Clinical Implications of Plasma-Based Genotyping with the Delivery of Personalized Therapy in Metastatic Non–Small Cell Lung Cancer

Supplementary Online Content

Aggarwal C, Thompson JC, Black TA, et al. Clinical implications of plasma-based genotyping with the delivery of personalized therapy in metastatic non–small cell lung cancer. JAMA Oncology. Published online October 11, 2018. doi:10.1001/jamaoncol.2018.4305

eTable 1. Plasma-based Circulating Tumor DNA and Tissue Next-Generation Sequencing Gene Panels

eTable 2. Clinically Relevant and Therapeutically Targetable Mutations

eTable 3. Liquid Biopsy–Detected Mutations for the 323 Patients Enrolled in the Study

eTable 4. Patient Characteristics

eTable 5. Forty-two Patients Who Received Targeted Therapy Indicated by Plasma

eFigure 1. Analysis of Mutations Detected in Plasma and/or Tissue NGS

eFigure 2. Correlation of Tissue AF for the Targeted Mutation and Depth of RECIST Response to Targeted Therapy in 10 Patients with Tissue and Plasma Available

This supplementary material has been provided by the authors to give readers additional information about their work.

Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable 1. Plasma-based Circulating Tumor DNA and Tissue Next-Generation Sequencing Gene Panels

A. Guardant360 Panel (73 genes) SNVs AKT1 ALK APC AR ARAF ARID1A ATM BRAF BRCA1 BRCA2 CCDN1 CCDN2 CCNE1 CDH1 CDK4 CDK6 CDKN2A CTNNB1 DDR2 EGFR ERBB2 ESR1 EZH2 FBXW7 FGFR1 FGFR2 FGFR3 GATA3 GNA11 GNAQ GNAS HNF1A HRAS IDH1 IDH2 JAK2 JAK3 KIT KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 MET MLH1 MPL MTOR MYC NF1 NFE2L2 NOTCH1 NPM1 NRAS NTRK1 NTRK3 PDGFRA PIK3CA PTEN PTPN11 RAF1 RB1 RET RHEB RHOA RIT1 ROS1 SMAD4 SMO STK11 TERT TP53 TSC1 VHL Indels ATM APC ARID1A BRCA1 BRCA2 CDH1 CDKN2A EGFR ERBB2 GATA3 KIT MET MLH1 MTOR NF1 PDGFRA PTEN RB1 SMAD4 STK11 TP53 TSC1 VHL Fusions ALK FGFR2 FGFR3 NTRK1 RET ROS1 B. Center for Personalized Diagnostics Panel v.2.0 (153 genes) –used as of 9/12/2016a ABL1 AKT1 AKT2 AKT3 ALK APC AR ARAF ARID1A ARID2 ATM ATRX AURKA BAP1 BRAF BRCA1 BRCA2 BRIP BTK CBP CCND1 CCND2 CCND3 CCNE1 CDH1 CDK4 CDK6 CDKN2A CHEK2 CIC CRKL CSF1R CTNNB1 DAXX DDR2 DNMT3A EGFR EIF1Ax EPHA3 ERBB2 ERBB3 ERBB4 ERCC2 ERG ESR1 ESR2 EZH2 FBXW7 FGF3 FGFR1 FGFR2 FGFR3 FGFR4 FLT3 FUBP1 GATA3 GNA11 GNAQ GNAS HRAS H3F3A IDH1 IDH2 IGF1R JAK1 JAK2 JAK3 KDM5A KDM5C KDM6A KDR KIT KMT2C KRAS MAP2K1 MAP2K2 MAP2K4 MAPK1 MAPK3 MAX MCL1 MDM2 MDM4 MED12 MEN1 MET MITF MLH1 MRE11A MSH2 MSH6 MTOR MYC MYCN NBN NF1 NF2 NTRK1 NTRK2 NTRK3 NKX2‐1 NOTCH1 NOTCH2 NOTCH3 NRAS EP300 PAK1 PALB2 PBRM1 PDGFRA PIK3CA PIKC3B PIK3R1 PTCH1 PTEN PTPN11 RAB35 RAC1 RAD50 RAD51 RAD51B RAD51C RAD51D RAF1 RB1 RET RHOA RNF43 SETD2 SF3B1 SLIT2 SMAD4 SMARCA4 SMO SPOP SRC STAG2 STK11 SUFU SUZ12 SYK TERT TET2 TGFBR2 TP53 TRAF7 TSC1 TSC2 TSHR U2AF1 VHL WT1 XRCC2 C. Penn Precision Panel (20 genes) AKT1 ALK BRAF CSF1R EGFR ERBB2 HRAS IDH1 IDH2 KIT KRAS MAP2K1 MET NOTCH1 NRAS PDGFRA PIK3CA PTEN RET TP53 aBolded: genes present in CPD Panel v.1.0 (47 genes) used prior to 9/12/2016. The following genes were present in CPD Panel v.1.0 but not v.2.0: HNF1A, MPL, NPM1, SMARCB1, STK.

Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable 2. Clinically Relevant and Therapeutically Targetable Mutations

Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable 3. Liquid Biopsy–Detected Mutations for the 323 Patients Enrolled in the Study

Patient Histology Gene Variant MAF Clonality Clonality ID calculation 00001 N ALK‐EML4 Fusion 0.20 1.00 clonal 00001 N CTNNB1 S45P 0.10 0.50 clonal 00002 N TP53 I254T 0.80 1.00 clonal 00002 N TP53 P177H 0.20 0.25 clonal 00008 N PTPN11 Q510H 1.50 1.00 clonal 00008 N KRAS G12V 0.20 0.13 subclonal 00009 N EGFR Exon19del 37.20 1.00 clonal 00009 N EGFR T790M 29.90 0.80 clonal 00009 N TP53 C182* 23.40 0.63 clonal 00009 N AR E213K 6.10 0.16 subclonal 00009 N BRCA1 T164A 3.80 0.10 subclonal 00012 N KRAS G13C 2.50 1.00 clonal 00012 N EGFR G197G 0.80 0.32 clonal 00012 N MET P1171L 0.80 0.32 clonal 00012 N RB1 I103I 0.70 0.28 clonal 00012 N RB1 I101I 0.60 0.24 clonal 00012 N CDKN2B R105Q 0.20 0.08 subclonal 00014 N EGFR T790M 1.50 1.00 clonal 00014 N EGFR Exon19del 1.00 0.67 clonal 00021 N PIK3CA V850G 0.50 1.00 clonal 00021 N RET V650M 0.30 0.60 clonal 00022 N TP53 H179Y 3.70 1.00 clonal 00022 N RB1 K94* 0.90 0.24 clonal 00022 N PIK3CA E545K 0.90 0.24 clonal 00022 N TP53 R196* 0.70 0.19 subclonal 00022 N EGFR Exon19del 0.50 0.14 subclonal 00022 N FGFR1 G697G 0.30 0.08 subclonal 00026 N NF1 R897Q 0.40 1.00 clonal 00027 N RB1 E748* 16.50 1.00 clonal 00027 N EGFR L858R 13.00 0.79 clonal 00027 N TP53 R213* 8.90 0.54 clonal 00027 N PTEN Q17* 6.10 0.37 clonal 00027 N APC D2663V 1.60 0.10 subclonal 00027 N EGFR T790M 1.30 0.08 subclonal 00027 N NOTCH1 A1650A 0.20 0.01 subclonal 00027 N AR E213K 0.20 0.01 subclonal 00027 N FGFR2 L258L 0.20 0.01 subclonal 00027 N NF1 L847P 0.20 0.01 subclonal 00031 N EGFR E709A 4.90 1.00 clonal 00031 N EGFR G719A 4.80 0.98 clonal 00031 N CTNNB1 S37F 1.00 0.20 clonal 00031 N NOTCH1 Q2416P 0.30 0.06 subclonal 00031 N ARID1A Q520P 0.30 0.06 subclonal 00031 N TP53 R248Q 0.2 0.04 subclonal

