Figure 3.
Designing AMBRE-68. (A) Candidate primers are uniformly distributed in CDKN2A locus, suggesting that good primer designs are possible. AmBre-design is tasked to capture CDKN2A deletion upstream and downstream breakpoints in regions chr9: 21,730,000–21,965,000 and chr9: 21,975,000–22,129,000 (GRCh37 coordinates), respectively. (B) Final low-cost 68-primer design to capture CDKN2A deletions in 380-kb breakpoint region. The solution has a 97.6% and a 99.7% coverage of breakpoint regions. The fraction of break pairs captured by the design (resulting in amplicon length <13 kb) is 99.99%.
