Fig. 1Overall survival (A-C) and progression-free survival (D-F) with respect to the epidermal growth factor receptor (EGFR) mutation status of non-small cell lung carcinoma patients as determined by direct sequencing (A, D), peptide nucleic acid (PNA) clamping (B, E), and pyrosequencing (C, F).
Table 1.Summary of discordant cases (n=15, 25%) of EGFR mutation profiles using direct sequencing, PNA clamping, and pyrosequencing according to clinicopathologic characteristics, including EGFR TKI responses
Case No. |
Direct sequencing |
PNA clamping |
Pyrosequencing |
TKI Response |
Sex |
Smoking |
Histology |
1 |
G719X, L861Q |
G719X, L861Q |
G719X |
SD
|
F |
N |
ADC |
2 |
Wild |
Wild |
Exon 19 del |
PR
|
M |
C |
ASC
|
3 |
Wild |
Wild |
Exon 19 del |
PD |
F |
N |
ADC |
4 |
Wild |
G719X |
Wild |
SD
|
M |
C |
ADC |
5 |
Wild |
Exon 19 del |
Exon 19 del |
PR
|
M |
C |
ADC |
6 |
Wild |
S768I |
Wild |
PD |
F |
N |
ADC |
7 |
Wild |
L858R |
L858R |
PR
|
M |
N |
ADC |
8 |
Exon 19 del |
Wild |
Wild |
PD |
F |
N |
ADC |
9 |
Exon 19 del |
Wild |
Wild |
PD |
M |
FS |
ASC
|
10 |
Exon 20 duplication |
Wild |
Wild |
PD |
F |
N |
ADC |
11 |
R776H |
Wild |
Wild |
PD |
M |
N |
LCC
|
12 |
L858R |
L858R |
Wild |
PD |
M |
N |
ADC |
13 |
L858R |
Wild |
L858R |
PR
|
F |
N |
ADC |
14 |
L858R |
Wild |
L858R |
SD
|
F |
N |
ADC |
15 |
L858R |
Wild |
L858R |
PD |
F |
N |
ADC |
Table 2.
EGFR mutation profiles as identified by direct sequencing, not designed by PNA clamp EGFR mutation detection kit or pyrosequencing
Case No. |
Exon |
Alteration |
Direct sequencing
|
TKI response |
Nucleotide alteration |
Amino acid alteration |
8 |
19 |
Deletion |
2239-2263del |
L747-755Adel |
PD |
9 |
19 |
Deletion |
2253-2276del |
S752_I759del |
PD |
10 |
20 |
Duplication |
dup 2311-2319 AACCCCCAC |
D770_N771insNPH |
PD |
11 |
20 |
Point mutation |
2327G>A |
R776H |
PD |
Table 3.Summary of concordant cases (n=46, 75%) of EGFR mutation profiles using direct sequencing, PNA clamping, and pyrosequencing according to clinicopathologic characteristics, including EGFR TKI responses
EGFR mutation |
TKI response |
Sex |
Smoking |
Histology |
Exon19 (n = 18, 29%) |
CR (n = 2,3%)
|
F |
N |
ADC |
PR (n = 3)
|
F |
N |
ADC |
|
F |
N |
SCC
|
|
M |
C |
ADC |
SD (n = 9)
|
F (n = 5) |
N |
ADC |
|
M (n = 2) |
FS |
ADC |
|
M (n = 2) |
C |
ADC |
PD (n = 5) |
F (n = 3) |
N |
ADC |
|
M (n = 2) |
C |
ADC |
Exon21 (n = 11, 18%) |
PR (n = 5)
|
F (n = 3) |
N |
ADC |
|
M |
N |
ADC |
|
M |
C |
ADC |
SD
|
M |
C |
ADC |
PD (n = 5) |
F (n = 3) |
N |
ADC |
|
F (n = 2) |
C |
ADC |
Wild (n = 17, 28%) |
PR
|
M |
FS |
ADC |
SD (n = 1,3%)
|
F |
N |
ADC |
PD (n = 15) |
F (n = 4) |
N |
ADC |
|
F |
N |
SCC
|
|
F |
C |
ADC |
|
F |
C |
LCNEC
|
|
M |
N |
SCC
|
|
M (n = 2) |
FS |
ADC |
|
M |
C |
ADC |
|
M (n = 2) |
C |
SCC
|
|
M (n = 2) |
C |
SarCa
|
Table 4.Patients' characteristics and EGFR mutation status using direct sequencing, PNA clamping, and pyrosequencing
|
n (%) |
Direct sequencing EGFR mutation
|
PNA clamping EGFR mutation
|
Pyrosequencing EGFR mutation
|
|
(+) |
(-) |
p-value |
(+) |
(-) |
p-value |
(+) |
(-) |
p-value |
Total |
61 (100) |
38 (62) |
23 (38) |
|
