Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.
Nature Genetics (Impact Factor: 29.65). 03/2012; 44(4):390-7, S1. DOI: 10.1038/ng.2202
Source: PubMed

ABSTRACT We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.

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Available from: Toshiro K. Ohsumi, Jul 07, 2015
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    • "Replication fork stalling and template switching has been hypothesized to underpin some of the complex genomic rearrangements found in constitutional genomic disorders (Liu et al. 2011b). One study, for example, showed that 19% of individuals with chromosomal abnormalities had evidence for complexity of genomic rearrangements at the breakpoints (Chiang et al. 2012). In many cases, these complexes of structural variation are driven by clustered rearrangements with a striking resemblance to those described here, and cause severe developmental disorders (Liu et al. 2011b). "
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    Genome Research 07/2014; 24(10). DOI:10.1101/gr.175547.114 · 13.85 Impact Factor
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    • "This mechanism generates complex rearrangements formed by the incorrect ligation of ends with little or no sequence of homology and the insertion of some nucleotides, with the further loss of some fragments to generate deletions (Kloosterman et al. 2011; Holland and Cleveland 2012). The other mechanism that can be involved in the formation of complex rearrangements is chromoanasynthesis, which is generally involved in constitutional rearrangements that show complexity, microhomology at breakpoints , and occasionally the fusions of distant sequences and is indicative of a DNA replication-based mechanism as the causative agent, including fork stalling and template switching (FoSTeS) and/or microhomology-mediated break-induced replication (MMBIR) (Zhang et al. 2009; Liu et al. 2011; Chiang et al. 2012; Holland and Cleveland 2012). FoSTeS occurs when the DNA replication forks stall due to a DNA lesion or an error, allowing the replication fork to invade another fork through an area of microhomology. "
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    ABSTRACT: Genome rearrangements are caused by the erroneous repair of DNA double-strand breaks, leading to several alterations that result in loss or gain of the structural genomic of a dosage-sensitive genes. However, the mechanisms that promote the complexity of rearrangements of congenital or developmental defects in human disease are unclear. The investigation of complex genomic abnormalities could help to elucidate the mechanisms and causes for the formation and facilitate the understanding of congenital or developmental defects in human disease. We here report one case of a patient with atypical clinical features of the 1p36 syndrome and the use of cytogenomic techniques to characterize the genomic alterations. Analysis by multiplex ligation-dependent probe amplification and array revealed a complex rearrangement in the 1p36.3 region with deletions and duplication interspaced by normal sequences. We also suggest that chromoanagenesis could be a possible mechanism involved in the repair and stabilization of this rearrangement.
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    • "Although new methods such as fluorescence in situ hybridization (FISH) and array-based comparative genomic hybridization have been used to detect BCA-associated breakpoints in conjunction with karyotyping and other cytogenetic techniques (i.e., chromosome sorting), they are laborious and also unable to achieve single base pair resolution [Veltman et al., 2003; Chen et al., 2010]. Massive parallel sequencing has been demonstrated to accurately detect BCA-associated breakpoints, but this technique is highly dependent on prior knowledge of the affected G-band region [Chen et al., 2008; Chen et al., 2010; Sobreira et al., 2011; Talkowski et al., 2011; Chiang et al., 2012; Talkowski et al., 2012; Schluth-Bolard et al., 2013]. Therefore, for the routine clinical detection of BCA events, and to facilitate mapping of BCA-associated breakpoints, a highly accurate, cost-effective, and robust detection approach is desirable. "
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