1
Supporting Information Legends
2
3
4
5
6
7
Figure S1. Reads per exon are shown. The histogram demonstrates the median read
count per exon for the 48 targeted genes. The results reflect the data from five NGS
runs.
Table S1. Overview of the run parameters for all five MiSeq runs. In run 5, the 23
samples with the lowest median coverage (<250) or insufficient representation of
some loci were re-sequenced.
Run 1
Run 2
Run 3
Run 4
Run 5
Samples [n]
23
24
23
24
23
Amplicons [n]
212
212
212
212
212
Average
339
1.211
498
454
705
641
Cluster PF
87.59%
56.88%
89.07%
89.64%
72.62%
79.16%
Reads
2.83 M
8.66 M
4.04 M
3.69 M
5.43 M
4.93 M
Reads PF
2.48 M
4.93 M
3.60 M
3.31 M
3.95 M
3.65 M
Total Yield
0.8 Gb
1.5 Gb
1.1 Gb
1.0 Gb
1.2 Gb
1.1 Gb
≥ Q30 Score
75.00%
42.90%
83.70%
85.30%
27.60%
62.90
Cluster
Density
[K/mm²]
PF: passed filter; M: million; Gb: giga bases; Q30 score: 0.1% chance of a wrong base call
8
1
Table S2. A complete list of non-synonymous mutations ≥5% allelic frequency. chr: chromosome; del: deletion; ins: insertion; fs: frame
shift; * stop gained; Freq. frequency; Cov: coverage; TC: typical carcinoid; AC: atypical carcinoid; LCNEC: large cell neuroendocrine
carcinoma; SCLC: small cell lung cancer.
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
ABL1
chr9:133738402
NM_007313
c.859G>C
p.V287L
23%
139
P089
LCNEC
ABL1
chr9:133747556
NM_007313
c.920C>T
p.A307V
21%
125
P200
TC
ABL1
chr9:133747594
NM_007313
c.958C>T
p.L320F
21%
121
P105
LCNEC
ABL1
chr9:133748382
NM_007313
c.1100C>T
p.S367L
21%
270
P185
SCLC
ABL1
chr9:133750389
NM_007313
c.1277C>T
p.A426V
22%
130
P185
SCLC
ALK
chr2:29432668
NM_004304
c.3820G>A
p.A1274T
16%
157
P185
SCLC
ALK
chr2:29432712
NM_004304
c.3776G>A
p.C1259Y
11%
247
P081
LCNEC
APC
chr5:112173983
NM_001127510
c.2692C>T
p.H898Y
12%
325
P189
SCLC
APC
chr5:112174658
NM_001127510
c.3367C>T
p.Q1123*
95%
35
P059
AC
APC
chr5:112174677
NM_001127510
c.3386T>C
p.L1129S
47%
396
P062
TC
APC
chr5:112175079
NM_001127510
c.3788G>A
p.C1263Y
16%
337
P053
AC
APC
chr5:112175079
NM_001127510
c.3788G>A
p.C1263Y
35%
164
P081
LCNEC
APC
chr5:112175594
NM_001127510
c.4303A>G
p.R1435G
11%
348
P189
SCLC
APC
chr5:112175747
NM_001127510
c.4456G>A
p.D1486N
28%
235
P185
SCLC
2
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
ATM
chr11:108137985
NM_000051
c.2554C>T
p.Q852*
13%
452
P189
SCLC
ATM
chr11:108204682
NM_000051
c.7997C>T
p.T2666I
11%
412
P185
SCLC
ATM
chr11:108225599
NM_000051
c.8848G>A
p.E2950K
28%
1,420
P180
LCNEC
ATM
chr11:108225599
NM_000051
c.8848G>A
p.E2950K
32%
1,346
P183
SCLC
ATM
chr11:108225599
NM_000051
c.8848G>A
p.E2950K
34%
359
P185
SCLC
ATM
chr11:108225599
NM_000051
c.8848G>A
p.E2950K
40%
1,863
P186
SCLC
ATM
chr11:108236167
NM_000051
c.9103C>T
p.L3035F
14%
408
P185
SCLC
BRAF
chr7:140453146
NM_004333
c.1789C>G
p.L597V
43%
975
P115
LCNEC
BRAF
chr7:140481458
NM_004333
c.1350G>A
p.W450*
15%
182
