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. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.

Piazza, R., Magistroni, V., Pirola, A., Redaelli, S., Spinelli, R., Redaelli, S., et al. (2013). CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data. PLOS ONE, 8(10), e74825 [10.1371/journal.pone.0074825].

CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data

PIAZZA, ROCCO GIOVANNI;MAGISTRONI, VERA;PIROLA, ALESSANDRA;REDAELLI, SARA;SPINELLI, ROBERTA;REDAELLI, SERENA;VALLETTA, SIMONA;Cazzaniga, G;GAMBACORTI PASSERINI, CARLO
2013

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. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.
Articolo in rivista - Articolo scientifico
Copy number alterations, Whole-Exome Sequencing, Comparative Genome Hybridization, Allelic Imbalance
English
e74825
Piazza, R., Magistroni, V., Pirola, A., Redaelli, S., Spinelli, R., Redaelli, S., et al. (2013). CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data. PLOS ONE, 8(10), e74825 [10.1371/journal.pone.0074825].
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/48519
Citazioni
  • Scopus 16
  • ???jsp.display-item.citation.isi??? 14
Social impact