CEQer A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data.docVIP
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CEQer A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data
CEQer:AGraphicalToolforCopyNumberandAllelic
ImbalanceDetectionfromWhole-ExomeSequencing
Data
RoccoPiazza1*,VeraMagistroni1,AlessandraPirola1,SaraRedaelli1,RobertaSpinelli1,SerenaRedaelli2,
MartaGalbiati3,SimonaValletta1,GiovanniGiudici3,GiovanniCazzaniga3,CarloGambacorti-Passerini1
1DepartmentofHealthSciences,UniversityofMilano-Bicocca,Monza,Italy,2DepartmentofNeurosciencesandBiomedicalTechnologies,UniversityofMilano-Bicocca,
Monza,Italy,3TettamantiResearchCenter,UniversityofMilano-Bicocca,SanGerardoHospital,Monza,Italy
Abstract
Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome
Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated
instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer
(Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled
analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital
exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance
detection.Thisdataisusedtobuildmixedstatistical/heuristicmodelsallowingtheidentificationofCNA/AIevents.Totest
our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic
specimensandcorrespondingmatchedcontrolsandweanalyzedtheresultsusingCEQer.Takenglobally,theseanalyses
showedthatthecombineduseofcomparativedigitalexonquantificationandLOH/AIallowsgeneratingveryaccurateCNA
data.Therefore,weproposeCEQerasanefficient,robustanduser-friendlygraphicaltoolfortheidentificationofCNA/AIin
thecontextofwhole-exomesequencingdata.
Citation:PiazzaR,MagistroniV,PirolaA,RedaelliS,SpinelliR,etal.(2013)CEQer:AGraphicalToolforCopyNumberandAllelicImbalanceDetectionfromWhole-
ExomeSequencingData.PLoSONE8(10):e74825.doi:10.1371/journal.
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