Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements
TLDR
The impact of massive chromosomal change for the development of diseases such as cancer and for evolution more generally is considered and current models for underlying mechanisms are summarized.Abstract:
Recent genome sequencing studies have identified several classes of complex genomic rearrangements that appear to be derived from a single catastrophic event. These discoveries identify ways that genomes can be altered in single large jumps rather than by many incremental steps. Here we compare and contrast these phenomena and examine the evidence that they arise "all at once." We consider the impact of massive chromosomal change for the development of diseases such as cancer and for evolution more generally. Finally, we summarize current models for underlying mechanisms and discuss strategies for testing these models.read more
Citations
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Journal ArticleDOI
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants
TL;DR: Mako as mentioned in this paper proposed a graph-based pattern growth approach, where the graph depicts potential breakpoint connections, and pattern growth enables CSV detection without pre-defined models; however, there has been limited progress for CSV discovery compared with simple structural variants.
Posted ContentDOI
Mako: a graph-based pattern growth approach to detect complex structural variants
Jiadong Lin,Xiaofei Yang,Walter A. Kosters,Tun Xu,Yanyan Jia,Songbo Wang,Qihui Zhu,Mallory Ryan,Li Guo,Chengsheng Zhang,Charles Lee,Scott E. Devine,Scott E. Devine,Evan E. Eichler,Evan E. Eichler,Kai Ye +15 more
TL;DR: Mako as discussed by the authors proposed a graph-based pattern growth approach, where the graph depicts potential breakpoint connections and pattern growth enables CSV detection without predefined models, and the validation rates of real data based on experimental and computational validations as well as manual inspections are around 70%.
Posted Content
The Combinatorics of Tandem Duplication
TL;DR: In this article, the authors introduce an algebraic formalism to represent the process of tandem duplication as a word producing automaton, from which the number of possible evolutions arising from n tandem duplications can then be recursively derived.
Journal ArticleDOI
Double-strand breaks induce short-scale DNA replication and damage amplification in the fully grown mouse oocytes.
TL;DR: In this article, the conditions for initiation of multi-invasion-mediated DSB amplification were investigated in the G2 phase oocyte of a mouse and the results showed that DNA DSBs in the fully grown oocytes can initiate short-scale BIR (ssBIR) using the DNA replication indicator 5-ethynyl-2'-deoxyuridine (EdU).
Dissertation
Characterization of structural chromosomal variants by massively parallel sequencing
TL;DR: Five studies, focused on the analysis of SV using whole genome sequencing (WGS), developed and tested tools suitable for WGS SV analysis in a clinical setting, and validate the use of SV calling from WGS as a routine test in rare disease diagnostics.
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