Downloaded From: https://jamanetwork.com/ on 10/01/2021 00031 N TP53 M246L 0.2 0.04 subclonal 00031 N TP53 R65fs 0.05 0.01 subclonal 00033 N TP53 Y220* 32.30 1.00 clonal 00033 N TP53 H193R 0.20 0.01 subclonal 00034 N TP53 N210K 9.90 1.00 clonal 00034 N TP53 F212F 9.90 1.00 clonal 00034 N TP53 T211I 9.80 0.99 clonal 00034 N EGFR L858R 9.60 0.97 clonal 00034 N MET E1390K 2.70 0.27 clonal 00034 N TP53 R273C 0.30 0.03 subclonal 00034 N TP53 C275Y 0.20 0.02 subclonal 00034 N BRAF D118D 0.20 0.02 subclonal 00034 N NTRK1 T470K 0.20 0.02 subclonal 00034 N HNF1A R263C 0.20 0.02 subclonal 00034 N NF1 R2450* 0.10 0.01 subclonal 00035 N TP53 G262V 5.60 1.00 clonal 00035 N KRAS G12D 2.80 0.50 clonal 00036 N ERBB2 Q178Q 1.00 1.00 clonal 00036 N AR A403V 0.20 0.20 clonal 00036 N EGFR L858R 0.10 0.10 subclonal 00038 N EGFR Exon19del 4.90 1.00 clonal 00038 N TP53 Q136* 1.90 0.39 clonal 00038 N EGFR T790M 1.60 0.33 clonal 00038 N NF1 M1409T 1.10 0.22 clonal 00038 N ERBB2 R351* 0.10 0.02 subclonal 00041 N N/A WT Report WT Report 00042 N TERT L38L 0.60 1.00 clonal 00043 N RB1 C278S 0.70 1.00 clonal 00043 N EGFR Exon19del 0.20 0.29 clonal 00043 N EGFR T790M 0.20 0.29 clonal 00043 N EGFR P644P 0.10 0.14 subclonal 00044 N ROS1 A1832T 2.60 1.00 clonal 00044 N TP53 R248Q 2.50 0.96 clonal 00044 N NF1 T2741T 0.20 0.08 subclonal 00044 N ARID1A D2229N 0.10 0.04 subclonal 00046 N TP53 P278A 1.80 1.00 clonal 00046 N TP53 R249S 1.40 0.78 clonal 00046 N TP53 R158L 0.30 0.17 subclonal 00046 N MET T67T 0.30 0.17 subclonal 00047 N CDKN2A S12L 0.50 1.00 clonal 00047 N KRAS G12C 0.40 0.80 clonal 00047 N PDGFRA R376Q 0.10 0.20 clonal 00050 N N/A WT Report WT Report 00051 N JAK2 V617F 0.60 1.00 clonal 00051 N ATM V3032E 0.40 0.67 clonal 00053 N ALK R1120W 0.10 1.00 clonal 00054 N N/A WT Report WT Report 00056 N PDGFRA D154N 0.20 1.00 clonal

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00057 N EGFR L858R 6.50 1.00 clonal 00057 N TP53 Q144P 2.30 0.35 clonal 00057 N AR R841G 2.00 0.31 clonal 00057 N CCND1 M113I 0.10 0.02 subclonal 00059 N TP53 Y163C 2.80 1.00 clonal 00059 N EGFR Exon19del 2.20 0.79 clonal 00059 N CDKN2A P48L 2.20 0.79 clonal 00060 N APC R2505Q 0.20 1.00 clonal 00060 N AR M750V 0.20 1.00 clonal 00067 N TP53 R273H 0.50 1.00 clonal 00067 N PIK3CA G106V 0.50 1.00 clonal 00068 N STK11 K44* 4.70 1.00 clonal 00068 N FGFR1 T82T 2.90 0.62 clonal 00069 N N/A WT Report WT Report 00074 N DDR2 R806* 0.40 1.00 clonal 00074 N EGFR Exon19del 0.20 0.50 clonal 00076 N ALK‐EML4 Fusion 0.10 1.00 clonal 00076 N EML4‐ALK Fusion 0.10 1.00 clonal 00077 S GNAS R201H 17.00 1.00 clonal 00077 S TP53 D259Y 14.10 0.83 clonal 00077 S CDKN2A D84Y 4.20 0.25 clonal 00077 S ARID1A T238P 0.70 0.04 subclonal 00077 S ERBB2 C584G 0.40 0.02 subclonal 00077 S TERT L681R 0.30 0.02 subclonal 00077 S ERBB2 V697G 0.20 0.01 subclonal 00078 N N/A WT Report WT Report 00081 N NF1 Exon32del 3.30 1.00 clonal 00081 N EGFR L858R 2.40 0.73 clonal 00081 N MET V854I 0.30 0.09 subclonal 00081 N MET R191Q 0.10 0.03 subclonal 00083 N EGFR L858R 21.10 1.00 clonal 00083 N EGFR T790M 4.70 0.22 clonal 00084 N N/A WT Report WT Report 00085 S ALK I1171I 0.90 1.00 clonal 00085 S GNAS R201C 0.90 1.00 clonal 00085 S ARID1A Q507* 0.70 0.78 clonal 00085 S NRAS G12A 0.60 0.67 clonal 00085 S MET E924K 0.30 0.33 clonal 00086 N TP53 H179Q 0.10 1.00 clonal 00087 N EGFR Exon19del 6.90 1.00 clonal 00087 N TP53 R273C 3.10 0.45 clonal 00087 N KIT G663R 1.20 0.17 subclonal 00087 N ARID1A R1656R 0.40 0.06 subclonal 00087 N EGFR L12R 0.30 0.04 subclonal 00087 N ERBB2 V314I 0.10 0.01 subclonal 00087 N FGFR2 K505* 0.10 0.01 subclonal 00089 N NF1 E1787* 6.80 1.00 clonal 00089 N TP53 Y205C 0.20 0.03 subclonal

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00091 N N/A WT Report WT Report 00092 N EGFR L858R 15.10 1.00 clonal 00092 N PDGFRA Y225C 0.60 0.04 subclonal 00094 S CCDC6‐RET Fusion 9.40 1.00 clonal 00094 S RET‐CCDC6 Fusion 7.70 0.82 clonal 00094 S RB1 H483H 4.50 0.48 clonal 00094 S PTEN T277K 2.90 0.31 clonal 00094 S CDKN2A G23G 0.80 0.09 subclonal 00096 N TP53 R175H 0.10 1.00 clonal 00098 N N/A WT Report WT Report 00100 N EGFR R334H 0.40 1.00 clonal 00101 N EGFR L858R 1.00 1.00 clonal 00101 N ALK I1522T 0.70 0.70 clonal 00101 N EGFR E709A 0.60 0.60 clonal 00101 N TP53 G244S 0.30 0.30 clonal 00101 N PIK3CA H1047R 0.20 0.20 clonal 00106 N EGFR R108K 6.10 1.00 clonal 00106 N EGFR G719S 5.00 0.82 clonal 00106 N TP53 N239S 2.20 0.36 clonal 00106 N PIK3CA E545K 1.80 0.30 clonal 00106 N FGFR2 R203C 0.80 0.13 subclonal 00107 N BRAF E24A 0.50 1.00 clonal 00107 N TP53 C238Y 0.10 0.20 clonal 00109 N STK11 E351K 0.20 1.00 clonal 00109 N ERBB2 R143Q 0.20 1.00 clonal 00111 N BRCA1 E597K 0.20 1.00 clonal 00112 N SMO G212C 1.70 1.00 clonal 00112 N FGFR2 P508L 0.20 0.12 subclonal 00113 N ATM E3007D 7.50 1.00 clonal 00113 N CTNNB1 S45P 0.40 0.05 subclonal 00113 N EGFR L858R 0.40 0.05 subclonal 00113 N EGFR T790M 0.30 0.04 subclonal 00113 N STK11 D284A 0.20 0.03 subclonal 00113 N RB1 S919R 0.10 0.01 subclonal 00116 N TP53 R282W 3.50 1.00 clonal 00116 N EGFR Exon19del 2.20 0.63 clonal 00118 N N/A WT Report WT Report 00120 N EGFR N1094T 0.20 1.00 clonal 00120 N TP53 G105V 0.20 1.00 clonal 00120 N ARID1A Q840* 0.20 1.00 clonal 00121 N PIK3CA E545K 1.60 1.00 clonal 00121 N KRAS G12R 0.80 0.50 clonal 00121 N CCND1 A16V 0.40 0.25 clonal 00122 N N/A WT Report WT Report 00123 N EGFR Exon19del 9.70 1.00 clonal 00123 N EGFR C797S 6.90 0.71 clonal 00123 N EGFR T790M 3.80 0.39 clonal 00123 N TP53 R175G 0.40 0.04 subclonal