P139
LCNEC
BRAF
chr7:140481458
NM_004333
c.1350G>A
p.W450*
12%
1,213
P185
SCLC
EGFR
chr7:55211068
NM_005228
c.311T>A
p.L104Q
86%
31
P049
AC
EGFR
chr7:55211068
NM_005228
c.311T>A
p.L104Q
75%
102
P049
AC
EGFR
chr7:55221843
NM_005228
c.887_888delinsTT
p.P296L
14%
413
P185
SCLC
EGFR
chr7:55241726
NM_005228
c.2174C>T
p.T725M
24%
120
P119
LCNEC
EGFR
chr7:55249020
NM_005228
c.2318A>C
p.H773P
14%
301
P076
TC
3
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
EGFR
chr7:55249153
NM_005228
c.2451_2452delinsTG
p.W817C
15%
283
P193
SCLC
EGFR
chr7:55259518
NM_005228
c.2576C>T
p.A859V
11%
344
P195
SCLC
ERBB2
chr17:37881026
NM_004448
c.2354_2355delinsGG
p.L785R
81%
7,685
P056
AC
ERBB2
chr17:37881026
NM_004448
c.2354_2355delinsGG
p.L785R
94%
10,654
P153
LCNEC
ERBB2
chr17:37881026
NM_004448
c.2354_2355delinsGG
p.L785R
87%
5,326
P005
SCLC
ERBB2
chr17:37881026
NM_004448
c.2354_2355delinsGG
p.L785R
98%
6,727
P068
TC
ERBB2
chr17:37881410
NM_004448
c.2602C>T
p.R868W
10%
295
P134
AC
ERBB2
chr17:37881410
NM_004448
c.2602C>T
p.R868W
13%
292
P097
LCNEC
ERBB2
chr17:37881410
NM_004448
c.2602C>T
p.R868W
13%
286
P183
SCLC
ERBB2
chr17:37881410
NM_004448
c.2602C>T
p.R868W
25%
177
P189
SCLC
ERBB2
chr17:37881410
NM_004448
c.2602C>T
p.R868W
11%
275
P194
SCLC
ERBB2
chr17:37881432
NM_004448
c.2624C>T
p.T875I
20%
364
P089
LCNEC
ERBB2
chr17:37881432
NM_004448
c.2624C>T
p.T875I
12%
215
P066
TC
ERBB4
chr2:212288982
NM_005235
c.2764G>A
p.D922N
41%
162
P185
SCLC
ERBB4
chr2:212289002
NM_005235
c.2744C>A
p.T915N
13%
291
P051
AC
ERBB4
chr2:212587144
NM_005235
c.857G>A
p.G286E
10%
676
P185
SCLC
4
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
ERBB4
chr2:212587216
NM_005235
c.785G>A
p.C262Y
14%
243
P139
LCNEC
ERBB4
chr2:212589833
NM_005235
c.709G>A
p.G237S
12%
447
P139
LCNEC
FGFR1
chr8:38282201
NM_001174067
c.855_856insG
p.P286fs
27%
103
P053
AC
FGFR1
chr8:38282201
NM_001174067
c.855_856insG
p.P286fs
26%
134
P119
LCNEC
FGFR2
chr10:123279642
NM_022970
c.790G>A
p.A264T
19%
139
P125
LCNEC
GNAS
chr20:57484407
NM_080425
c.2516_2517insC
p.D839fs
20%
207
P049
AC
GNAS
chr20:57484421
NM_080425
c.2531G>A
p.R844H
31%
821
P074
TC
HNF1A
chr12:121432115
NM_000545
c.862delG
p.G288fs
13%
268
P132
AC
IDH1
chr2:209113176
NM_005896
c.331G>A
p.A111T
12%
789
P185
SCLC
IDH1
chr2:209113208
NM_005896
c.299G>A
p.R100Q
15%
786
P185
SCLC
IDH1
chr2:209113233
NM_005896
c.274T>A
p.W92R
18%
150
P076
TC
IDH1
chr2:209113240
NM_005896
c.267A>C
p.K89N
43%
79
P005
SCLC
IDH1
chr2:209113240
NM_005896
c.267A>C
p.K89N
45%
162
P076
TC
JAK3
chr19:17945790
NM_000215
c.2070G>A
p.W690*
38%
118
P193
SCLC
KDR
chr4:55946247
NM_002253
c.3932C>T
p.S1311F
16%
243
P081
LCNEC
KDR
chr4:55972974
NM_002253
c.1416_1417delinsTA
p.QA472_473HT
48%
565
P050
AC
5
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
KDR
chr4:55972974
NM_002253
c.1416_1417delinsTA
p.QA472_473HT
65%
399
P081
LCNEC
KIT
chr4:55593481
