Identification of Germline Variants in a Cohort of South Africa Paediatric Cancer Patients

Abstract

Paediatric cancers, which affect individuals under 18 years of age, are often attributed to inherited germline genetic variants due to the limited time for the accumulation of DNA alterations. Variants in cancer predisposition genes- such as tumour suppressor genes (TSGs), proto-oncogenes and DNA repair genes- are known to increase cancer risk. This study aimed to identify germline single nucleotide variants (SNVs) in paediatric cancer patients using Whole Exome Sequencing (WES), with a focus on four common childhood solid tumours; nephroblastoma, retinoblastoma, rhabdomyosarcoma and osteosarcoma. DNA was extracted from blood samples of 14 patients diagnosed with one of these cancers, and a virtual gene panel consisting of 64 cancer predisposition genes was used to analyse WES data. A total of 212,825 variants were processed, with the majority being intronic, followed by synonymous, missense, splice-site and indel variants. Variants were prioritised based on factors such as minor allele frequencies, variant types, locations and in silico prediction scores. These variants were further assessed using databases like ClinVar and AlphaMissense database (AMDB) and visualised using Integrative Genomics Viewer (IGV). Two heterozygous missense variants in TSGs were classified as variants of uncertain significance (VUSs) according to ACMG/ AMP guidelines: one in the TP53 gene (NM_000546.6:c.923T>C) in a retinoblastoma patient (PC79) and another in the SDHB gene (NM_003000.3:c.455C>T) in a rhabdomyosarcoma patient (PC2), both of African ancestry. While the identification of these VUSs provide valuable insights into potential germline genetic causes of paediatric cancers, the absence of definitive pathogenic variants underscores the need for further investigation. This study also highlights the challenges of interpreting genetic data in underrepresented populations, such as those of African descent, where VUSs are more prevalent. Despite these challenges, WES proved to be valuable in identifying germline variants and advancing our understanding of paediatric cancer genetics in South Africa.