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00123 N TP53 R175H 0.10 0.01 subclonal 00123 N EGFR I462T 0.10 0.01 subclonal 00123 N EGFR C797S 0.05 0.01 subclonal 00125 N N/A WT Report WT Report 00127 N TP53 C176F 3.50 1.00 clonal 00127 N STK11 E199* 2.40 0.69 clonal 00127 N KRAS G12D 1.30 0.37 clonal 00127 N PTPN11 D94N 0.60 0.17 subclonal 00127 N NF1 N2659S 0.20 0.06 subclonal 00127 N CCND1 D25A 0.20 0.06 subclonal 00130 N GNAS R201H 22.70 1.00 clonal 00131 N EGFR Exon20ins 0.10 1.00 clonal 00132 N EGFR L858R 0.50 1.00 clonal 00134 N AR N235K 1.30 1.00 clonal 00134 N KRAS G12C 1.20 0.92 clonal 00134 N APC E2428V 0.60 0.46 clonal 00134 N EGFR S186R 0.20 0.15 subclonal 00134 N RET D631N 0.10 0.08 subclonal 00136 N EGFR L858R 0.80 1.00 clonal 00136 N TP53 E294* 0.40 0.50 clonal 00136 N ARID1A R2233Q 0.20 0.25 clonal 00136 N TP53 R267W 0.10 0.13 subclonal 00137 N EGFR L858R 55.50 1.00 clonal 00137 N TP53 L257P 7.20 0.13 subclonal 00137 N EGFR Q40Q 1.50 0.03 subclonal 00137 N TP53 S241C 0.30 0.01 subclonal 00138 N TP53 R249K 1.40 1.00 clonal 00138 N KRAS G12A 1.10 0.79 clonal 00138 N CDKN2A Q50H 0.50 0.36 clonal 00140 N N/A WT Report WT Report 00141 N N/A WT Report WT Report 00143 N TP53 R282W 0.50 1.00 clonal 00143 N CCND2 M81V 0.50 1.00 clonal 00144 S KRAS G12C 29.90 1.00 clonal 00144 S CCNE1 V37F 0.40 0.01 subclonal 00147 N MYC L114R 0.90 0.03 subclonal 00147 N KIT N400S 0.70 0.02 subclonal 00147 N EGFR L11R 0.50 0.02 subclonal 00147 N CCND1 L254R 0.30 0.01 subclonal 00149 N IDH2 R140Q 0.20 1.00 clonal 00149 N TP53 P153P 0.10 0.50 clonal 00152 N AR R608Q 0.20 1.00 clonal 00152 N PTEN E256K 0.20 1.00 clonal 00152 N NOTCH1 I2109I 0.20 1.00 clonal 00152 N BRCA1 S784L 0.10 0.50 clonal 00152 N MET R417* 0.10 0.50 clonal 00152 N CCNE1 S302L 0.10 0.50 clonal 00152 N NF1 R440Q 0.10 0.50 clonal

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00153 N TP53 R248W 12.60 1.00 clonal 00153 N KRAS Q61H 9.80 0.78 clonal 00153 N EGFR V599V 9.30 0.74 clonal 00153 N PTEN R234L 5.60 0.44 clonal 00154 N N/A WT Report WT Report 00157 N KRAS G12C 1.20 1.00 clonal 00157 N CDKN2A A76S 1.00 0.83 clonal 00157 N TP53 R273L 0.70 0.58 clonal 00158 N EGFR L858R 0.30 1.00 clonal 00159 S PTEN R233* 3.80 1.00 clonal 00159 S EGFR L858R 3.80 1.00 clonal 00159 S EGFR L62R 3.60 0.95 clonal 00159 S MLH1 S368L 0.40 0.11 subclonal 00159 S ARID1A S1623L 0.20 0.05 subclonal 00159 S FGFR1 E294K 0.20 0.05 subclonal 00159 S PIK3CA R108H 0.20 0.05 subclonal 00159 S STK11 E357K 0.10 0.03 subclonal 00159 S RET E623K 0.10 0.03 subclonal 00160 N TP53 R282W 22.50 1.00 clonal 00160 N CCND1 V27V 2.80 0.12 subclonal 00160 N ERBB2 P391P 2.60 0.12 subclonal 00160 N TP53 R273H 0.50 0.02 subclonal 00160 N TP53 C176Y 0.30 0.01 subclonal 00160 N ATM K2717T 0.20 0.01 subclonal 00160 N BRCA1 A675A 0.10 0.00 subclonal 00160 N PDGFRA I497I 0.10 0.00 subclonal 00160 N MET R413C 0.10 0.00 subclonal 00161 N TP53 R175H 4.20 1.00 clonal 00161 N EGFR Exon19del 1.60 0.38 clonal 00163 N N/A WT Report WT Report 00164 N TP53 S241F 2.80 1.00 clonal 00164 N EGFR Exon19del 1.90 0.68 clonal 00164 N NF1 I1845S 0.90 0.32 clonal 00166 N EGFR Exon19del 30.20 1.00 clonal 00166 N TP53 R337C 7.10 0.24 clonal 00166 N EGFR T790M 3.00 0.10 subclonal 00169 N TP53 R213* 0.20 1.00 clonal 00170 N TP53 R267W 20.00 1.00 clonal 00170 N GNAS R201S 0.70 0.04 subclonal 00170 N NFE2L2 R43Q 0.20 0.01 subclonal 00171 N N/A WT Report WT Report 00173 N KRAS G12C 11.90 1.00 clonal 00173 N CDK6 V234L 8.10 0.68 clonal 00173 N CDK4 G300A 5.80 0.49 clonal 00173 N CDK4 G247A 5.20 0.44 clonal 00173 N KIT T385T 1.73 0.15 subclonal 00176 N TP53 P151T 1.20 1.00 clonal 00177 N TP53 D281N 35.60 1.00 clonal

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00177 N EGFR L858R 25.30 0.71 clonal 00177 N EGFR T790M 10.40 0.29 clonal 00177 N ERBB2 M833I 2.10 0.06 subclonal 00177 N PDGFRA R981H 0.10 0.00 subclonal 00178 N EGFR Exon19del 65.70 1.00 clonal 00179 N EGFR L858R 6.90 1.00 clonal 00179 N TP53 P278S 2.70 0.39 clonal 00179 N PIK3CA H1047R 2.50 0.36 clonal 00179 N ARID1A Q393* 0.20 0.03 subclonal 00179 N FGFR3 F767F 0.10 0.01 subclonal 00180 N KRAS G12C 5.60 1.00 clonal 00180 N TP53 E287* 4.20 0.75 clonal 00180 N KIT N370S 3.80 0.68 clonal 00180 N JAK2 V617F 0.20 0.04 subclonal 00182 N EGFR L858R 33.40 1.00 clonal 00182 N CTNNB1 S33F 0.20 0.01 subclonal 00184 N N/A WT Report WT Report 00186 N NRAS Q61R 0.70 1.00 clonal 00186 N TP53 V218G 0.30 0.43 clonal 00186 N TP53 R158H 0.20 0.29 clonal 00187 N ARID1A Q1095* 6.50 1.00 clonal 00187 N EGFR T790M 0.90 0.14 subclonal 00187 N APC N1953N 0.30 0.05 subclonal 00187 N NF1 K2265K 0.30 0.05 subclonal 00187 N EGFR R149W 0.10 0.02 subclonal 00188 N EGFR L858R 0.20 1.00 clonal 00188 N PIK3CA E545K 0.20 1.00 clonal 00190 N ERBB2 Exon20ins 3.80 1.00 clonal 00190 N GNAS R201H 0.20 0.05 subclonal 00190 N GNAS R201G 0.10 0.03 subclonal 00192 N GNAQ T224T 3.50 1.00 clonal 00194 N CDKN2A Q50H 2.40 1.00 clonal 00194 N TP53 P177S 2.20 0.92 clonal 00194 N TP53 M246I 2.10 0.88 clonal 00194 N STK11 E199* 2.10 0.88 clonal 00194 N NF1 Q2434R 2.00 0.83 clonal 00194 N TP53 G105C 1.90 0.79 clonal 00194 N CCNE1 P407P 1.90 0.79 clonal 00194 N APC R1105Q 1.80 0.75 clonal 00194 N BRCA1 R979L 1.70 0.71 clonal 00194 N KIT A7A 1.70 0.71 clonal 00194 N SMO R628L 1.50 0.63 clonal 00194 N ARAF P216P 1.40 0.58 clonal 00194 N NF1 G629A 1.20 0.50 clonal 00194 N NF1 L1659L 0.30 0.13 subclonal 00195 N ATM N3003S 0.50 1.00 clonal 00195 N TP53 Y220C 0.20 0.40 clonal 00196 N PTEN Y225S 2.00 1.00 clonal

