Effect of algorithms on the identification of copy number variants in healthy Finnish individuals and individuals with autism spectrum disorder

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dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.advisorJärvelä, Irma 
dc.contributor.authorKanduri, Chakravarthi
dc.contributor.departmentTietojenkäsittelytieteen laitosfi
dc.contributor.schoolPerustieteiden korkeakoulufi
dc.contributor.schoolSchool of Scienceen
dc.contributor.supervisorLähdesmäki, Harri 
dc.date.accessioned2020-12-28T10:14:58Z
dc.date.available2020-12-28T10:14:58Z
dc.date.issued2012 
dc.description.abstractCopy Number Variations, a form of genomic structural variation, are known to alter the gene expression, thereby causing phenotypic variation and increasing the risk of disease susceptibility. In order to understand the role of CNVs in the genetic variation of human populations, it has become increasingly common to incorporate CNV maps in disease-association studies. Yet, there is neither an experimental method nor an algorithm that can accurately identify a CNV. In addition to this void, population-specific differences exist in CNV maps making it more complicated to get the big picture of genomic variations. To address some of these issues, this study makes an assessment of two most popular algorithms available for Illumina-based platforms alongside contributing to the global variation map with Finnish population-specific CNVs. Illumina HumanOmniExpress-12 v1 beadchip was used for genotyping 203 trios (father, mother, offspring) of healthy individuals and 90 other trios, in which the offspring is affected with autism spectrum disorder (ASD). CNVs were identified using PennCNV and QuantiSNP, two most popular algorithms for Illumina-based platforms, which uses Hidden Markov Models to detect CNVs. Comparisons were made to check the agreement in CNV-calls, differences in size statistics and size disen
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/100039
dc.identifier.urnURN:NBN:fi:aalto-2020122858870
dc.language.isoenen
dc.programme.majorInformaatiotekniikkafi
dc.programme.mcodeT-61fi
dc.rights.accesslevelclosedAccess
dc.titleEffect of algorithms on the identification of copy number variants in healthy Finnish individuals and individuals with autism spectrum disorderen
dc.type.okmG2 Pro gradu, diplomityö 
dc.type.ontasotMaster's thesisen
dc.type.ontasotPro gradu -tutkielmafi
dc.type.publicationmasterThesis 
local.aalto.digiauthask
local.aalto.digifolderAalto_91174
local.aalto.idinssi44735
local.aalto.openaccessno
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