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Reports (Research Report) Year : 2008

Precise detection of rearrangement breakpoints in mammalian chromosomes


Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely locate rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to investigate the breakpoints themselves in order to refine them. By aligning each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarity inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Since this method requires as input synteny blocks with some properties which, though they appear natural, are not verified by current methods for detecting such blocks, we further give a formal definition and provide an algorithm to compute them. The whole method is applied to locate breakpoints on the human genome when compared to the mouse and dog genomes. Among the 355 human-mouse and 240 human-dog breakpoints, 168 and 146 respectively span less than 50 Kb. We compared the resulting breakpoints with some publicly available ones and show that we achieve a better resolution. Furthermore, we suggest that breakpoints are rarely reduced to a point, and instead consist in often large regions that can be distinguished from the sequences around in terms of segmental duplications, similarity with related species, and transposable elements. We hope that this new result may provide some insight into the mechanism and evolutionary properties of chromosomal rearrangements.
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Dates and versions

inria-00278553 , version 1 (13-05-2008)
inria-00278553 , version 2 (14-05-2008)


  • HAL Id : inria-00278553 , version 2


Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot. Precise detection of rearrangement breakpoints in mammalian chromosomes. [Research Report] RR-6533, INRIA. 2008, pp.26. ⟨inria-00278553v2⟩
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