Electronic Theses and Dissertations (Masters)
Permanent URI for this collectionhttps://hdl.handle.net/10539/38221
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Item Germline Cancer Predisposition Variants in Paediatric Rhabdomyosarcoma(University of the Witwatersrand, Johannesburg, 2023) Pillhofer, Gabriella Peta; Lamola, Lindie; Mnika, KhuthalaRhabdomyosarcoma (RMS) is cancer that originates from undifferentiated skeletal muscle cells. RMS is the most common tissue sarcoma in children and adolescents and has over 50% of cases occurring in individuals under the age of 10 and thus there is reason to suspect that RMS may have a hereditary predisposition. However, much of the existing research of germline predisposition in paediatric RMS is focused on ethnically European populations, and currently very little data is available from African populations. In this study, we aimed to identify RMS predisposition variants by performing whole exome sequencing (WES) on germline DNA from eight paediatric patients diagnosed with RMS. Following WES, variant annotation and filtering was performed to identify variants in genes of interest that were potentially germline causes of malignancy. Filtered variants were then classified according to American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines. This study identified four variants of uncertain significance (VUSs) in four patients. Two of these were in genes that have previously been associated with an RMS phenotype (SDHB and BRCA1), and two were in genes that have been associated with a hereditary cancer syndrome that is not linked to RMS (CBL and CREBBP). While the highlighted variants are not of clinical significance, this study emphasises the importance of cataloguing and reporting VUSs in research in Africa. By expanding the genomic database on African patients, the analysis of variants on the continent may be made more accurate and efficient. It is the goal that the knowledge gained from this study will contribute to the information base of hereditary paediatric cancers in Africa, and that it may encourage similar research so that the field may continue to expand.Item Mutation Profiling of Paediatric Solid Tumours in a Cohort of South African Patients(University of the Witwatersrand, Johannesburg, 2023) Manolas, Erin; Krause, Amanda; Lamola, LindieChildhood cancers are an emerging global health burden, with the highest increase in incidence and mortality rates occurring in low-middle income countries, such as South Africa (SA). Adding to this burden is the contribution of cancer-predisposing genes (CPGs), whose germline variants increase the risk of cancer development in childhood. These genes are largely associated with a set of disorders, known as cancer-predisposing syndromes (CPSs), which are characterised by an increased likelihood of cancer development and/or additional phenotypic malignant/non- malignant features. Next-Generation Sequencing (NGS) technologies have been key in determining the occurrence and contribution of such germline variants to paediatric cancer development across international research and diagnostic settings. However, these technologies have not been applied to paediatric cohorts in SA and thus there is a paucity of data regarding the contribution of germline variants to childhood cancer development in this setting. Through the design and evaluation of an NGS targeted-CPG panel, this study aimed to generate germline variant profiles of SA paediatric cancer patients, thereby gaining insight into their potential role in the pathogenesis of childhood cancers. NGS was performed on the genomic DNA from 32 solid-tumour paediatric cancer patients using an Ion Ampliseq 50 CPG panel design and the Ion Torrent S5 sequencing instruments. Germline variants were called using the Ion Torrent Suite™ software (v.5.12.0) and annotated using the Ensembl Variant Effect Predictor. Variants were filtered using a bioinformatics pipeline assessing variant data from population and public databases, computational data, functional studies data, genetic pedigrees indicating family history and phenotypic data. Variant evidence was further interpreted for variant prioritisation and classification according to the ACMG-AMP guidelines. All putative pathogenic/likely-pathogenic (P/LP) variants identified were validated via Sanger Sequencing. Seven pathogenic and/or likely pathogenic germline variants were identified and validated in seven patients. Three of these variants, identified in the NF1, RET, and TP53 genes, were detected in patients who presented with phenotypes consistent with their genetic findings and are associated with well-known CPSs (diagnostic yield - 3/32, ~9.4%). The remaining four variants, identified in the BRCA1, ERCC3, FAH, and RB1 genes, have not been previously associated with the patient’s cancer phenotype and therefore require further investigation. At the time of this project’s data generation, this is the first global report of the novel heterozygous, likely pathogenic FAH p.R162H variant. Additionally, although reported elsewhere, the majority of the variants identified in this study (6/7, ~86.7%) have been reported for the first time within the SA paediatric population. To our knowledge, this is the first study to utilise NGS technologies in the germline variant profiling of paediatric solid-tumour patients in SA and therefore has greatly added to filling the current knowledge gap. In addition, these findings have contributed towards the foundation for the development of a CPG sequencing panel suitable for implementation in a SA diagnostic setting