Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation

Abstract

Most balanced translocations are thought to result mechanistically from non-homologous endjoining (NHEJ) or, in rare cases of recurrent events, by nonallelic homologous recombination (NAHR). Here, we use low coverage mate pair whole genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n=4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated-insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by the error prone replication-based repair mechanisms (RBMs). Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

“…Recent studies highlighted that ABCRs are more complex than expected, with more breakpoints and cryptic deletions/duplications than expected Redin et al, 2017). They confirmed that ABCRs can lead to gene disruption and/or positional effect, and explain some phenotypes, such as MCA/ID for example (Nilsson et al, 2017;Redin et al, 2017;Schluth-Bolard et al, 2013). Moreover, these approaches revealed potential mechanisms of breakpoint formation, improving our knowledge about the genome and its anomalies Nilsson et al, 2017;Redin et al, 2017).…”

Induction of Chromosomal Translocations with CRISPR-Cas9 and Other Nucleases: Understanding the Repair Mechanisms That Give Rise to Translocations

“…Larger deletions (>1000 bp) are also observed at lower frequency, arising either by resection or possibly as the result of several breaks. Notably, perfect joining of ends has also been reported (e.g., 37% of junctions (Nilsson et al, 2017)). Microhomologies have been observed in 20–40% of translocation breakpoint junctions from tumors (Mattarucchi et al, 2008; Nilsson et al, 2017; Weckselblatt et al, 2015).…”

“…Oftentimes, only the junction sequences for the oncogenic translocation have been reported, although several publications include both junctions from the reciprocal (balanced) translocation. Concerning deletions, while most of the breakpoints are accompanied by deletions, the median deletion length remains short (e.g., 1 bp, (Nilsson et al, 2017); 5 bp, (Reiter et al, 2003); 14 bp, (Gillert et al, 1999)). Larger deletions (>1000 bp) are also observed at lower frequency, arising either by resection or possibly as the result of several breaks.…”

“…Microhomologies have been observed in 20–40% of translocation breakpoint junctions from tumors (Mattarucchi et al, 2008; Nilsson et al, 2017; Weckselblatt et al, 2015). The definition of microhomology can differ, however, as authors have sometimes considered there to be microhomologies when short repeated sequences are found after short (templated or not) insertions but not exactly corresponding to the 2 original breakpoint sequences (Mattarucchi et al, 2008; Nilsson et al, 2017), making it difficult to compare various studies. Particularly, a mechanism of template switching potentially use microhomologies to facilitate ligation of templated insertions with the partner chromosome, not reflecting altNHEJ activity.…”

“…More complex junctions, albeit happening to a lesser extent, can also be recovered in these this model and are likely to arise by similar repair mechanisms as in tumor cells from patients. In some cases, a plausible mechanism for their formation is replication primed by one of the DNA ends using microhomology reminiscence of the template switching mechanism described in patient cells (Mattarucchi et al, 2008; Nilsson et al, 2017). Of note the use of nCas9 provides more flexibility in DNA end structures potentially leading to more complex rearrangements found in certain type of tumors, i.e., duplications (Ghezraoui et al, 2014; Renouf et al, 2014)…”