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00196 N FGFR3 T753T 2.00 1.00 clonal 00196 N FGFR2 L306L 2.00 1.00 clonal 00196 N MYC E162E 1.80 0.90 clonal 00197 N EGFR R831S 5.40 1.00 clonal 00197 N KRAS G12A 3.30 0.61 clonal 00198 N BRAF G469V 2.60 1.00 clonal 00198 N STK11 D194Y 1.60 0.62 clonal 00199 S BRAF G469A 0.40 1.00 clonal 00199 S TP53 I195T 0.20 0.50 clonal 00199 S BRCA1 L358L 0.20 0.50 clonal 00200 N MET R412C 0.20 1.00 clonal 00201 N RB1 A22A 1.20 1.00 clonal 00201 N ARID1A Q766P 0.80 0.67 clonal 00202 N TP53 P177H 1.50 1.00 clonal 00202 N TP53 Y220C 0.50 0.33 clonal 00202 N TP53 C176W 0.10 0.07 subclonal 00202 N EGFR P644P 0.10 0.07 subclonal 00203 N EGFR T790M 22.20 1.00 clonal 00203 N EGFR Exon19del 20.80 0.94 clonal 00203 N PTEN F154L 0.80 0.04 subclonal 00204 N EGFR Exon19del 2.50 1.00 clonal 00204 N EGFR T790M 1.70 0.68 clonal 00204 N CCNE1 F307F 0.70 0.28 clonal 00205 N ARAF E195A 0.60 1.00 clonal 00205 N ARID1A R693R 0.50 0.83 clonal 00205 N ARID1A Q1584* 0.30 0.50 clonal 00205 N FGFR2 D304N 0.30 0.50 clonal 00205 N NOTCH1 E159K 0.20 0.33 clonal 00205 N KIT R830* 0.20 0.33 clonal 00205 N APC E1317G 0.20 0.33 clonal 00206 N PIK3CA E453K 12.10 1.00 clonal 00206 N TP53 F113S 6.50 0.54 clonal 00206 N EGFR Exon19del 5.00 0.41 clonal 00207 N GNAQ E245Q 19.60 1.00 clonal 00207 N CDKN2A P81R 19.40 0.99 clonal 00207 N CDKN2A G89G 19.00 0.97 clonal 00207 N TP53 E298* 18.00 0.92 clonal 00207 N SMAD4 D493H 16.30 0.83 clonal 00207 N CTNNB1 S37C 8.80 0.45 clonal 00207 N EGFR R889K 8.10 0.41 clonal 00207 N AR E187K 0.20 0.01 subclonal 00207 N CCND2 L118L 0.10 0.01 subclonal 00208 N KRAS G12C 27.70 1.00 clonal 00208 N KRAS A11A 27.50 0.99 clonal 00208 N STK11 Q170* 26.40 0.95 clonal 00208 N RET F924L 18.30 0.66 clonal 00208 N MYC E424Q 17.90 0.65 clonal 00209 N BRAF E26A 1.40 1.00 clonal

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00209 N NF1 K936* 0.50 0.36 clonal 00209 N MYC D173A 0.40 0.29 clonal 00209 N NF1 Y1625C 0.40 0.29 clonal 00209 N CCNE1 R3R 0.40 0.29 clonal 00209 N FGFR3 E768A 0.30 0.21 clonal 00209 N TP53 A161S 0.30 0.21 clonal 00209 N NOTCH1 L1559R 0.20 0.14 subclonal 00209 N RAF1 P235T 0.20 0.14 subclonal 00210 N TP53 R175H 0.70 1.00 clonal 00210 N TP53 R248G 0.20 0.29 clonal 00210 N EGFR E736K 0.20 0.29 clonal 00211 N EGFR Exon19del 27.70 1.00 clonal 00211 N PIK3CA E542K 0.90 0.03 subclonal 00211 N EGFR T790M 0.30 0.01 subclonal 00211 N NF1 S1150* 0.20 0.01 subclonal 00211 N CDKN2A E26E 0.20 0.01 subclonal 00212 N GNAS R201C 0.50 1.00 clonal 00212 N NF1 R1534* 0.40 0.80 clonal 00212 N KRAS A146V 0.40 0.80 clonal 00212 N SMAD4 Q442L 0.30 0.60 clonal 00213 N ERBB2 R340Q 0.10 1.00 clonal 00214 N IDH1 R132L 4.40 1.00 clonal 00214 N TP53 V216M 3.00 0.68 clonal 00214 N BRAF G464V 2.60 0.59 clonal 00214 N NF1 L2232P 2.20 0.50 clonal 00214 N CDKN2A A85D 1.80 0.41 clonal 00214 N NRAS Q61L 1.80 0.41 clonal 00214 N NF1 Q1987Q 0.10 0.02 subclonal 00215 N N/A WT Report WT Report 00216 N TP53 G154V 18.60 1.00 clonal 00216 N VHL S65A 0.70 0.04 subclonal 00216 N NF1 V2839M 0.20 0.01 subclonal 00217 N NOTCH1 Q2376R 1.10 1.00 clonal 00217 N APC E763* 0.20 0.18 subclonal 00217 N ERBB2 L1017R 0.20 0.18 subclonal 00218 N BRCA2 Q3126R 0.20 1.00 clonal 00219 N NF1 P2516A 6.00 1.00 clonal 00220 N TP53 Y126N 0.50 1.00 clonal 00220 N KRAS Q61H 0.50 1.00 clonal 00220 N TP53 C277Y 0.30 0.60 clonal 00220 N AKT1 G162G 0.30 0.60 clonal 00220 N DDR2 E779V 0.20 0.40 clonal 00220 N TP53 T211I 0.10 0.20 clonal 00221 N KRAS G12C 1.50 1.00 clonal 00221 N TP53 E286* 1.40 0.93 clonal 00221 N APC K2445R 0.60 0.40 clonal 00222 N EGFR L858R 0.30 1.00 clonal 00222 N TP53 H214R 0.20 0.67 clonal

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00222 N EGFR T790M 0.20 0.67 clonal 00223 N EGFR L858R 1.10 1.00 clonal 00223 N ALK G1133S 0.20 0.18 subclonal 00223 N EGFR T354M 0.20 0.18 subclonal 00223 N FGFR2 Y91Y 0.10 0.09 subclonal 00224 N EGFR Exon19del 4.10 1.00 clonal 00224 N TP53 F341Y 3.50 0.85 clonal 00224 N AR G373G 0.50 0.12 subclonal 00224 N NOTCH1 S1541R 0.30 0.07 subclonal 00224 N CDKN2A E88A 0.10 0.02 subclonal 00224 N APC K1437* 0.10 0.02 subclonal 00225 N AR Q114Q 0.30 1.00 clonal 00225 N PIK3CA D915N 0.10 0.33 clonal 00226 N EGFR G1161C 0.70 1.00 clonal 00226 N EGFR Exon20ins 0.50 0.71 clonal 00226 N APC S2607S 0.20 0.29 clonal 00227 N ALK G1123S 0.20 1.00 clonal 00228 N RB1 W78* 52.00 1.00 clonal 00228 N ERBB2 Exon20ins 47.90 0.92 clonal 00228 N RB1 K715K 0.40 0.01 subclonal 00228 N PTPN11 I54I 0.20 0.00 subclonal 00229 N KRAS G12C 5.20 1.00 clonal 00229 N NF1 L2766L 3.20 0.62 clonal 00229 N TP53 A138V 2.60 0.50 clonal 00229 N BRCA2 D191H 0.40 0.08 subclonal 00229 N ARID1A A2110A 0.10 0.02 subclonal 00230 N KRAS G12C 11.00 1.00 clonal 00230 N TP53 E271K 6.60 0.60 clonal 00230 N ROS1 C1811W 2.80 0.25 clonal 00230 N GATA3 P394P 1.80 0.16 subclonal 00230 N BRCA1 S1101N 0.20 0.02 subclonal 00231 N MET V892L 0.40 1.00 clonal 00232 N EGFR A647T 0.40 1.00 clonal 00233 N TP53 R158C 0.40 1.00 clonal 00233 N BRAF V600E 0.30 0.75 clonal 00234 N BRAF E26A 3.00 1.00 clonal 00234 N BRCA1 E1250K 1.00 0.33 clonal 00234 N BRAF S37A 0.70 0.23 clonal 00234 N EGFR P518L 0.40 0.13 subclonal 00235 N NF1 Exon53del 1.30 1.00 clonal 00237 N TP53 V272M 1.50 1.00 clonal 00237 N RAF1 T260K 0.80 0.53 clonal 00239 N N/A WT Report WT Report 00240 N TP53 F113V 0.40 1.00 clonal 00240 N FGFR2 G182R 0.20 0.50 clonal 00241 N KRAS G12C 1.70 1.00 clonal 00241 N FGFR2 R111G 0.30 0.18 subclonal 00241 N PIK3CA R140* 0.10 0.06 subclonal

