or cloud seeding had significantly more SCNAs (4.64±4.76) than eyes with dust or no vitreous seeding (2.70±3.72; P=0.022). Eyes with an endophytic tumor growth pattern (without retinal detachment; RD) were significantly more likely to have one or more SCNA (84.6%) than eyes with an exophytic tumor growth pattern (with RD) (57.5%; P=0.030).

Conclusions : The AH liquid biopsy platform is an efficient method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB.

This is a 2021 ARVO Annual Meeting abstract.

 

Fig 1. Prevalence of non-highly recurrent RB SCNAs in primarily and secondarily enucleated eyes.