Expanding the RB1 variant landscape of heritable retinoblastoma: unlocking precision oncology potential in Southern Africa

Abstract

Background: Retinoblastoma (Rb) is the most common childhood intraocular cancer, with heritable forms caused by pathogenic germline variants in the RB1 (or retinoblastoma 1) gene, which necessitate intensive and costly lifelong surveillance. Genetic testing enables precise risk prediction and individualized clinical management, yet data on the RB1 variant spectrum in African populations remains scarce. This study investigated the molecular landscape of clinically presumed heritable Rb in a Southern African cohort and evaluated the potential healthcare and economic benefits of implementing genetic testing.

Methods: Fifty-eight patients with clinically presumed heritable Rb were recruited from two tertiary hospitals in South Africa. Comprehensive RB1 gene analysis was performed using next-generation sequencing (NGS) to detect single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs), and was supplemented by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). A cost comparison model was developed to evaluate conventional clinical screening versus a genetically guided approach.

Results: RB1 pathogenic and/or likely pathogenic variants were identified in 84.5% (49/58) of patients, including eleven novel variants. The variant spectrum included frameshift, nonsense, splicing, intronic, and missense changes, with a notable concentration in the pocket domain region of the Rb associated protein (pRb). CNVs were detected in 10.3% of probands. Our cost analysis demonstrated significant savings associated with genetic testing, reducing surveillance-related expenses by up to US$228,989 across extended family generations in the private sector and US$166,489 in the public sector. Implementing genetic testing would also minimize unnecessary examinations and promote more efficient allocation of healthcare resources.

Conclusions: Comprehensive RB1 genetic testing in this Southern African cohort revealed a diverse variant landscape, including novel pathogenic changes, and demonstrated the clinical and economic value of integrating genetic testing into Rb management. These findings contribute to the global understanding of genetic variation within the RB1 gene and support tailored care strategies that can reduce the surveillance burden, optimize healthcare resources, and improve outcomes for affected families.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12885-026-15789-7.

Keywords: Cancer genetics; Copy number variant analysis; Health economics; Molecular diagnosis; Next-generation sequencing; Retinoblastoma.

Fig. 1

Distribution of the variant subtypes in the RB1 gene included in the gnomAD non-cancer dataset. Below each variant subtype is the percentage of that subtype in the dataset. UTR untranslated region

Fig. 2

Distribution of the variant subtypes in the RB1 gene identified in the in-house control dataset (n = 80). Below each variant subtype is the percentage of that subtype in the dataset. UTR untranslated region

Fig. 3

Distribution of the RB1 single nucleotide variants and small insertions and deletions detected in this study. Below each variant subtype is the percentage of that subtype in the dataset

Fig. 4

Schematic representation of the spectrum of causal RB1 single nucleotide variants and small insertions and deletions identified. The cyclin fold domains (CYCA and CYCB) are highlighted in blue, the linker domain (LD) in green, and the pocket domains (PA and PB) in pink. Identical recurrent variants are represented once