Childhood Cancer Data Initiative Annual Symposium (Abstract Registration): Submission #33

Abstract: Background: Retinoblastoma (RB), the most common intraocular malignancy in children, laid the foundation for cancer genetics through the discovery of the RB1 tumor suppressor gene and the "two-hit" hypothesis. However, precision oncology has largely bypassed RB due to the risks associated with intraocular tumor biopsy. To overcome this, we developed an aqueous humor (AH) liquid biopsy platform for genomic profiling using tumor-derived cell-free DNA (cfDNA).

Methods: We established LBSeq4Kids, a CLIA-certified laboratory-developed test combining low-pass whole genome sequencing (LP-WGS) for detecting somatic copy number alterations (CNAs) and a custom pediatric targeted sequencing panel (TSP) for single nucleotide variants and fusions. A total of 147 AH samples from 60 patients (75 eyes) with suspected intraocular malignancy were analyzed.

Results: In 41 RB patients, LP-WGS detected CNAs in 94% of diagnostic samples and 100% of recurrent cases, achieving an overall sensitivity of 97%. No CNAs or pathogenic variants were detected in 14 patients with benign mimickers, demonstrating 100% specificity. Serial testing showed CNA clearance in 61% of eyes after two treatment cycles, aligning with clinical remission. TSP identified RB1 mutations in 92% of germline variant cases and was valuable in CNA-negative tumors.

Conclusions: LBSeq4Kids enables safe, repeatable molecular profiling in RB, transforming it into a genomically accessible cancer. This approach offers precise diagnosis, risk assessment, treatment monitoring, and recurrence detection, marking a significant advance in pediatric precision oncology.