Figure 2.

Mutation detection using formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tumor specimens. Variants were detected by AmpliSeq (A) and SimpliSeq (B) in 44 FFPE genomic DNA samples. The red shade stands for variants with VF >5%; blue shade for variants with VF between 1% and 5%; and green shade for variants within a single gene containing multiple hotspot mutations, with VFs of both 1%–5% and >5%. Gray shade indicates no variants detected. The y-axis indicates the gene name, and the x-axis the identification of the matched pairings, i.e., the microdissected epithelial tumor and stroma tissues. False-negative variants in p53 and PTEN are marked with a circle (B). (C–E): Correlation of high-frequent variants (VF >5%) (C, D) and low-frequent variants (VF 1%–5%) (E) between AmpliSeq and SimpliSeq. Open circles within the marked area represent “true positive” and open circles on the x-axis represent “false positive.” Note that JAK2 was excluded from the above analysis and the outstanding “false-positive genes” (PIK3CA, NRAS, FGFR2) have been removed in (D, E). The percentage of bona fide variants (marked in red) was calculated based on SimpliSeq and AmpliSeq variant calls, and is provided in the upper right corner of each figure (C–E).

Abbreviation: VF, variant frequency.