SupplementaryTable 1.Mutation analysis in 103 matching tissue and plasma samples

Patient / Biopsy type / Disease stage / Gene / Mutation / Tissue
ARMS-PCR assay / Plasma
cSMART assay
Mutation ratio / Mutation templatesper2 ml / Total templatesper2 ml
Positive concordant samples (n = 57)
1* / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 85 / 1240
5 / Cervical lymph node biopsy / IIIB / KRAS / G12A / > 0.05 / 4 / 694
8 / Surgical specimen / IV / KRAS / G12S / > 0.05 / 74 / 2408
11* / Pleural effusion / IV / EGFR / L858R / > 0.05 / 1 / 2020
12 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 2 / 2706
15 / Pleural effusion / IV / EGFR / E20ins / > 0.05 / 1 / 2144
16 / Bronchoscopic biopsy / IIIB / EGFR / E746_A750del / > 0.05 / 326 / 2877
18 / Percutaneous lung biopsy / IIIB / EGFR / E746_A750del / > 0.05 / 942 / 2898
20 / Cervical lymph node biopsy / IIIB / KRAS / G12C / > 0.05 / 39 / 595
23* / Pleural effusion / IV / EGFR / L858R / > 0.05 / 37 / 2844
25 / Pleural effusion / IV / KRAS / G12C / > 0.05 / 1540 / 3846
26* / Cerebrospinal fluid / IV / EGFR / E746_A750del / > 0.05 / 4 / 1634
EGFR / T790M / > 0.05 / 2 / 1433
27 / Bone biopsy / IV / ERBB2 / E20ins
exon20:c.2310_2311insGCATACGTGATG:p.E770delinsEAYVM / > 0.05 / 2414 / 7465
28 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 1 / 1546
29 / Cervical lymph node biopsy / IV / EGFR / L858R / > 0.05 / 42 / 1991
30 / Sputum / III / ALK / fusion / > 0.05 / 6 / 3475
32 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 4 / 2594
33 / Bronchial brushbiopsy sample / IIIB / EGFR / E20ins exon20:c.2296_2297insTGGCCAGCG:p.M766delinsMASV / > 0.05 / 1046 / 4632
35 / Supraclavicular lymph node biopsy / IIIB / EGFR / E746_A750del / > 0.05 / 4512 / 7535
37 / Bronchoscopic biopsy / IIIB / EGFR / E19del exon19:c.2236_2244del:p.746_748del / > 0.05 / 21 / 1412
38 / Sputum / IIIB / EGFR / L858R / > 0.05 / 6 / 6479
39 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 5 / 5900
42 / Pleural effusion / IV / EGFR / E20ins exon20:c.2300_2301insCAGCGTGGA:p.A767delinsASVD / > 0.05 / 67 / 2995
EGFR / E20ins exon20:c.2296_2297insTGGCCAGCG:p.M766delinsMASV / > 0.05 / 1 / 2958
43 / Bone biopsy / IV / KRAS / G12C / > 0.05 / 27 / 1665
44 / Sputum / IV / EGFR / L858R / > 0.05 / 5 / 3093
45 / Bronchoscopic biopsy / III / EGFR / L858R / > 0.05 / 17 / 2404
46 / Percutaneous lung biopsy / IV / EGFR / L858R / > 0.05 / 1449 / 3419
49 / Pleural effusion / IV / KRAS / G12C / > 0.05 / 573 / 2176
51 / Sputum / IV / EGFR / E19del exon19:c.2236_2244del:p.746_748del / > 0.05 / 28 / 854
54 / Pleural effusion / IV / BRAF / V600E / > 0.05 / 4 / 1505
55 / Sputum / IV / KRAS / G12C / > 0.05 / 64 / 1423
56 / Pleural effusion / IV / EGFR / L747_P753>S / > 0.05 / 10 / 3055
58 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 231 / 3746
61 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 1 / 1453
62 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 57 / 3666
63 / Bronchoscopic biopsy / III / KRAS / G12C / > 0.05 / 54 / 2093
69 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 3 / 2281
70 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 5 / 1997
71 / Pleural effusion / IV / KRAS / G12S / > 0.05 / 782 / 2259
72 / Sputum / IV / EGFR / G719A / > 0.05 / 892 / 5993
77 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 10 / 1648
80 / Hydropericardium / IV / EGFR / L858R / > 0.05 / 1905 / 3729
82 / Percutaneous lung biopsy / IIIB / EGFR / L858R / > 0.05 / 25 / 1791
84* / Liver biopsy / IV / EGFR / L858R / > 0.05 / 1404 / 2308
EGFR / T790M / > 0.05 / 622 / 2048
85 / Lung wedge resection / III / EGFR / E746_A750del / > 0.05 / 2 / 4093
88* / Pleural effusion / IV / EGFR / E746_S752>A / > 0.05 / 1708 / 4890
89 / Pleural effusion / IV / BRAF / V600E / > 0.05 / 11 / 2704
91 / Pleural effusion / IV / EGFR / G719S / > 0.05 / 35 / 2423
EGFR / S768I / > 0.05 / 41 / 2445
92 / Bronchoscopic biopsy / IV / EGFR / E746_A750del / > 0.05 / 6 / 1229
93 / Pleural effusion / IV / KRAS / G12A / > 0.05 / 5 / 1409
94 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 3 / 1832
