1. Supplemental Figure 1 A B Alteration Time 1 (AF) Time 2 (AF)
EGFR L858R
5.3%
0.6%
18.1%
EGFR T790M
50.9%
49.2%
54.4%
EGFR C797S ND
1.3%
EGFR Q787Q
51.5%
48.7%
54.8%
TP53 P278R
3.8%
19.7%
Supplemental Figure 1: Case of advanced NSCLC with high level EGFR T790M mutation on plasma next-generation sequencing (NGS). (A) Initial plasma NGS detected EGFR L858R at 5.3% AF and T790M at 50.9% AF. Plasma NGS was repeated after progression on osimertinib, showing EGFR L858R at 0.6% AF and T790M at 49.2% AF. After further progression, repeat plasma NGS detected EGFR L858R at 18.1%, T790M at 54.4%, and a new EGFR C797S mutation at 1.3%. (B) AF plot of coding and noncoding variants detected at all three timepoints (AF of the TP53 mutation at time 2 imputed at 0%). The EGFR T790M mutation is seen within a band of variants that includes the common SNP (EGFR Q787Q), suspicious for an incidentally detected germline EGFR T790M.

2. Supplemental Figure 2 B A
Supplemental Figure 2: Distribution of variant AFs between 25% and 75% across 105 cases of plasma NGS. For both the (A) standard deviation and (B) mean, a normal curve can be fit with outliers evident. A B

3. Supplemental Figure 3
Supplemental Figure 3: Plasma NGS cases positive for EGFR T790M submitted for blinded validation. Among 11 cases (Cohort A) designated with low copy number variation and high AF of EGFR T790M (left), all 11 were confirmed to be germline (100% positive predictive value). Among 10 cases (Cohort B) with high copy number variation and high AF of EGFR T790M (right), one was positive for a germline T790M mutation.