Characteristics of the germ-line Copy Number Variations (CNVs) in colorectal cancer patients

Werdyani, Salem (2016) Characteristics of the germ-line Copy Number Variations (CNVs) in colorectal cancer patients. Masters thesis, Memorial University of Newfoundland.

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Abstract

INDELs and CNVs are types of structural variations. This project aimed to computationally predict and examine the possible biological consequences of the INDELs/CNVs in colorectal cancer patient genomes using the QuantiSNP and PennCNV algorithms. A total of 69,290 INDELs/CNVs were identified in 495 patients and satisfied the quality control criteria. These variations constituted 3,486 distinct INDELs/CNVs and clustered in 1,527 CNV regions. The majority of the variations were CNVs (~79%) and deletions (~81%). Around 63% of the distinct variations were identified to completely or partially cover the sequences of 1,673 genes, and a large number of these genes were observed to act in cancer related biological pathways. In summary, this project detected a number of biologically interesting INDELs/CNVs in the genomes of colorectal cancer patients. Further studies in the Savas lab will investigate these variants in detail including their possible associations with the disease characteristics and outcomes in colorectal cancer.

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