Study of the role of SETD2 mutations in clear cell renal cell carninoma (ccRCC)
Year: 2013
Type: dissertation
Abstract: Clear cell Renal Cell Carcinoma, ccRCC, is the most common form of Renal Cancer, accounting for 90% of these cancers cases. It is well established that the majority of these cancers happen when both alleles of VHL (Von Hippel Lindau) tumour suppressor gene are mutated. It has also been observed that patients with this form of cancer present mutations on the SETD2 gene which applies its functions during transcription. In the last few years the growth within sequencing technologies has been astonishing. Next Generation Sequencing technology, NGS, provides tools for assessing full genomes to a reference sequence in a matter of days, being extremely accurate, while also increasingly cost effective. One of its many applications is RNA-Sequencing, a method for transcriptome analysis. Throughout this thesis we aimed at analysing RNA-Seq data from six samples: four with mutations on the SETD2 gene and two control samples. The main goal was to understand how the remaining genes on the transcriptome respond to these genes mutations. In the first part of this work we aimed at analysing several forms to normalize the data, resorting to R software packages (EDASeq, DESeq and edgeR). Data normalization is a crucial step on NGS techniques, as these techniques have some inherent bias that need to be accounted for. DESeq proved to be the most selective, while EDASeq is not as stringent. The second part of this work aimed at identifying deferentially expressed genes, to infer which genes behave in a significant way in the samples, packages edgeR, DESeq and RankProd. We identified six new genes as differentially expressed.
Author: Catarina Faria de Almeida
Language: Portuguese
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W22591660