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

// Duarte Mendes Oliveira 1, * , Gianluca Santamaria 1, * , Carmelo Laudanna 1 , Simona Migliozzi 1 , Pietro Zoppoli 1 , Michael Quist 4 , Catie Grasso 5 , Chiara Mignogna 2 , Laura Elia 3 , Maria Concetta Faniello 1 , Cinzia Marinaro 1 , Rosario Sacco 3 , Francesco Corcione 6 , Giuseppe Viglietto 1 , Donatella Malanga 1 and Antonia Rizzuto 3 1 Dipartimento di Medicina Sperimentale e Clinica, Universita Magna Graecia, Catanzaro, Italy 2 Dipartimento di Scienze della Salute, Universita Magna Graecia, Catanzaro, Italy 3 Dipartimento di Scienze Mediche e Chirurgiche, Universita Magna Graecia, Catanzaro, Italy 4 Fred Hutchinson Cancer Research Center, Seattle, WA, USA 5 University of California Los Angeles (UCLA), Los Angeles, CA, USA 6 UOC Chirurgia Generale, Azienda Ospedaliera dei Colli, Napoli, Italy * These authors contributed equally to this work Correspondence to: Giuseppe Viglietto, email: viglietto@unicz.it Donatella Malanga, email: malanga@unicz.it Keywords: colon cancer; Next generation sequencing; copy number alteration Received: April 04, 2017      Accepted: February 28, 2018      Published: April 17, 2018 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.