Browsing by Author "Alkodsi, Amjad"

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Comparison of somatic copy number alteration detection algorithms in whole-genome and whole-exome data
(2013) Alkodsi, Amjad
School of Science | Master's thesis
Somatic copy number alterations (SCNAs) constitute an important type of structural variations that affect cancer pathogenesis. Accurate detection of SCNAs is a crucial task as it can lead to identification of events driving cancer development. The advent of next-generation sequencing technologies has revolutionized the field of genomics and variant analysis. While whole-genome sequencing can give a broader view of the genome, whole-exome sequencing has the advantage of time and cost efficiency. Several algorithms have been developed to detect SCNAs from whole-genome and whole-exome sequencing data. However, their relative performance was not well described. In this thesis, we present a comparative analysis of six SCNA detection algorithms in sequencing data including ControlFreeC, BICseq, HMMcopy, CNAnorm, ExomeCNV and VarScan2. We use simulated data as well as a real dataset of 11 breast cancer samples subjected to whole-genome, whole-exome sequencing and SNP array genotyping. We address the relative strengths and limitations of each algorithm, and we explore the relative merits of using whole-genome over whole-exome sequencing data.