Molecular Changes in Retinoblastoma beyond RB1: Findings from Next-Generation Sequencing

Abstract

This investigation uses hybridization capture-based next-generation sequencing to deepen our understanding of genetics that underlie retinoblastoma. Eighty-three enucleated retinoblastoma specimens were evaluated using a MSK-IMPACT clinical next-generation sequencing panel to evaluate both somatic and germline alterations. Somatic copy number variations (CNVs) were also identified. Genetic profiles were correlated to clinicopathologic characteristics. RB1 inactivation was found in 79 (97.5%) patients. All specimens had additional molecular alterations. The most common non-RB1 gene alteration was BCOR in 19 (22.9%). Five (11.0%) had pathogenic germline mutations in other non-RB1 cancer predisposition genes. Significant clinicopathologic correlations included: vitreous seeds associated with 1q gains and 16q loss of heterozygosity (BH-corrected p-value = 0.008, 0.004; OR = 12.6, 26.7, respectively). BCOR mutations were associated with poor prognosis, specifically metastases-free survival (MFS) (nominal p-value 0.03). Furthermore, retinoblastoma patients can have non-RB1 germline mutations in other cancer-associated genes. No two specimens had the identical genetic profile, emphasizing the individuality of tumors with the same clinical diagnosis.

Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature

“…Mutations included 4 small indels resulting in frameshift mutations and a large 588 Kb deletion disrupting the 5′UTR. This frequency is in line with previous reports of loss of function mutations in BCOR (10-23%) [18,[20][21][22]. Three patients, PD34259, PD37492 and PD37518 were male and since BCOR is located on chromosome X p11.4, these mutations were hemizygous in nature.…”

“…Focal amplifications of the orthodenticle homeobox 2 gene (OTX2) were observed in 3% and focal deletions of the BCL6 Corepressor (BCOR) observed in 4% of the same cohort of retinoblastoma tumours [19]. Truncating point mutations in BCOR have been also reported in 10-17% of Rb [18,[20][21][22]. In addition, a number of studies have identified consistent large-scale copy number changes including gains of 1q, 2p and 6p and losses of 16q [19,20,23].…”

“…To date, the majority of studies investigating genomic aberrations in Rb have focused on copy number aberrations [23], whole-exome sequencing [20] or targeted gene panels [18,22]. Very limited numbers of whole-genome sequencing (WGS) experiments have been performed.…”

Clinical evaluation of RB1 genetic testing reveals novel mutations in Vietnamese patients with retinoblastoma

“…The present study also supported the potential use of age at diagnosis as a risk factor for inherited RB. Recently, NGS is considered a highly sensitive and efficient approach for the detection of RB1 mutations due to increasing use of NGS in gene mutation analysis of RB; especially screening and identification of RB1 mutations with NGS substantially benefits the prepotency, early diagnosis and treatment of retinoblastoma (20)(21)(22)(23)(24)(25). Furthermore, the sensitivity rate of NGS in the present study was similar with that reported to previous studies.…”

“…The combination of the aforementioned methods is essential for detecting all possible RB1 mutations (17)(18)(19). Recently, Next Generation Sequencing (NGS) has been implemented as rapid and effective strategy for identification of RB1 mutations since all variations can be detected in a single test, thus providing a number of advantages, including high sensitivity and cost-effectiveness (20)(21)(22)(23)(24)(25). In Vietnam, Sanger sequencing coupled with MLPA (SS-MLPA) could detect germline RB1 mutations in 82-84% of bilateral cases (26,27).…”