Detection of somatic copy number alterations in cancerusing targeted exome capture sequencing

Robert J. Lonigro, Catherine S. Grasso, Dan R. Robinson, Xiaojun Jing, Yi Mi Wu, Xuhong Cao, Michael J. Quist, Scott A. Tomlins, Kenneth J. Pienta, Arul M. Chinnaiyan

Research output: Contribution to journalArticle

Abstract

The research community at large is expending considerable resources to sequence the coding region of the genomes of tumors and other human diseases using targeted exome capture (i.e., "whole exome sequencing"). The primary goal of targeted exome sequencing is to identify nonsynonymous mutations that potentially have functional consequences. Here, we demonstrate that whole-exome sequencing data can also be analyzed for comprehensively monitoring somatic copy number alterations (CNAs) by benchmarking the technique against conventional array CGH. A series of 17 matched tumor and normal tissues from patients with metastatic castrate-resistant prostate cancer was used for this assessment. We show that targeted exome sequencing reliably identifies CNAs that are common in advanced prostate cancer, such as androgen receptor (AR) gain and PTEN loss. Taken together, these data suggest that targeted exome sequencing data can be effectively leveraged for the detection of somatic CNAs in cancer.

Original languageEnglish (US)
Pages (from-to)1019-1025
Number of pages7
JournalNeoplasia
Volume13
Issue number11
DOIs
StatePublished - Nov 2011
Externally publishedYes

    Fingerprint

ASJC Scopus subject areas

  • Cancer Research

Cite this

Lonigro, R. J., Grasso, C. S., Robinson, D. R., Jing, X., Wu, Y. M., Cao, X., Quist, M. J., Tomlins, S. A., Pienta, K. J., & Chinnaiyan, A. M. (2011). Detection of somatic copy number alterations in cancerusing targeted exome capture sequencing. Neoplasia, 13(11), 1019-1025. https://doi.org/10.1593/neo.111252