Breakpoint reuse rate in rearrangement scenarios

CREATED: 200810140800 Speaker: Anne Bergeron ** Rearrangement of chromosome 17 in Bourque, Pevzner and Tesler

• position of breakpoints depends on order of operation ** Classical view of breakpoint reuse rate, $r = 2D/b$
• $D$ is the rearrangement distance
• $b$ is the number of adjacencies in B that are no adjacencies in A
• Assumes that each operation makes 2 cuts ** if genomes are linear, they must have the same number of chromosomes ** chromosomes must be co-tailed
• In practice ** empty chromosomes are added as necessary ** caps are added to make chromosomes co-tailed ** chromosomes are circularized (Alekseyev and Pevzner) ** New view of breakpoint reuse rate
• Operations that make 0 or 1 cut
• Linear chromosomes: semi translocation, semi inversion, fission, fusion (0 cut)
• Linear and circular chromosomes
• Now, $r = C/b$ where C is the number of cuts, $0 \le r \le 2$ ** Understanding the reuse rate
• Adjacency graph, BB path, cycle, AB path and AA path
• Long cycles induces breakpoint reuse ** Conclusion
• reuse rate depends on how genomes and telomares are modeled