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00243 N N/A WT Report WT Report 00244 N EGFR L858R 10.20 1.00 clonal 00244 N TP53 R175H 3.50 0.34 clonal 00244 N APC T1556fs 2.00 0.20 clonal 00244 N EGFR T790M 1.60 0.16 subclonal 00245 N TP53 H193P 17.70 1.00 clonal 00245 N CTNNB1 V22L 14.70 0.83 clonal 00245 N MET T579S 14.30 0.81 clonal 00245 N EGFR E245D 8.30 0.47 clonal 00245 N CDKN2A L45F 7.40 0.42 clonal 00245 N PIK3CA E149K 0.30 0.02 subclonal 00246 N STK11 Exon5del 17.20 1.00 clonal 00246 N NRAS Q61K 12.00 0.70 clonal 00246 N TP53 L26I 10.10 0.59 clonal 00246 N JAK2 V617F 2.00 0.12 subclonal 00246 N KRAS Q61H 0.20 0.01 subclonal 00247 N FGFR2 P508S 0.80 1.00 clonal 00248 N EGFR Exon19del 0.90 1.00 clonal 00248 N EGFR T790M 0.60 0.67 clonal 00248 N TP53 K132R 0.30 0.33 clonal 00248 N CDKN2A Exon1ins 0.20 0.22 clonal 00249 N NF1 R1412K 2.50 1.00 clonal 00249 N TP53 R213* 2.10 0.84 clonal 00249 N NF1 R1612S 1.80 0.72 clonal 00249 N EGFR S1042R 0.50 0.20 clonal 00249 N KIT N130N 0.30 0.12 subclonal 00249 N KRAS R135K 0.20 0.08 subclonal 00250 N STK11 Y60* 0.40 1.00 clonal 00250 N BRAF M23V 0.40 1.00 clonal 00250 N ALK G1202G 0.20 0.50 clonal 00251 N N/A WT Report WT Report 00252 N EGFR S768I 2.30 1.00 clonal 00252 N EGFR G719C 2.20 0.96 clonal 00252 N CDK6 R214L 1.80 0.78 clonal 00252 N BRCA1 V1181I 1.10 0.48 clonal 00252 N TP53 Y220C 0.30 0.13 subclonal 00253 N EGFR T790M 1.50 1.00 clonal 00253 N EGFR L858R 0.90 0.60 clonal 00253 N EGFR C797S 0.90 0.60 clonal 00254 N TP53 Q136* 0.30 1.00 clonal 00254 N KRAS G12C 0.20 0.67 clonal 00255 N TERT Q73P 13.80 1.00 clonal 00255 N EGFR Exon19del 6.00 0.43 clonal 00255 N SMAD4 Exon9del 3.30 0.24 clonal 00255 N CTNNB1 S33C 2.70 0.20 clonal 00255 N MYC S265R 2.70 0.20 clonal 00255 N TP53 L93R 1.30 0.09 subclonal 00255 N CCND1 D25A 1.10 0.08 subclonal

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00255 N EGFR A310T 0.09 0.01 subclonal 00256 N TP53 Exon11del 48.10 1.00 clonal 00257 N KRAS G12C 8.70 1.00 clonal 00257 N TP53 R273C 3.60 0.41 clonal 00257 N TP53 C176Y 1.80 0.21 clonal 00257 N PIK3CA E542K 1.10 0.13 subclonal 00257 N MAP2K1 K57N 1.10 0.13 subclonal 00257 N APC Exon10del 0.90 0.10 subclonal 00257 N PDGFRA H116Q 0.70 0.08 subclonal 00257 N MYC A454A 0.70 0.08 subclonal 00257 N FGFR2 P413P 0.30 0.03 subclonal 00258 N EGFR Exon19del 6.00 1.00 clonal 00258 N TP53 T284P 4.10 0.68 clonal 00258 N RB1 Splice Site SNV 3.90 0.65 clonal 00259 N EGFR L858R 0.50 1.00 clonal 00259 N FGFR2 A284G 0.20 0.40 clonal 00260 N KRAS G12V 0.40 1.00 clonal 00260 N MAP2K1 P124Q 0.30 0.75 clonal 00261 N N/A WT Report WT Report 00262 N EGFR L858R 0.50 1.00 clonal 00263 N ALK I1171S 3.20 1.00 clonal 00263 N ALK F1174L 0.10 0.03 subclonal 00264 N KRAS G12V 0.50 1.00 clonal 00264 N STK11 E256* 0.30 0.60 clonal 00264 N AR Q405Q 0.30 0.60 clonal 00264 N TP53 I195T 0.10 0.20 clonal 00264 N ERBB2 R1230W 0.10 0.20 clonal 00265 N KRAS G12V 45.50 1.00 clonal 00265 N DDR2 N615K 5.30 0.12 subclonal 00265 N EGFR R252C 4.90 0.11 subclonal 00266 N EGFR Exon19del 1.70 1.00 clonal 00266 N RB1 Exon1del 1.30 0.76 clonal 00266 N TP53 Exon8ins 1.10 0.65 clonal 00266 N PDGFRA R718Q 0.60 0.35 clonal 00267 N TP53 I195T 3.20 1.00 clonal 00267 N NF1 W837* 2.80 0.88 clonal 00267 N EGFR L858R 2.50 0.78 clonal 00267 N TERT Promoter SNV 0.50 0.16 subclonal 00267 N NTRK1 Q660Q 0.50 0.16 subclonal 00267 N AR H664R 0.30 0.09 subclonal 00267 N BRCA2 L639L 0.30 0.09 subclonal 00267 N PDGFRA A978T 0.30 0.09 subclonal 00267 N ARID1A Q393* 0.20 0.06 subclonal 00267 N KIT I54M 0.20 0.06 subclonal 00268 N EGFR Exon19del 0.80 1.00 clonal 00268 N EGFR T790M 0.40 0.50 clonal 00268 N TP53 R273H 0.30 0.38 clonal 00268 N TP53 C277F 0.20 0.25 clonal

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00268 N TP53 S241F 0.20 0.25 clonal 00269 N TP53 Q192* 0.50 1.00 clonal 00269 N EGFR Exon19del 0.50 1.00 clonal 00270 N KRAS G12C 0.10 1.00 clonal 00270 N TP53 F54fs 0.10 1.00 clonal 00271 N BRCA1 I90fs 1.00 1.00 clonal 00271 N ALK G1202R 0.70 0.70 clonal 00271 N BRCA1 N743S 0.10 0.10 subclonal 00272 N N/A WT Report WT Report 00275 N TP53 A159P 82.10 1.00 clonal 00275 N KIT Q347K 6.70 0.08 subclonal 00275 N NF1 R2812Q 0.20 0.00 subclonal 00275 N KIT E53K 0.10 0.00 subclonal 00275 N TERT D685N 0.10 0.00 subclonal 00275 N DDR2 D710H 0.10 0.00 subclonal 00276 N STK11 Q100* 44.50 1.00 clonal 00276 N TP53 R249M 40.10 0.90 clonal 00276 N KRAS Q61H 36.30 0.82 clonal 00276 N ALK M1328T 22.40 0.50 clonal 00276 N TERT PromoterSNV 12.20 0.27 clonal 00276 N FBXW7 N621K 7.60 0.17 subclonal 00276 N AR E643D 0.60 0.01 subclonal 00276 N ERBB2 V25A 0.50 0.01 subclonal 00276 N VHL R79G 0.20 0.00 subclonal 00277 N PTEN Y46fs 0.50 1.00 clonal 00277 N EGFR L858R 0.40 0.80 clonal 00277 N TP53 R156P 0.20 0.40 clonal 00278 N EGFR Exon19del 8.70 1.00 clonal 00278 N CTNNB1 S37F 6.50 0.75 clonal 00278 N VHL G212A 6.30 0.72 clonal 00278 N EGFR T790M 4.80 0.55 clonal 00278 N ALK L1571L 1.00 0.11 subclonal 00278 N ATM S3027R 0.60 0.07 subclonal 00278 N TP53 R273H 0.50 0.06 subclonal 00278 N TP53 H168fs 0.10 0.01 subclonal 00282 N NF1 V288M 2.20 1.00 clonal 00282 N EGFR Exon19del 1.80 0.82 clonal 00282 N EGFR V769M 1.30 0.59 clonal 00282 N AR Q196* 0.40 0.18 subclonal 00282 N RB1 A10A 0.30 0.14 subclonal 00282 N PIK3CA R88Q 0.10 0.05 subclonal 00283 N MET Exon14 skipping SNV 0.30 1.00 clonal 00283 N AR R856H 0.30 1.00 clonal 00283 N MET L824L 0.20 0.67 clonal 00283 N KRAS L113L 0.10 0.33 clonal 00284 N TP53 T155P 0.80 1.00 clonal 00284 N BRCA2 V1504M 0.10 0.13 subclonal 00285 N KRAS Q22K 0.90 1.00 clonal

