Fig 2. Patient #1 mutation calls and validation.

A) Using a cutoff of 1.5% variant allele percentage, 46 of the 47 mutations present in the tumor were identified in the cfDNA. Estimating from the average variant allele percentage of 3.8%, 7.5% of the cfDNA was derived from the tumor. B) Fifteen additional mutations were called in the cfDNA which were not called in the tumor sample. Four of these are present in the tumor, but below our calling cutoff of 10% for the tumor. Genes highlighted in red were successfully validated via sequencing on the Ion Torrent PGM. Approximately 4,000 genomes of cfDNA were used as input to the validations, giving us a lower sensitivity bound of 0.025–0.5% depending on the site-specific background error rate.