Fragile Breakage Model

CREATED: 200710030547 Speaker: Glenn Tesler, UCSD

• breakpoint distance underestimate the reversal distance AND mistakenly assumes bps are never reused
• GRIMM-Synteny ** noise vs synteny blocks ** microrearrangements vs macrorearrangements ** do alignment, then find “clusters” (at least 1Mbp and at most 85 micro rearrangements)
• 2D breakpoint graph
• Human vs Mouse ** Chromosome X: d_r = 7, but only 11 bp so >= 3 bp reuse ** Whole genome: at least 190 bp reuse
• Breakpoint Reuse Rate = {2d} / b, for parsimonious scenarios 1 <= "BRR" <= 2 ** for Human-Mouse comparison, BRR = 1.63
• Potential problem with Random Breakage Model ** unit of length on a chromosome depends on technology used, usually not linearly related ** uniform in one unit is not uniform in another unit.