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00285 N TP53 S106fs 0.30 0.33 clonal 00286 N N/A WT Report WT Report 00287 N BRCA2 N2458T 0.40 1.00 clonal 00288 N N/A WT Report WT Report 00290 N BRAF V600E 1.30 1.00 clonal 00290 N TP53 P152Q 0.40 0.31 clonal 00290 N MTOR A1340A 0.40 0.31 clonal 00290 N EGFR T354T 0.20 0.15 subclonal 00290 N TP53 R248Q 0.10 0.08 subclonal 00290 N TP53 Y205C 0.10 0.08 subclonal 00290 N APC C1578fs 0.06 0.05 subclonal 00291 N GATA3 R330M 1.10 1.00 clonal 00291 N TP53 R175L 1.00 0.91 clonal 00291 N STK11 E223* 0.90 0.82 clonal 00291 N JAK3 H588Q 0.90 0.82 clonal 00291 N RET R817C 0.60 0.55 clonal 00291 N ROS1 R2042R 0.50 0.45 clonal 00291 N TP53 R158H 0.10 0.09 subclonal 00291 N BRCA2 T325fs 0.08 0.07 subclonal 00292 N KRAS G12C 14.90 1.00 clonal 00292 N BRCA1 E1694* 11.70 0.79 clonal 00293 N EGFR H835L 1.90 1.00 clonal 00293 N EGFR L833V 1.80 0.95 clonal 00293 N APC T1074T 1.10 0.58 clonal 00293 N TP53 R158L 0.80 0.42 clonal 00294 N NF1 Splice Site SNV 1.80 1.00 clonal 00294 N TP53 G245V 1.50 0.83 clonal 00294 N NOTCH1 R1586C 1.30 0.72 clonal 00294 N MET C624C 0.90 0.50 clonal 00294 N RET R886L 0.90 0.50 clonal 00294 N CDKN2A R128P 0.80 0.44 clonal 00298 N EGFR N1112S 1.70 1.00 clonal 00298 N KRAS Q61H 0.80 0.47 clonal 00298 N CDKN2A R138T 0.80 0.47 clonal 00298 N ALK N1140N 0.60 0.35 clonal 00298 N SMAD4 E538K 0.10 0.06 subclonal 00299 N EGFR Exon19del 0.10 1.00 clonal 00300 N AR D496V 0.70 1.00 clonal 00300 N NF1 Splice Site SNV 0.30 0.43 clonal 00301 N EML4‐ALK Fusion 0.70 1.00 clonal 00301 N ALK‐EML4 Fusion 0.50 0.71 clonal 00302 S FGFR3 L406M 0.10 1.00 clonal 00302 S DDR2 R806* 0.09 0.90 clonal 00303 N ROS1 T1723I 0.10 1.00 clonal 00304 N EGFR R832C 8.70 1.00 clonal 00304 N KRAS G12C 0.30 0.03 subclonal 00304 N TP53 C275F 0.20 0.02 subclonal 00305 N EGFR Exon19Del 2.00 1.00 clonal

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00305 N TP53 P250L 0.40 0.20 clonal 00305 N SMAD4 D415fs 0.40 0.20 clonal 00305 N PDGFRA V527V 0.40 0.20 clonal 00305 N TP53 P278A 0.20 0.10 subclonal 00306 N TP53 P177R 0.30 1.00 clonal 00307 N MET V794A 6.00 1.00 clonal 00307 N KRAS G13D 0.20 0.03 subclonal 00307 N TP53 C275Y 0.10 0.02 subclonal 00308 S ERBB2 L161L 0.40 1.00 clonal 00308 S MET H476Y 0.20 0.50 clonal 00309 N N/A WT Report WT Report 00310 S TP53 V173M 10.20 1.00 clonal 00311 N TP53 P278S 2.40 1.00 clonal 00311 N KRAS T58I 1.70 0.71 clonal 00311 N BRAF D594N 1.70 0.71 clonal 00311 N EGFR G649E 0.80 0.33 clonal 00311 N TP53 C176Y 0.70 0.29 clonal 00312 N STK11 K78N 9.70 1.00 clonal 00312 N MET R426C 0.30 0.03 subclonal 00313 N TP53 V272L 2.80 1.00 clonal 00313 N CDKN2A E10* 1.80 0.64 clonal 00314 N BRCA1 E842* 26.30 1.00 clonal 00314 N MAPK1 A2G 7.00 0.27 clonal 00314 N NF1 R192* 2.80 0.11 subclonal 00314 N ATM R2691P 1.00 0.04 subclonal 00314 N MAPK1 L244F 0.50 0.02 subclonal 00314 N EGFR A647T 0.30 0.01 subclonal 00314 N MET E746Q 0.20 0.01 subclonal 00314 N KRAS K117N 0.03 0.00 subclonal 00316 N ATM Y332C 0.50 1.00 clonal 00316 N ARID1A S1085P 0.40 0.80 clonal 00316 N AR R727C 0.30 0.60 clonal 00318 N EGFR L858R 12.00 1.00 clonal 00318 N TP53 R273L 3.90 0.33 clonal 00318 N NF1 R2637* 0.40 0.03 subclonal 00318 N CDK6 D275E 0.10 0.01 subclonal 00319 N EGFR Exon19del 1.10 1.00 clonal 00319 N SMAD4 R531W 0.60 0.55 clonal 00319 N TP53 H179Q 0.50 0.45 clonal 00320 N TP53 V274F 5.20 1.00 clonal 00320 N TERT R672L 0.90 0.17 subclonal 00321 N EGFR L858R 6.40 1.00 clonal 00321 N CTNNB1 G34V 3.30 0.52 clonal 00321 N FGFR2 M400T 0.10 0.02 subclonal 00322 N KRAS G13C 26.00 1.00 clonal 00322 N TP53 R337L 8.70 0.33 clonal 00323 N EGFR L858R 7.60 1.00 clonal 00323 N PIK3CA E545K 4.40 0.58 clonal

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00323 N TP53 Splice Site SNV 2.60 0.34 clonal 00323 N BRCA1 D1152V 1.10 0.14 subclonal 00323 N GNAS R201H 0.10 0.01 subclonal 00324 N TP53 S313fs 3.30 1.00 clonal 00324 N STK11 L282fs 2.60 0.79 clonal 00324 N TP53 L257V 1.90 0.58 clonal 00324 N FGFR2 D479N 1.10 0.33 clonal 00324 N ARAF Y493C 0.60 0.18 subclonal 00324 N FGFR2 A97T 0.20 0.06 subclonal 00325 S NF1 D1527fs 1.40 1.00 clonal 00325 S STK11 F309F 0.10 0.07 subclonal 00326 N TP53 Splice Site SNV 0.30 1.00 clonal 00326 N NF1 I2026fs 0.20 0.67 clonal 00327 N BRAF D594G 4.70 1.00 clonal 00327 N STK11 E145fs 2.70 0.57 clonal 00327 N TP53 R273H 0.60 0.13 subclonal 00328 N BRCA1 K325K 0.80 1.00 clonal 00328 N CDKN2A A109T 0.30 0.38 clonal 00328 N APC P114A 0.30 0.38 clonal 00329 N KRAS G12D 0.80 1.00 clonal 00329 N CTNNB1 D32N 0.20 0.25 clonal 00329 N APC S246P 0.20 0.25 clonal 00330 N MAP2K1 P124P 3.50 1.00 clonal 00330 N EGFR L372L 0.40 0.11 subclonal 00330 N KRAS G12C 0.20 0.06 subclonal 00330 N ARID1A L1659L 0.20 0.06 subclonal 00330 N TP53 Y220C 0.10 0.03 subclonal 00331 N TP53 N247I 0.30 1.00 clonal 00331 N APC V2194fs 0.20 0.67 clonal 00331 N FGFR2 N184S 0.10 0.33 clonal 00332 N TP53 R273H 9.40 1.00 clonal 00332 N NF1 Q2686* 6.80 0.72 clonal 00333 N N/A WT Report WT Report 00334 N TP53 Q104* 37.70 1.00 clonal 00334 N TP53 L130F 0.30 0.01 subclonal 00334 N MET R987Q 0.10 0.00 subclonal 00335 N TP53 H179L 1.90 1.00 clonal 00335 N IDH2 R140Q 0.40 0.21 clonal 00335 N KRAS Q61H 0.20 0.11 subclonal 00336 N N/A WT Report WT Report 00338 N STK11 L282fs 4.60 1.00 clonal 00338 N EGFR L858R 2.70 0.59 clonal 00338 N RB1 Splice Site SNV 2.30 0.50 clonal 00338 N TP53 Splice Site SNV 1.80 0.39 clonal 00338 N MYC S298P 1.20 0.26 clonal 00338 N MYC P297P 1.10 0.24 clonal 00338 N AR A122S 0.60 0.13 subclonal 00338 N MET T750T 0.60 0.13 subclonal

