Figure 3

Effect of amplifiable FFPE DNA copy number on the detection of mutational load by targeted NGS. The amplifiable DNA copy number (Cp#) for two clinical FFPE samples was calculated to be 370 and 289 copies based on the QFI (9% for both samples) and a well-characterized mutation frequency of 30.0 ± 3.4% for BRAF V600E or 38.4 ± 4.6% for PIK3CA H1047R, respectively. BRAF and PIK3CA loci were enriched using PCR [14] and sequenced on the MiSeq. The graph shows a dilution series of the DNA, from 24 to 3,030 amplifiable DNA copies and each point (blue, BRAF; red, PIK3CA) represents the fraction of reads with the target mutation.