Abstract 186: Gain of chromosome 6p is a molecular biomarker for prognostication of retinoblastoma ocular survival: The aqueous humor surrogate tumor biopsy
Authors: Berry Jesse L. , Xu Liya , Polski Ashley , Prabakar Rishvanth , Reid Mark , Kim Jonathan , Kuhn Peeter , Hicks James 
Published: September 2020

Abstract
Purpose: Aqueous humor (AH) is a novel source of tumor-derived cell-free DNA (cfDNA) and can serve as a surrogate tumor biopsy, or liquid biopsy, for retinoblastoma (RB). We previously identified a somatic copy number alteration (SCNA) gain of chromosome 6p as associated with a 10-fold increased risk of enucleation. In this study, we provide a 2-year extended update to further explore 6p gain as a prognostic biomarker for ocular survival.
Methods: Patients diagnosed with RB from 12/2014 - 7/2019 from whom AH was sampled were included. AH was extracted via clear corneal paracentesis at diagnosis, during intravitreal injection of chemotherapy or enucleation. CfDNA was extracted; shallow whole genome sequencing was performed to assess for cfDNA tumor fractions and highly recurrent RB SCNAs (gain of 1q, 2p, 6p, loss of 13q, 16q). Patient demographics, treatment regimen and globe salvage were recorded.
Results: 50 eyes from 46 patients were included: 27 eyes were salvaged and 23 were enucleated. Most eyes (36/50,72%) were TNM stage cT2b. 116 samples of AH were analyzed. There were no cases of orbital relapse or metastatic spread. The median follow-up was 30 months (range 6-64 mos). After genomic evaluation, 33 / 50 eyes (66%) demonstrated one or more highly-recurrent RB SCNAs and 39/50 (78%) demonstrated any measurable SCNA. Gain of 6p was the most prevalent RB SCNA among all 50 eyes (50%), followed by 1q gain (38%), 16q loss (30%), 2p gain (including 3 focal MYCN gains; 18%), and 13q loss (16%). RB SCNAs were significantly more prevalent in enucleated eyes (21/23, 91.3%) than in salvaged eyes (12/27, 44.4%; Fisher's exact, P=0.0007). Of these, 6p gain was particularly more prevalent in enucleated eyes (17/23, 73.9%) than in salvaged eyes (8/27, 29.6%; Chi-squared, P=0.002) Of all the RB SCNAs, the presence of 6p gain in the cfDNA in the AH portended nearly 10 times greater odds of being enucleated (OR=9.87,95% CI=1.75-55.65, P=0.009). No single other SCNA had a statistically significant power to predict enucleation although there was a trend towards significance for 2p/focal MYCN gain (P=0.09) limited by the few number of eyes with this SCNA.
Conclusions: Although we previously identified chromosomal gain of 6p as a potential indicator of an aggressive phenotype in RB, that study included a smaller cohort of patients and limited follow-up. With extended follow-up and nearly double the number of eyes and AH samples, the data continue to demonstrate that AH is a high-yield surrogate tumor biopsy, and the presence of RB-specific SCNAs–specifically gain of 6p–has the potential to serve as a prognostic biomarker for RB.
Citation Format: Jesse L. Berry, Liya Xu, Ashley Polski, Rishvanth Prabakar, Mark Reid, Jonathan Kim, Peeter Kuhn, James Hicks. Gain of chromosome 6p is a molecular biomarker for prognostication of retinoblastoma ocular survival: The aqueous humor surrogate tumor biopsy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 186.