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00338 N BRCA2 N3168_D3170del 0.10 0.02 subclonal 00339 N TP53 Q317* 19.40 1.00 clonal 00339 N RB1 E554K 14.20 0.73 clonal 00339 N PTEN G127V 1.20 0.06 subclonal 00339 N PTEN Y155fs 1.20 0.06 subclonal 00340 N EGFR Exon19del 5.70 1.00 clonal 00340 N PIK3CA E545K 5.00 0.88 clonal 00340 N TP53 V73fs 4.90 0.86 clonal 00341 N KRAS G12D 34.10 1.00 clonal 00341 N MET E1325K 0.20 0.01 subclonal 00341 N NF1 A208V 0.20 0.01 subclonal 00342 N BRAF T241M 12.10 1.00 clonal 00342 N KRAS G12V 4.70 0.39 clonal 00342 N TP53 D288fs 3.00 0.25 clonal 00342 N ERBB2 P562P 0.30 0.02 subclonal 00342 N BRCA2 K2244Q 0.30 0.02 subclonal 00343 N TP53 G244V 0.40 1.00 clonal 00343 N CCNE1 K315N 0.40 1.00 clonal 00343 N SMAD4 I478K 0.10 0.25 clonal 00344 N PIK3CA Q546R 2.20 1.00 clonal 00344 N MAP2K1 K57N 0.90 0.41 clonal 00344 N ALK R1061W 0.40 0.18 subclonal 00345 N TSC1 E1044fs 0.60 1.00 clonal 00345 N NOTCH1 G2299G 0.40 0.67 clonal 00345 N ATM C353W 0.20 0.33 clonal 00346 N KRAS G12V 1.60 1.00 clonal 00346 N MAPK1 E322* 1.00 0.63 clonal 00346 N AR R31H 0.20 0.13 subclonal 00346 N PDGFRA P32P 0.20 0.13 subclonal 00346 N CDKN2A Q50H 0.10 0.06 subclonal 00347 S EGFR Exon19del 2.40 1.00 clonal 00347 S BRAF G464G 0.90 0.38 clonal 00347 S NF1 E1694 0.20 0.08 subclonal 00348 N EGFR L858R 0.50 1.00 clonal 00348 N TP53 P278L 0.30 0.60 clonal 00349 N EGFR T790M 0.30 1.00 clonal 00350 N TP53 R196P 0.40 1.00 clonal 00350 N KRAS G12V 0.20 0.50 clonal 00350 N PDGFRA S461S 0.20 0.50 clonal 00350 N TP53 K120 0.10 0.25 clonal 00350 N EGFR G665D 0.10 0.25 clonal 00350 N TP53 A119A 0.10 0.25 clonal 00351 N TP53 P152L 0.90 1.00 clonal 00351 N CDK4 F31F 0.10 0.11 subclonal 00352 N EGFR T430T 0.50 1.00 clonal 00352 N ESR1 H547R 0.10 0.20 clonal 00353 N EGFR L858R 1.00 1.00 clonal 00354 N ALK V1023V 1.20 1.00 clonal

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00354 N MTOR T237I 0.20 0.17 subclonal 00355 N GNAS R201H 0.30 1.00 clonal 00355 N HNF1A A269A 0.10 0.33 clonal 00356 N N/A WT Report WT Report 00357 S TP53 Y234C 23.80 1.00 clonal 00357 S ERBB2 R811P 0.20 0.01 subclonal 00357 S ARID1A P418L 0.10 0.00 subclonal 00358 S STK11 D53fs 0.70 1.00 clonal 00358 S KRAS G12C 0.40 0.57 clonal 00358 S TP53 C238F 0.30 0.43 clonal 00359 N TP53 Splice Site SNV 0.30 1.00 clonal 00360 N N/A WT Report WT Report 00361 N ALK L1196Q 0.40 1.00 clonal 00361 N KIF5B‐ALK Fusion 0.20 0.50 clonal 00361 N ALK G1202R 0.20 0.50 clonal 00361 N PIK3CA R617P 0.20 0.50 clonal 00361 N EGFR G663G 0.10 0.25 clonal 00362 N ARID1A P1392P 0.60 1.00 clonal 00362 N TP53 H214R 0.30 0.50 clonal 00363 N NF1 S1443* 0.90 1.00 clonal 00364 N MET S796* 2.20 1.00 clonal 00364 N JAK2 V617F 1.00 0.45 clonal 00364 N KRAS G12C 0.20 0.09 subclonal 00365 N EGFR L858R 0.90 1.00 clonal 00366 N GNAQ S233T 7.10 1.20 clonal 00366 N JAK2 V617F 5.90 1.00 clonal 00366 N AR P146T 5.10 0.86 clonal 00366 N CCNE1 G342W 3.40 0.58 clonal 00366 N CCNE1 T341T 3.30 0.56 clonal 00366 N MET Exon14 skipping SNV 3.20 0.54 clonal 00366 N FGFR2 A97P 0.30 0.05 subclonal 00367 N TP53 S241F 0.30 1.00 clonal 00367 N TSC1 S579I 0.30 1.00 clonal 00367 N MET Exon14 skipping SNV 0.20 0.67 clonal 00367 N MAPK1 Splice site SNV 0.20 0.67 clonal 00368 N N/A WT Report WT Report 00369 N PTEN L193_F195del 1.10 1.00 clonal 00369 N ARID1A A2235fs 0.80 0.73 clonal 00370 N N/A WT report WT Report 00371 N N/A WT report WT Report 00372 N TP53 R175H 9.10 1.00 clonal 00372 N KRAS G12C 8.50 0.93 clonal 00372 N IDH2 R140Q 0.40 0.04 subclonal 00372 N PDGFRA C49S 0.10 0.01 subclonal 00373 S MET Exon14 skipping SNV 0.50 1.00 clonal 00374 N STK11 D176Y 6.90 1.00 clonal 00374 N BRAF G469A 5.00 0.72 clonal 00374 N RHOA E40K 1.80 0.26 clonal

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00374 N JAK2 V617F 0.50 0.07 subclonal 00374 N BRCA1 Splice Site SNV 0.20 0.03 subclonal 00375 N N/A WT Report WT Report 00376 N KRAS G12A 4.00 1.00 clonal 00376 N TP53 R273L 2.20 0.55 clonal 00376 N PIK3CA E453K 1.70 0.43 clonal 00376 N ERBB2 L651V 1.10 0.28 clonal 00378 N KRAS G12F 0.50 1.00 clonal 00378 N ARID1A R1287fs 0.30 0.60 clonal 00379 N TP53 R249M 3.20 1.00 clonal 00379 N KRAS G12C 0.50 0.16 subclonal 00379 N TP53 R273H 0.30 0.09 subclonal 00379 N GNAS R201H 0.10 0.03 subclonal 00379 N BRCA2 N3318S 0.10 0.03 subclonal 00380 N KRAS G12R 0.90 1.00 clonal 00380 N TP53 S90fs 0.30 0.33 clonal 00380 N TP53 Splice Site SNV 0.20 0.22 clonal 00383 N TP53 R273L 24.10 1.00 clonal 00383 N KRAS G12C 23.20 0.96 clonal 00383 N APC A703T 7.70 0.32 clonal 00383 N AR D266A 7.00 0.29 clonal 00384 N STK11 E57fs 20.70 1.00 clonal 00384 N BRAF G469A 19.70 0.95 clonal 00384 N PIK3CA H1047R 0.50 0.02 subclonal 00384 N BRCA1 F1798F 0.20 0.01 subclonal 00386 N BRCA2 L2805L 0.30 1.00 clonal 00387 N TP53 R158L 19.70 1.00 clonal 00387 N PTEN I33del 0.40 0.02 subclonal 00388 N BRAF K483E 1.10 1.00 clonal 00388 N TP53 G262V 0.60 0.55 clonal 00389 N TP53 R196* 30.10 1.00 clonal 00389 N NF1 K1752E 0.10 0.00 subclonal 00390 N EGFR Exon19del 52.60 1.00 clonal 00390 N EGFR T594N 20.50 0.39 clonal 00390 N TP53 R273C 6.70 0.13 subclonal 00390 N CDKN2A W110* 1.70 0.03 subclonal 00391 N EGFR Exon19del 8.70 1.00 clonal 00391 N TP53 L201* 3.40 0.39 clonal 00391 N SMAD4 R445* 2.10 0.24 clonal 00391 N SMAD5 D537E 0.20 0.02 subclonal 00391 N PIK3CA E545K 0.10 0.01 subclonal 00392 N TP53 Splice Site indel 0.20 1.00 clonal 00393 N TP53 G266* 8.50 1.00 clonal 00393 N NTRK3 V606V 6.00 0.71 clonal 00393 N CDKN2A E149* 5.70 0.67 clonal 00394 N EGFR T790M 0.20 1.00 clonal 00394 N DDR2 R752H 0.20 1.00 clonal 00395 N EGFR Exon19del 20.00 1.00 clonal

