GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes

Remond J.A. Fijneman*, Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Sanne Abeln

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R ( and is available from Bioconductor (
Original languageEnglish
Article number2340
Pages (from-to)1-8
Number of pages8
Early online date19 Sept 2016
Publication statusPublished - 6 Jul 2017


  • Cancer genome
  • Computational method
  • Copy number aberration profile
  • Molecular characterization
  • Recurrent breakpoint genes
  • Structural chromosomal aberrations


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