Abstract 4285: Structural variant breakpoint detection in advanced colorectal cancer
Authors: Broek E van den , Krijgsman O , Sie D , Haan JC , Komor M , Traets J , Heideman DAM , Wiel MA van de , Nagtegaal ID , Punt CJA , Carvalho B , Ylstra B , Meijer GA , Fijneman RJA 
Published: May 2015

Abstract
Introduction
Development of colorectal cancer (CRC) is accompanied by genomic alterations that drive tumor initiation and progression. Gains and losses of large chromosome segments result in DNA copy number alterations and subsequently quantitative changes in mRNA and protein expression levels. Interestingly, the accompanying chromosome breakpoints represent structural variants (SV) that may affect gene architecture and thereby normal gene function.
Aim
The aim of this study was to identify recurrent SV breakpoints in advanced CRC.
Methods
Previously a series of 352 advanced CRC samples from CAIRO and CAIRO2 clinical studies [Koopman et al. Lancet 2007; Tol et al. N Engl J Med 2009] was characterized for genome-wide DNA copy number alterations. DNA from formalin-fixed paraffin-embedded (FFPE) tumor and patient-matched normal tissue was subjected to high-resolution array-Comparative Genomic Hybridization (Agilent 180K arrays). Using these data, we now determined the prevalence of recurrent breakpoints in genes in CRC by computational analysis. In addition, multiplexed amplicon analysis involving 48 cancer-related genes (Illumina TruSeq Amplicon Cancer Panel) was applied to determine mutation frequencies. Multi-Dendrix was used to identify modules of (mutually exclusively mutated) cancer driver genes.
Results
We identified 748 recurrent SV breakpoints in genes (FDR&lt;0.1). The highest frequency of recurrent breakpoints was detected in MACROD2, in up to ∼40% of CRC samples. Most recurrent breakpoints occurred in less than 5% of all tumors, and have not been reported before in CRC. Mutation frequencies in APC, TP53 and KRAS were conform expectations (60%, 58%, and 48%, respectively). Multi-Dendrix analysis revealed modules of cancer driver genes that included both the commonly mutated CRC cancer genes as well as genes with recurrent breakpoints, suggesting that several of the SV breakpoint genes are candidate drivers of the carcinogenic process.
Conclusions
We were able to pinpoint the prevalence of 748 recurrent SV breakpoint regions in genes using array-CGH data from 352 CRC samples. Moreover, our studies revealed several breakpoints in genes that are mutually exclusive with the commonly mutated APC, KRAS, and TP53 genes, and therefore represent novel candidate cancer driver genes. Further studies are required to investigate their functional and clinical significance.
Citation Format: E van den Broek, O Krijgsman, D Sie, JC Haan, M Komor, J Traets, DAM Heideman, MA van de Wiel, ID Nagtegaal, CJA Punt, B Carvalho, B Ylstra, GA Meijer, RJA Fijneman. Structural variant breakpoint detection in advanced colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4285. doi:10.1158/1538-7445.AM2014-4285