A Distinct Class of Chromoanagenesis Events Characterized by Focal Copy Number Gains

Abstract

Chromoanagenesis is the process by which a single catastrophic event creates complex rearrangements confined to a single or a few chromosomes. It is usually characterized by the presence of multiple deletions and/or duplications, as well as by copy neutral rearrangements. In contrast, an array CGH screen of patients with developmental anomalies revealed three patients in which a single chromosome carries from 8 to 11 large copy number gains confined to a single chromosome or chromosomal arm, but the absence of deletions. Subsequent fluorescence in situ hybiridization and massive parallel sequencing revealed the duplicons to be clustered together in distinct locations across the altered chromosomes. Breakpoint junction sequences showed both microhomology and non-templated insertions of up to 40 bp. Hence, these patients each demonstrate a single altered chromosome of clustered insertional duplications, no deletions, and breakpoint junction sequences showing microhomology and/or non-templated insertions. These observations are difficult to reconcile with current mechanistic descriptions of chromothripsis and chromoanasynthesis. Therefore, we hypothesize those rearrangements to be of a mechanistically different origin. In addition, we suggest that large untemplated insertional sequences observed at breakpoints are driven by a non-canonical non-homologous end joining mechanism.

Of Simple and Complex Genome Rearrangements, Chromothripsis, Chromoanasynthesis, and Chromosome Chaos

“…The latter finding cannot be reconciled with classical NHEJ. On the other hand, the highly dispersed nature of the rearrangements cannot be accounted for by assuming a single fork stalling and template-switching event during DNA replication [Liu et al, 2011;Masset et al, 2016]. Since no triplications and quadruplications were found, these cases are clearly distinct from the homology-driven DNA repair mechanism mediated by multiple template switches recently documented for the PLP1 locus [Beck et al, 2015].…”

“…Since no triplications and quadruplications were found, these cases are clearly distinct from the homology-driven DNA repair mechanism mediated by multiple template switches recently documented for the PLP1 locus [Beck et al, 2015]. Therefore, the authors invoke an alternative NHEJ mechanism, probably mediated by DNA Polθ , to account for the CCRs in their cases [Masset et al, 2016].…”

“…Such chromosome fragmentation, 116 this process of chromoanasynthesis, i.e., chromosome reconstitution, results in clustered CNVs, including deletions, duplications, and triplications [Liu et al, 2011]. Recently, 3 cases of chromoanasynthesis with rearrangements of a single chromosome involving duplications and insertion translocations as well as a novel cell-division independent mechanism of chromothripsis have been reported [Masset et al, 2016;Nazaryan-Petersen et al, 2016].…”

“…Using array-CGH screening, 3 patients with 8-11 copy number gains dispersed across a single chromosome were found [Masset et al, 2016]. By FISH analyses, the copy number gains proved to be insertion-duplications of DNA segments at distant locations within the same chromosome.…”

Break‐induced replication links microsatellite expansion to complex genome rearrangements

“…A) Polymerase stuttering at microsatellite repeats leads to excess nascent strand microsatellite sequence (expansion). B) Terminal transferase-like nontemplated synthesis (dashed line) across a hairpin abasic gap [114–120] or C ) Template hairpin isomerization following destabilization of a stalled polymerase [121] leads to contraction. D) Polymerase stalling leads to replication stress, fork collapse, single-ended DSB (seDSB).…”