Figure 2

Significant levels of C>T/G>A sequencing artefacts in FFPE samples. (A) Assessment of sequence artefacts in cell line DNA and FFPE samples. The prevalence of each type of nucleotide change in the 1-10% allele frequency range was computed. Likely true variants identified through the Varscan2 variant caller were operationally removed to enrich for sequencing artefact changes. The graph shows all FFPE samples sorted according to the counts of C>T/G>A changes. Zoomed view: HL-60 and H1975 cell lines were used as good quality DNA controls. (B) The prevalence of each type of nucleotide change in the 10-25% allele frequency range. The graph shows all FFPE samples sorted according to the counts of C>T/G>A changes.