95 / Pleural effusion / IV / EGFR / L747_P753>S / > 0.05 / 31 / 1355
97 / Bronchoalveolar lavage fluid / IV / EGFR / E746_A750del / > 0.05 / 202 / 1539
98 / Percutaneous lung biopsy / IIIB / KRAS / A146P / > 0.05 / 2 / 1918
100 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 1045 / 2862
101 / Pleural effusion / IV / EGFR / L861Q / > 0.05 / 3 / 1974
102 / Pleural effusion / IV / ALK / KIF5B-ALK fusion / > 0.05 / 8 / 1588
Partially concordant samples (n = 9)
4 / Percutaneous lung biopsy / IV / EGFR / L747_P753>S / > 0.05 / 1406 / 6207
EGFR / T790M / < 0.01 (neg) / 2 / 5809
7* / Pleural effusion / IV / EGFR / E746_S752>A / > 0.05 / 42 / 3067
KRAS / G12V / > 0.05 / 1 (neg) / 1817
9 / Pleural effusion / IV / ALK / fusion / > 0.05 / 1 / 2222
EGFR / T790M / < 0.01 (neg) / 3 / 3206
47 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 84 / 10066
EGFR / G719S / < 0.01 (neg) / 3 / 12367
50 / Metastasis biopsy / IV / EGFR / G719A / > 0.05 / 277 / 2037
EGFR / T790M / < 0.01 (neg) / 74 / 1270
53* / Pleural effusion / IV / EGFR / L858R / > 0.05 / 85 / 3258
EGFR / T790M / < 0.01 (neg) / 5 / 1855
64* / Pleural effusion / IV / EGFR / L858R / > 0.05 / 274 / 10622
EGFR / T790M / < 0.01 / 170 / 7637
EGFR / G719S / < 0.01 (neg) / 3 / 9690
66 / Pleural effusion / IV / EGFR / L747_A750>P / > 0.05 / 6 / 2037
KRAS / G12C / > 0.05 / 1 (neg) / 1180
87 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 15 / 1473
EGFR / G719S / < 0.01 (neg) / 1 / 1676
Discordant samples (n = 19)
3 / Pleural effusion / IV / EGFR / T790M / < 0.01 (neg) / 2 / 6363
10 / Pleural effusion / IV / ALK / Fusion / > 0.05 / 0 (neg) / NC
13 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 0 (neg) / 666
17 / Pleural effusion / IV / EGFR / T790M / < 0.01 (neg) / 2 / 2427
21 / Pulmonary lobectomy / IIIB / KRAS / G12V / > 0.05 / 0 (neg) / 1352
24 / Bronchoscopic biopsy / III / EGFR / L858R / > 0.05 / 0 (neg) / 2871
31 / Cervical lymph node biopsy / IIIB / ALK / Fusion / > 0.05 / 0 (neg) / NC
36 / Bronchoscopic biopsy / IIIB / EGFR / 19del / > 0.05 / 0 (neg) / 3183
41 / Pleural effusion / IV / EGFR / G719C / < 0.01 (neg) / 3 / 14536
EGFR / T790M / < 0.01 (neg) / 6 / 8772
48 / Pleural effusion / IV / EGFR / L858R / > 0.05 / 0 (neg) / 2706
EGFR / E20ins exon20:c.2365_2366insGGGTCG:p.I789delinsRVV / < 0.01 (neg) / 1 / 2019
52 / Pleural effusion / IV / EGFR / E746_A750del / > 0.05 / 0 (neg) / 1344
57 / Pleural effusion / IV / KRAS / G12V / > 0.05 / 0 (neg) / 2140
65 / Pleural effusion / IV / KRAS / G12A / > 0.05 / 0 (neg) / 1095
67 / Percutaneous lung biopsy / IIIB / KRAS / G12D / > 0.05 / 0 (neg) / 1724
74 / Pleural effusion / IV / ALK / fusion / > 0.05 / 0 (neg) / NC
75* / Pleural effusion / IV / EGFR / E19del exon19:c.2238_2252del:p.746_751del / > 0.05 / 0 (neg) / 1721
EGFR / T790M / > 0.05 / 0 (neg) / 1281
76 / Pulmonarylobectomy / IIIA / EGFR / L858R / > 0.05 / 0 (neg) / 1095
79* / Pleural effusion / IV / EGFR / 19del / > 0.05 / 0 (neg) / 1196
EGFR / T790M / > 0.05 / 0 (neg) / 806
103 / Pleural effusion / IV / KRAS / G12V / > 0.05 / 0 (neg) / 711
Negative concordant samples (n = 18)
2 / Pleural effusion / IV / None / None
6 / Pleural effusion / IV / None / None
14 / Percutaneous lung biopsy / IV / None / None
19 / Cervical lymph node biopsy / IIIB / None / None
22 / Cervical lymph node biopsy / III / None / None
34 / Percutaneous lung biopsy / IIIB / None / None
40 / Pleural effusion / IV / None / None
59 / Pleural effusion / IV / None / None
60 / Pleural effusion / IV / None / None
68 / Pleural effusion / IV / None / None
73 / Pleural effusion / IV / None / None
78 / Sputum / IV / None / None
81 / Pleural effusion / IV / None / None
83 / Pleural effusion / IV / None / None
86 / Supraclavicular lymph node biopsy / IV / None / None
90 / Pleural effusion / IV / None / None
96 / Lobectomy specimen / IIIA / None / None
99 / Pleural effusion / IV / None / None

NC =Not calculable. There was no specific site of fusion to count the corresponding normal sequence templates.*EGFR-TKI treatment.