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00395 N EGFR T790M 10.20 0.51 clonal 00395 N TP53 P278S 1.60 0.08 subclonal 00397 N EGFR Exon19del 0.10 1.00 clonal 00398 N MTOR H1454H 0.60 1.00 clonal 00400 N MET Exon14 skipping SNV 9.80 1.00 clonal 00400 N TP53 R337H 5.80 0.59 clonal 00400 N NF1 Splice site SNV 4.50 0.46 clonal 00400 N TERT Promoter SNV 0.20 0.02 subclonal 00402 N EGFR A647T 0.30 1.00 clonal 00403 N STK11 Splice Site SNV 1.60 1.00 clonal 00403 N TP53 T125K 1.50 0.94 clonal 00403 N NOTCH1 N2389N 1.30 0.81 clonal 00403 N NF1 G1133V 1.20 0.75 clonal 00404 N NF1 K686* 27.60 1.00 clonal 00404 N TP53 G154V 22.70 0.82 clonal 00404 N NTRK1 G620G 0.30 0.01 subclonal 00404 N BRAF G258D 0.10 0.00 subclonal 00405 N EGFR Exon19del 0.10 1.00 clonal 00405 N TP53 C141fs 0.08 0.80 clonal 00406 N KRAS G12A 0.50 1.00 clonal 00406 N SMAD4 D351Y 0.40 0.80 clonal 00407 N ATM R3008H 0.50 1.00 clonal 00407 N TP53 H179Q 0.20 0.40 clonal 00407 N TP53 R196P 0.20 0.40 clonal 00407 N TP53 C238Y 0.10 0.20 clonal 00408 N NF1 S2309S 0.60 1.00 clonal 00409 N N/A WT Report WT Report 00410 N PDGFRA D444N 2.30 1.00 clonal 00410 N TP53 R213P 1.00 0.43 clonal 00410 N MET Exon14 skipping SNV 0.80 0.35 clonal 00410 N NF1 D2095V 0.60 0.26 clonal 00410 N HNF1A T196T 0.20 0.09 subclonal 00410 N EGFR D256D 0.20 0.09 subclonal 00412 N TP53 R283P 0.80 1.00 clonal 00412 N STK11 H107P 0.50 0.63 clonal 00412 N CDKN2A Splice site SNV 0.20 0.25 clonal 00412 N CDK6 P55Q 0.20 0.25 clonal 00412 N KRAS G12D 0.10 0.13 subclonal 00412 N CDH1 G78C 0.10 0.13 subclonal 00412 N FGFR2 K296N 0.10 0.13 subclonal 00412 N ARID1A L2266fs 0.06 0.08 subclonal 00414 N PIK3CA C420R 3.40 1.00 clonal 00414 N TP53 R342fs 3.20 0.94 clonal 00414 N ERBB2 T479T 2.70 0.79 clonal 00414 N TERT Promoter SNV 2.30 0.68 clonal 00414 N FGFR2 S252 0.20 0.06 subclonal 00415 N IDH2 R140L 0.40 1.00 clonal 00415 N KRAS G12D 0.40 1.00 clonal

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00415 N ARID1A Q2219 0.20 0.50 clonal 00416 N TP53 E336 0.40 1.00 clonal 00416 N KRAS G12V 0.20 0.50 clonal 00416 N PDGFRA R293H 0.10 0.25 clonal 00416 N KRAS G12D 0.08 0.20 clonal 00417 N MET Exon14 skipping SNV 27.10 1.00 clonal 00417 N MET Splice Site SNV 9.70 0.36 clonal 00417 N ERBB2 R34Q 0.20 0.01 subclonal 00417 N KIT M1? 0.10 0.00 subclonal 00418 N EGFR Exon19del 1.10 1.00 clonal 00418 N PIK3CA E545K 0.20 0.18 subclonal 00418 N MET Exon14 skipping SNV 0.03 0.03 subclonal 00419 N SMAD4 L551fs 0.04 1.00 clonal 00420 N PIK3CA Q75E 8.20 1.00 clonal 00420 N STK11 E293 4.20 0.51 clonal 00420 N MET F523F 2.90 0.35 clonal 00420 N ARID1A S1992S 0.30 0.04 subclonal 00420 N TSC1 E1044fs 0.30 0.04 subclonal 00420 N TP53 Splice site SNV 0.10 0.01 subclonal 00465 N TP53 E349* 7.20 1.00 clonal 00465 N EGFR L858R 5.00 0.69 clonal 00465 N TP53 R273V 0.70 0.10 subclonal 00465 N TP53 Y220C 0.60 0.08 subclonal 00482 N N/A WT Report WT Report 00483 S BRAF G466E 0.20 1.00 clonal 00486 N TP53 I162F 0.40 1.00 clonal 00486 N MPL W515R 0.40 1.00 clonal 00486 N KRAS G12C 0.20 0.50 clonal 00486 N PTEN R41I 0.10 0.25 clonal 00486 N KIT V960F 0.10 0.25 clonal 00488 N EGFR Exon20ins 0.40 1.00 clonal 00488 N PIK3CA F128L 0.40 1.00 clonal 00488 N PIK3CA E545K 0.30 0.75 clonal 00488 N BRCA2 L3346F 0.30 0.75 clonal 00490 N SMAD4 G352V 0.70 1.00 clonal 00490 N ALK‐EML4 Fusion 0.50 0.71 clonal 00490 N SMAD4 R361H 0.50 0.71 clonal 00490 N EML4‐ALK Fusion 0.30 0.43 clonal 00491 N N/A WT Report WT Report 00492 N MET Exon14 skipping SNV 4.80 1.00 clonal 00492 N CDKN2A T77fs 0.90 0.19 subclonal 00493 N GATA3 P337H 1.50 1.00 clonal 00493 N STK11 G242V 1.50 1.00 clonal 00493 N KRAS G13D 1.30 0.87 clonal 00493 N ERBB2 A440T 0.30 0.20 clonal 00494 N TP53 Splice site SNV 2.20 1.00 clonal 00494 N EGFR K754E 1.10 0.50 clonal 00494 N EGFR Exon19del 1.00 0.45 clonal

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00494 N EGFR T790M 0.50 0.23 clonal 00494 N PTEN I8_E18del 0.30 0.14 subclonal 00495 N EGFR Exon18del 0.70 1.00 clonal 00495 N PIK3CA E545K 0.50 0.71 clonal 00495 N TP53 R337fs 0.40 0.57 clonal 00495 N TP53 R248W 0.30 0.43 clonal 00495 N MAPK1 E197K 0.20 0.29 clonal 00496 N BRAF V600E 0.20 1.00 clonal 00497 N PTEN C136R 0.40 1.00 clonal 00497 N ERBB2 L123L 0.20 0.50 clonal 00498 N STK11 S216F 0.60 1.00 clonal 00498 N KRAS G12C 0.30 0.50 clonal 00504 N N/A WT Report WT Report ‐ This spreadsheet contains all liquid biopsy‐detected mutations for the 323 patients enrolled in this study ‐ The number of patients with targetable or clinically relevant mutations found in plasma is higher in this table than in Figure 1 because patients at progression with driver mutations detected by plasma but resistance mutations detected by tissue only, are captured in the "Tissue only" category of Figure 1.

All such patients had testing ordered at the time of progression for the purpose of detecting a resistance mutation.

‐ Histology: S = Squamous, N = Non‐squamous ‐ MAF = Mutation Allele Fraction ‐ Clonality is calculated using the approach described in Blakely CM et al., Nature Genetics, Dec. 2017. In brief, a clonal mutation is defined as > 0.2 mutational allele frequency (MAF)/maximum (max.) MAF) and subclonal (<0.2 MAF/maximum MAF).

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eFigure 1. Analysis of Mutations Detected in Plasma and/or Tissue NGS

A. Mutational profile as determined by plasma NGS for 323 patients (green = insertions/deletions/fusions, blue = synonymous mutation, red = nonsynonymous mutation). B. Comparison of mutation prevalence for the 10 most frequently detected mutations for 128 patients who had both plasma (gray bars) and tissue (black bars) NGS completed. C. Among the 128 patients, 31 had a therapeutically targetable mutation detected in both plasma and tissue. Shown is a comparison of the tissue and plasma AFs (ρ = 0.40, P = .023). Four of the 27 patients had both a driver and a resistance mutation detected, so 31 data points are shown in the figure.

TP53 PTEN Tissue APC EGFR Plasma KRAS BRCA1 NF1 NF1 MET MET PIK3CA PIK3CA STK11 STK11 AR KRAS ARID1A TP53 CDKN2A EGFR ALK 0 5 0 5 0 1 1 2 ERBB2 BRAF % Total M utations Detected RB1 APC BRCA1 FGFR2 ins/del/fusions PDGFRA PTEN synonymous C 100 CTNNB1 nonsynonymous SMAD4 KIT 80 MYC ATM 60 BRCA2 NOTCH1 GNAS 40 CCNE1 TERT 20 CCND1

0 50 100 150 200 250 (%) Fraction Allele Tissue 0 Number of variants 0 20406080100 Plasma Allele Fraction (%)

Downloaded From: https://jamanetwork.com/ on 10/01/2021 eFigure 2. Correlation of Tissue AF for the Targeted Mutation and Depth of RECIST Response to Targeted Therapy in 10 Patients with Tissue and Plasma Available

Among the 42 patients shown in Figure 3 for whom RECIST response was measured, 10 had the targetable mutation detected in both plasma and tissue. Shown here is the correlation of tissue AF for the targeted mutation and depth of RECIST response to targeted therapy (n = 10 patients; r = 0.216, P = .176).

60 40 20 Tissue AF Mutations 0 Ex19del (driver) 20 40 60 80 T790M (resistance) -20 MET Exon14 skip -40

-60 2500 2000 -80 1500 1000 % Change in Target Lesion% Change in Target -100 500 0 02468

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