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Retinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited.

To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses.

Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors.

Targeted therapy based on these subclonal events might be insufficient for complete tumor control. Retinoblastoma is a childhood cancer of the retina. Although the disease is relatively rare accounting for 2% of childhood cancers, retinoblastoma is the most common intra-ocular malignancy in children. From a clinical genetics perspective, three retinoblastoma types can be distinguished: familial (10%), sporadic heritable (30%) and non-heritable (60%). Patients with familial or sporadic heritable retinoblastoma have a germ line mono-allelic RB1 mutation and have acquired a second RB1 hit in the retina. While familial patients have inherited the mutant allele, sporadic heritable patients have acquired a de novo RB1 mutation.

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The majority of non-heritable retinoblastoma (95%) is also caused by bi-allelic inactivation of RB1 but in this case occurring through two subsequent somatic events in the developing retina. A minority of non-heritable retinoblastoma (2%) is caused by amplification of the oncogene MYCN. Recently, chromothrypsis of chromosome 13 disrupting the RB1 locus has been described as an alternative mechanism for RB1 inactivation. Possibly, 13q chromothrypsis accounts for the remaining patients for whom no RB1 or MYCN alterations can be found by Sanger sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA) or RB1 promotor methylation assays. Yet, while inactivation of RB1 in the developing retina is sufficient for neoplastic onset, it has been suggested that additional genetic alterations are required for malignant progression. In agreement, based on comprehensive genome-wide next-generation sequencing (NGS) efforts, it was claimed that two to eight genetic alterations are required to drive tumorigenesis.

Throughout the last decade, useful insights about secondary genetic alterations in retinoblastoma have been obtained by studies profiling large (>50 Kb) somatic copy number alterations (SCNAs). Unlike many other cancers, very little is known about smaller genetic alterations (. Identification of significantly mutated genes by somatic SNV/INDEL analysis To identify genes relevant for retinoblastoma carcinogenesis, we compared SNVs/INDELs observed in 71 primary retinoblastoma samples with a variant database established from blood DNA of the same patients (N = 70, from one bilateral patient, one tumor sample per eye was analyzed). Sequencing, alignment and enrichment statistics are provided (). The number of exonic variants ranged between 18,510 and 23,772 variants per tumor sample, adding up to a total of 1,386,285 variants in the tumor cohort. By comparing tumor variants with the pooled blood variant database, only 5,797/1,386,285 (0.41%) variants were considered somatically acquired.