Supplementary Materials and Methods; Supplementary Tables 1-3; Supplementary Figures 1-2 from BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System

Supplementary Table 1. Emergence of BRAF mutations in cfDNA; Supplementary Table 2. Patients with BRAF V600K mutations in FFPE tumor and plasma cfDNA samples; Supplementary Table 3. Experimental therapies in 34 patients with longitudinal collection of plasma cfDNA; Supplementary Figure 1. A. Among the 160 patients whose cfDNA samples were tested for BRAF mutations, the median overall survival duration of the 113 patients with a BRAF-mutant cfDNA percentage of 0% (10.0 months, 95% confidence interval [CI], 7.2-12.8 months; blue) was longer than that of the 47 patients with a BRAF-mutant cfDNA percentage of >0% (7.0 months, 95% CI, 2.5-11.5 months; red), but this difference was not significant (P=0.09). B. Among these same 160 patients, the median overall survival duration of the 126 patients with a BRAF-mutant cfDNA percentage of <1% (10.5 months, 95% CI, 8.4-12.6 months; blue) was significantly longer than that of the 34 patients with a BRAF-mutant cfDNA percentage of greater than or equal to 1%(5.5 months, 95% CI, 3.4-7.6 months; red; P=0.006). C. Among the 47 patients with cfDNA BRAF mutations, the median overall survival duration of the 21 patients with a BRAF-mutant cfDNA percentage of less than or equal to 2% (11.2 months, 95% CI, 10.4-12.0 months; blue) was longer than that of the 26 patients with a BRAF-mutant cfDNA percentage of >2% (4.4 months, 95% CI, 3.2-5.6 months; red), but this difference was not statistically significant (P=0.05). D. Among the 62 patients whose formalin-fixed paraffin-embedded tumor samples had BRAF mutations, the median overall survival duration of the 37 patients with a BRAF-mutant cfDNA percentage of less than or equal to 2% (14.6 months, 95% CI, 9.4-19.8 months; blue) was significantly longer than that of 25 patients with a BRAF-mutant cfDNA percentage of >2% (4.5 months, 95% CI, 3.0-6.0 months; P=0.001). Supplementary Figure 2. A. The median amount of cfDNA in plasma of the 160 patients whose cfDNA was tested for BRAF mutations was 60 ng/ml. The median overall survival duration of the 81 patients with a cfDNA amount in plasma less than or equal to 60 ng/ml (8.9 months, 95% confidence interval [CI], 4.8-13.0 months; blue)was similar to that of the 79 patients with a cfDNA amount in plasma >60 ng/ml (8.7 months, 95% CI, 5.2-12.2 months; red; P=0.91). B. The median cfDNA concentration of these same 160 patients was 4.6 ng/μl. The median overall survival duration of the 82 patients with a cfDNA concentration <5 ng/IJI (9.5 months, 95% Cl, 5.8-13.2 months; blue) was similar to that of the 78 patients with cfDNA concentrations 5 ng/ml (8.7 months, 95% Cl, 5.4-12.0 months; red), but this difference was not significant (P=0.89).