The Genetic And Cell Free Dna Characteristics Of Soft Tissue Sarcomas
thesisposted on 2019-04-17, 08:52 authored by Nicholas C. Eastley
Soft tissue sarcomas (STSs) are a group of rare, malignant tumours with a relatively poor prognosis. Although they have been broadly classified as complex or simple based on their karyotype, only a few studies have investigated the genetic characteristics of STSs in detail. To further explore STS genomics we analysed a group of primary STSs using Illumina Next Generation Sequencing. This analysis revealed several characteristics of the analysed tumours including 1) a low single nucleotide variant and insertion/deletion mutational burden, 2) a high number of recurrent amplifications/deletions, 3) significant inter-tumoural heterogeneity regardless of histopathological classification and 4) complex genotypes in the vast majority of STSs analysed. Currently no circulating STS biomarkers exist. Short fragments of DNA termed cell free DNA (cfDNA) can be found in the bloodstream. Some cancer patient cfDNA is tumour derived (circulating tumour derived DNA / ctDNA) and in several malignancies this ctDNA appears to correlate with disease behaviour. Despite this, very few studies have investigated STS patient cfDNA/ctDNA. To address this paucity of work we next used quantitative PCR, semiconductor targeted NGS and digital droplet PCR to characterise the cfDNA/ctDNA characteristics of two groups of metastatic and non-metastatic STS patients. This analysis revealed elevated cfDNA levels in the metastatic patients, which weakly correlated with disease burden suggesting a potential diagnostic role. Overall ctDNA was also identified in 27% (non-metastatic) - 36% (metastatic) of the analysed patients suggesting either that 1) the experimental approach used was not specific enough to detect ctDNA in tumours as genetically heterogeneous as STSs, or that 2) not all STSs shed ctDNA. Moving forwards although this analysis highlights a potential role for the use of ctDNA profiling in STS patients, it has also identified several significant challenges that must be addressed before ctDNA can be proposed as a realistic source for novel biomarkers.
Supervisor(s)Royle, Nicola; Ashford, Robert; Shaw, Jacqui; Esler, Claire
Date of award2019-03-08
Author affiliationDepartment of Genetics
Awarding institutionUniversity of Leicester