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Author:Alkodsi, Amjad
Title:Comparison of somatic copy number alteration detection algorithms in whole-genome and whole-exome data
Publication type:Master's thesis
Publication year:2013
Pages:56      Language:   eng
Department/School:Perustieteiden korkeakoulu
Main subject:Informaatiotekniikka   (T-61)
Supervisor:Rousu, Juho ; Lundeberg, Joakim
Instructor:Hautaniemi, Sampsa ; Louhimo, Riku
OEVS:
Electronic archive copy is available via Aalto Thesis Database.
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Location:P1 Ark Aalto     | Archive
Keywords:somatic copy number alteration
exome sequencing
whole-genome sequencing
SNP arrays
Abstract (eng): 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.
ED:2013-09-25
INSSI record number: 47247
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