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A chromosomal rearrangement (CR) event occurs as a consequence of double-strand breaks (DSBs) of the DNA, followed by abnormal rejoining of the non-homologous ends, producing a new chromosomal arrangement (van Gent et al., 2001). Alternatively, a CR event can result from crossing-over between repetitive DNA sequences (Shrivastav et al., 2008). CR events may lead to disruption of genes and other functional structures. They have been implicated in many tumor and non-tumor human diseases (Stephens et al., 2009; Muhle et al., 2004), and are frequently examined in clinical diagnosis, treatment and prognosis (Stilgenbauer et al., 2002; Helmrich et al., 2005; Mullighan et al., 2008).