Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data.

Duarte Mendes Oliveira,Rosario Sacco,Chiara Mignogna,Carmelo Laudanna,Francesco Corcione,Maria Concetta Faniello,Giuseppe Viglietto,Antonia Rizzuto,Cinzia Marinaro,Gianluca Santamaria,Catie Grasso,Pietro Zoppoli,Simona Migliozzi,Donatella Malanga,Michael Quist,Laura Elia

doi:10.18632/oncotarget.24912

Duarte Mendes Oliveira, Rosario Sacco + Show 14 more

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https://doi.org/10.18632/oncotarget.24912

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Abstract

The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined “common genes”) and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined “site-associated genes”). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL1 was associated with good prognosis.

Highlights

The development of cancer is driven by the acquisition of somatic genetic alterations that include single nucleotide variations (SNVs), gene fusions and copy-number alterations (CNAs)
We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm
We have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments and the presence of copy number alterations in 14 genes that were significantly associated to one specific site

Summary

Introduction

The development of cancer is driven by the acquisition of somatic genetic alterations that include single nucleotide variations (SNVs), gene fusions and copy-number alterations (CNAs). CNAs are somatic changes that cause the gain or loss of DNA fragments [1,2,3], and represent the most common alterations of cancer cells [4,5,6,7,8,9]. They contribute to both onset and progression of cancer by inappropriate activation of proto-oncogenes and/or inactivation of tumor suppressor genes [4, 10,11,12,13,14,15]. Many of these studies had inherent limitations due to small sample size, low-resolution assays and/or lack of associated clinical annotation, for early-stage CC

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