Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis

Translocation is one of the most common structural chromosome abnormalities found in humans, with a de novo frequency of 1 in 2000 (Warburton 1991). Unbalanced translocations lead to monosomy and trisomy for segments of different chromosomes and account for ∼1% of cases of developmental delay and intellectual disability (Ravnan et al. 2006; Ballif et al. 2007; Shao et al. 2008). The initial exchange of genetic material between two nonhomologous chromosomes can occur during premeiotic mitoses, meiotic recombination in the parental germline, or post-zygotic mitoses in the early embryo (Vanneste et al. 2009; Robberecht et al. 2013). Unbalanced translocations detected in affected children may be inherited from a parent who carries the balanced form of the rearrangement or may arise de novo. Recurrent translocations may be mediated by nonallelic homologous recombination (NAHR) between segmental duplications (Giglio et al. 2002; Ou et al. 2011) or paralogous interspersed repeats (Luo et al. 2011; Hermetz et al. 2012; Robberecht et al. 2013). Palindromic AT-rich repeats on Chromosomes 3, 8, 11, 17, and 22 also generate recurrent translocations, the most common of which is the recurrent t(11;22) that causes Emanuel syndrome (Edelmann et al. 2001; Kurahashi et al. 2003; Gotter et al. 2007; Kato et al. 2012, 2014). Most germline translocations, however, are not recurrent, and sequencing of translocation breakpoints has revealed features of nonhomologous end-joining (NHEJ) and microhomology-mediated break-induced replication (MMBIR) at more than 60 unique translocation junctions (Chen et al. 2008; Higgins et al. 2008; Sobreira et al. 2011; Chiang et al. 2012; Robberecht et al. 2013). Recently, a study of 12 de novo unbalanced translocations, nine of which were sequenced, concluded that NAHR between paralogous repeats is the predominant mechanism of de novo unbalanced translocation formation (Robberecht et al. 2013). Sequencing translocation breakpoints can also identify physically disrupted and fused genes. In the case of balanced translocations, genes altered at translocation breakpoints are strong candidates to explain neurodevelopmental phenotypes (Baptista et al. 2005; Higgins et al. 2008; Backx et al. 2011). On the other hand, the clinical features of individuals with unbalanced translocations may be explained by copy number changes in genes within monosomic and trisomic segments. In either case, identifying unique gene fusions is important for understanding the consequences of translocations. Sequence analysis of breakpoint junctions can also reveal more complex rearrangement structures than expected from copy number studies alone (Luo et al. 2011; Chiang et al. 2012; Carvalho et al. 2013; Brand et al. 2014; Newman et al. 2015). Though most germline translocations involve only two chromosomes, some are the product of many breakpoints on three to five different chromosomes. Originally seen in cancer (Stephens et al. 2011), chromosome shattering or chromothripsis is now recognized as a cause of some germline translocations (Kloosterman et al. 2011, 2012; Chiang et al. 2012; Nazaryan et al. 2014; Pellestor et al. 2014; de Pagter et al. 2015). Here we investigate translocation structure, genes fused at breakpoints, and rearrangement mechanisms by analyzing a group of 57 unbalanced translocations, the largest cohort to date. Using a combination of array comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH), SureSelect sequence capture, and whole-genome sequencing (WGS), we provide a comprehensive sequence analysis of unbalanced translocations.