35 (57) |
26 (43) |
|
37 (61) |
24 (39) |
|
Sex |
|
|
|
|
|
|
|
|
|
|
Female |
35 (57) |
25 (71) |
10 (29) |
0.113 |
21 (60) |
14 (40) |
0.794 |
24 (69) |
11 (31) |
0.188 |
Male |
26 (43) |
13 (50) |
13 (50) |
|
14 (54) |
12 (46) |
|
13 (50) |
13 (50) |
|
Smoking historya
|
|
|
|
|
|
|
|
|
|
|
Never |
36 (59) |
26 (72) |
10 (28) |
0.066b
|
22 (61) |
14 (39) |
0.600b
|
24 (67) |
12 (33) |
0.294b
|
Former |
6 (10) |
3 (50) |
3 (50) |
|
2 (33) |
4 (67) |
|
2 (33) |
4 (67) |
|
Current |
19 (31) |
9 (47) |
10 (53) |
|
11 (58) |
8 (42) |
|
11 (58) |
8 (42) |
|
Histology |
|
|
|
|
|
|
|
|
|
|
ADC |
50 (82) |
35 (70) |
15 (30) |
0.014c
|
34 (68) |
16 (32) |
<0.001c
|
35 (70) |
15 (30) |
0.002c
|
SCC |
5 (8) |
1 (20) |
4 (80) |
|
1 (20) |
4 (80) |
|
1 (20) |
4 (80) |
|
Others |
6 (10) |
2 (33) |
4 (67) |
|
0 |
6 (100) |
|
1 (17) |
5 (83) |
|
Tumor size (cm) |
|
|
|
|
|
|
|
|
|
|
≤ 3 |
26 (43) |
21 (81) |
5 (19) |
0.016 |
19 (73) |
7 (27) |
0.040 |
21 (81) |
5 (19) |
0.008 |
> 3 |
35 (57) |
17 (49) |
18 (51) |
|
16 (46) |
19 (54) |
|
16 (46) |
19 (54) |
|
Operation method |
|
|
|
|
|
|
|
|
|
|
Biopsy |
1 (2) |
1 (100) |
0 |
1.000 |
1 (100) |
0 |
1.000 |
1 (100) |
0 |
1.000 |
Resection |
60 (98) |
37 (62) |
23 (38) |
|
34 (57) |
26 (43) |
|
36 (60) |
24 (40) |
|
EGFR TKI response |
|
|
|
|
|
|
|
|
|
|
CR |
1 (2) |
1 (100) |
0 |
0.537d
|
1 (100) |
0 |
0.122d
|
1 (100) |
0 |
0.005d
|
PR |
13 (21) |
9 (69) |
4 (31) |
|
10 (77) |
3 (23) |
|
12 (92) |
1 (8) |
|
SD |
14 (23) |
12 (86) |
2 (14) |
|
12 (86) |
2 (14) |
|
12 (86) |
2 (14) |
|
PD |
33 (54) |
16 (48) |
17 (52) |
|
12 (36) |
21 (64) |
|
12 (36) |
21 (64) |
|
Table 5.Clinical outcomes among subgroups of patients who are treated with EGFR TKIs
|
n (%) |
Objective responsea
|
p-value |
Disease control rateb
|
p-value |
Median TTP (mo) |
p-value |
MST (mo) |
p-value |
Total |
61 (100) |
14 (23) |
|
28 (46) |
|
16.0 |
|
30.0 |
|
Sex |
|
|
|
|
|
|
|
|
|
Female |
35 (57) |
7 (20) |
0.553 |
15 (43) |
0.613 |
18.0 |
0.440 |
29.0 |
0.445 |
Male |
26 (43) |
7 (27) |
|
13 (50) |
|
13.5 |
|
35.0 |
|
Smoking historyc
|
|
|
|
|
|
|
|
|
|
Never |
36 (59) |
9 (25) |
0.762d
|
17 (47) |
1.000d
|
17.0 |
0.300d
|
32.0 |
0.795d
|
Former |
6 (10) |
1 (17) |
|
3 (50) |
|
19.5 |
|
44.5 |
|
Current |
19 (31) |
4 (21) |
|
8 (42) |
|
11.0 |
|
28.0 |
|
Histology |
|
|
|
|
|
|
|
|
|
ADC |
50 (82) |
12 (24) |
0.726e
|
26 (52) |
0.051e
|
17.5 |
0.043e
|
30.0 |
0.100e
|
SCC |
5 (8) |
1 (20) |
|
1 (20) |
|
11.0 |
|
28.0 |
|
Others |
6 (10) |
1 (17) |
|
1 (17) |
|
10.0 |
|
28.0 |
|
Direct sequencing |
|
|
|
|
|
|
|
|
|
EGFR mutation (+) |
38 (62) |
10 (26) |
0.537 |
22 (58) |
0.019 |
20.0 |
0.008 |
34.5 |
0.428 |
EGFR mutation (-) |
23 (38) |
4 (17) |
|
6 (26) |
|
10.0 |
|
24.0 |
|
PNA clamping |
|
|
|
|
|
|
|
|
|
EGFR mutation (+) |
35 (57) |
11 (31) |
0.122 |
23 (66) |
0.001 |
19.0 |
0.020 |
34.0 |
0.606 |
EGFR mutation (-) |
26 (43) |
3 (12) |
|
5 (23) |
|
10.5 |
|
24.0 |
|
Pyrosequencing |
|
|
|
|
|
|
|
|
|
EGFR mutation (+) |
37 (61) |
13 (35) |
0.005 |
25 (68) |
<0.001 |
19.0 |
0.018 |
35.0 |
0.294 |
EGFR mutation (-) |
24 (39) |
1 (4) |
|
3 (13) |
|
12.0 |
|
25.0 |
|