Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles

Abstract

Reciprocal chromosome translocations are often not exactly reciprocal. Most familiar are deletions at the breakpoints, up to megabases in extent. We describe here the opposite phenomenon-duplication of tens or hundreds of kilobases at the breakpoint junction, so that the same sequence is present on both products of a translocation. When the products of the translocation are mapped on the genome, they overlap. We report several of these ''overlapping-breakpoint'' duplications in breast cancer cell lines HCC1187, HCC1806, and DU4475. These lines also had deletions and essentially balanced translocations. In HCC1187 and HCC1806, we identified five cases of duplication ranging between 46 kb and 200 kb, with the partner chromosome showing deletions between 29 bp and 31 Mb. DU4475 had a duplication of at least 200 kb. Breakpoints were mapped using array painting, i.e., hybridization of chromosomes isolated by flow cytometry to custom oligonucleotide microarrays. Duplications were verified by fluorescent in situ hybridization (FISH), PCR on isolated chromosomes, and cloning of breakpoints. We propose that these duplications are the counterpart of deletions and that they are produced at a replication bubble, comprising two replication forks with the duplicated sequence in between.

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

“…The replication-associated mechanism MMBIR can also generate alterations with multiple breakpoints (Hastings et al, 2009a). The lack of templated insertions at the breakpoint junctions, however, which are thought to result from abortive attempts to use another template during replication (Hastings et al, 2009b; Howarth et al, 2011), does not substantiate the involvement of a replication-associated rearrangement mechanism in the complex alterations we observed.…”

Mechanisms of Gene Duplication and Amplification

“…Switches at both diverging forks produces a head-to-head dimeric circle, which can be extracted and integrated into the chromosome to yield a symmetrical TID. Fork interactions at replication bubbles were also proposed to explain duplication by unequal translocation in human cancer cell lines (Howarth et al 2011). The formation of TID duplications has also been explained using a template-switching model that does not restrict template switches to replication fork regions (Hastings et al 2009b;Carvalho et al 2011).…”

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

“…There are two general models: (1) template switching at a DNA replication fork (FoSTeS/MMBIR) (Lee et al 2007;Hastings et al 2009a) or bubble (Howarth et al 2011); and (2) chromothripsis, which involves chromosome shattering followed by nonhomologous or microhomology-mediated end-joining (NHEJ/MMEJ) (Stephens et al 2011). There is evidence for both models.…”