1. A B Supplementary Figure S1. T790M CTC PointMan genotyping assay. (A) Test characteristics of PointMan CTC T790M genotyping assay. The assay was validated using dilutions of the T790M allele derived from H1975 gDNA in a background of wild- type template derived from normal human peripheral blood leukocytes. Of 14 total wild-type control reactions, no false positives were observed. (B) Sample chromatogram of a T790M-positive CTC case.

2. Concurrent tumor biopsy genotyping +- CTC genotyping +55 -47 All tumor biopsy genotyping +- ctDNA genotyping +105 -79 CTC genotyping +- ctDNA genotyping +63 -59 All tumor biopsy genotyping +- CTC genotyping +112 -59 Percent agreement = 57% (95%CI: 34-78%) Kappa = 0.137 McNemar = 1.0 Percent agreement = 74% (95%CI: 54-89%) Kappa = 0.485 McNemar = 0.45 Percent agreement = 65% (95%CI: 43-84%) Kappa = 0.298 McNemar = 0.73 Percent agreement = 61% (95%CI: 42-78%) Kappa = 0.228 McNemar = 0.77 Concurrent tumor biopsy genotyping +- ctDNA genotyping +66 -49 Percent agreement = 60% (95%CI: 39-79%) Kappa = 0.194 McNemar = 0.75 All tumor biopsy genotyping +- CTC/ctDNA genotyping +176 -58 Percent agreement = 69% (95%CI: 52-84%) Kappa = 0.349 McNemar = 1.0 Supplementary Figure S2. T790M concordance by genotyping method.

3. Tumor biopsy Ex 19 deletions +- Plasma Ex 19 deletions +50 -28 Percent agreement = 87% (95%CI: 60-98%) Kappa = 0.727 McNemar = 0.50 Tumor biopsy L858R +- Plasma L858R +80 -122 Percent agreement = 97% (95%CI: 83-100%) Kappa = 0.919 McNemar = 1.0 Supplementary Figure S3. Concordance of L858R and Ex 19 deletion genotyping by ctDNA and tissue biopsy