Estimation of copy number alterations from exome sequencing data.

Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliab...

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Autores principales:	Rafael Valdés-Mas, Silvia Bea, Diana A Puente, Carlos López-Otín, Xose S Puente
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2b0816cc8fb04c548861415947af7041
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spelling	oai:doaj.org-article:2b0816cc8fb04c548861415947af70412021-11-18T08:04:34ZEstimation of copy number alterations from exome sequencing data.1932-620310.1371/journal.pone.0051422https://doaj.org/article/2b0816cc8fb04c548861415947af70412012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284693/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.Rafael Valdés-MasSilvia BeaDiana A PuenteCarlos López-OtínXose S PuentePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51422 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rafael Valdés-Mas Silvia Bea Diana A Puente Carlos López-Otín Xose S Puente Estimation of copy number alterations from exome sequencing data.
description	Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.
format	article
author	Rafael Valdés-Mas Silvia Bea Diana A Puente Carlos López-Otín Xose S Puente
author_facet	Rafael Valdés-Mas Silvia Bea Diana A Puente Carlos López-Otín Xose S Puente
author_sort	Rafael Valdés-Mas
title	Estimation of copy number alterations from exome sequencing data.
title_short	Estimation of copy number alterations from exome sequencing data.
title_full	Estimation of copy number alterations from exome sequencing data.
title_fullStr	Estimation of copy number alterations from exome sequencing data.
title_full_unstemmed	Estimation of copy number alterations from exome sequencing data.
title_sort	estimation of copy number alterations from exome sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2b0816cc8fb04c548861415947af7041
work_keys_str_mv	AT rafaelvaldesmas estimationofcopynumberalterationsfromexomesequencingdata AT silviabea estimationofcopynumberalterationsfromexomesequencingdata AT dianaapuente estimationofcopynumberalterationsfromexomesequencingdata AT carloslopezotin estimationofcopynumberalterationsfromexomesequencingdata AT xosespuente estimationofcopynumberalterationsfromexomesequencingdata
_version_	1718422217608396800

Estimation of copy number alterations from exome sequencing data.

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