NM_000222
c.1637_1638delinsGG
p.K546R
48%
1,792
P152
AC
KIT
chr4:55594209
NM_000222
c.1912delA
p.M638fs
19%
182
P049
AC
KRAS
chr12:25380276
NM_033360
c.182A>T
p.Q61L
31%
3,899
P100
LCNEC
KRAS
chr12:25380346
NM_033360
c.112G>A
p.D38N
23%
127
P059
AC
KRAS
chr12:25398284
NM_033360
c.35G>A
p.G12D
30%
1,284
P128
LCNEC
MET
chr7:116423402
NM_001127500
c.3730_3731insC
p.A1244fs
14%
426
P053
AC
MET
chr7:116423402
NM_001127500
c.3730_3731insC
p.A1244fs
19%
235
P201
AC
MET
chr7:116423402
NM_001127500
c.3730_3731insC
p.A1244fs
25%
102
P081
LCNEC
NRAS
chr1:115258732
NM_002524
c.50G>A
p.S17N
27%
244
P185
SCLC
NRAS
chr1:115258744
NM_002524
c.38G>A
p.G13D
16%
244
P185
SCLC
PDGFRA
chr4:55141055
NM_006206
c.1701_1702delinsGT
p.D568Y
100%
1,148
P161
LCNEC
PDGFRA
chr4:55144156
NM_006206
c.1985G>A
p.G662E
12%
390
P193
SCLC
PDGFRA
chr4:55144165
NM_006206
c.1994C>T
p.T665I
100%
40
P185
SCLC
PDGFRA
chr4:55152039
NM_006206
c.2471_2472delinsCT
p.V824A
97%
923
P079
TC
PIK3CA
chr3:178916887
NM_006218
c.274C>T
p.L92F
14%
279
P152
AC
6
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
PIK3CA
chr3:178916887
NM_006218
c.274C>T
p.L92F
14%
221
P139
LCNEC
PIK3CA
chr3:178916893
NM_006218
c.280C>T
p.L94F
11%
1,131
P185
SCLC
PIK3CA
chr3:178928055
NM_006218
c.1333C>T
p.L445F
15%
269
P185
SCLC
PIK3CA
chr3:178952052
NM_006218
c.3107T>C
p.L1036S
30%
2,394
P190
SCLC
PIK3CA
chr3:178952052
NM_006218
c.3107T>C
p.L1036S
39%
702
P191
SCLC
PIK3CA
chr3:178952052
NM_006218
c.3107_3108delinsCT
p.L1036S
9%
751
P193
SCLC
PIK3CA
chr3:178952052
NM_006218
c.3107T>C
p.L1036S
22%
1,821
P193
SCLC
PTEN
chr10:89720864
NM_000314
c.1015C>T
p.P339S
48%
81
P049
AC
RB1
chr13:49027217
NM_000321
c.1784C>T
p.P595L
12%
401
P185
SCLC
RB1
chr13:49033880
NM_000321
c.2017C>T
p.H673Y
17%
246
P189
SCLC
RET
chr10:43609994
NM_020975
c.1946_1947delinsTA
p.S649L
23%
2,043
P195
SCLC
RET
chr10:43615632
NM_020975
c.2711_2713delinsTTG
p.SY904_905FD
15%
267
P193
SCLC
RET
chr10:43615633
NM_020975
c.2712_2713delinsGG
p.Y905D
99%
45
P055
AC
RET
chr10:43615633
NM_020975
c.2712_2713delinsGG
p.Y905D
53%
277
P115
LCNEC
RET
chr10:43615633
NM_020975
c.2711_2713delinsTGG
p.SY904_905LD
93%
469
P061
TC
RET
chr10:43617406
NM_020975
c.2742_2743insG
p.V915fs
13%
319
P185
SCLC
7
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
RET
chr10:43617452
NM_020975
c.2789C>T
p.T930M
14%
601
P185
SCLC
SMAD4
chr18:48581201
NM_005359
c.505C>T
p.Q169*
14%
296
P200
TC
SMARCB1
chr22:24134016
NM_003073
c.167C>T
p.T56I
11%
325
P152
AC
SMARCB1
chr22:24134016
NM_003073
c.167C>T
p.T56I
12%
932
P193
SCLC
SMO
chr7:128846170
NM_005631
c.1100T>G
p.L367R
46%
94
P134
AC
TP53
chr17:7577046
NM_000546
c.892G>T
p.E298*
11%
666
P097
LCNEC
TP53
chr17:7577058
NM_000546
c.879_880delinsTT
p.E294*
51%
680
P153
LCNEC
TP53
chr17:7577120
NM_000546
c.818G>T
p.R273L
34%
701
P120
LCNEC
TP53
chr17:7577539
NM_000546
c.742_743delinsTA
p.R248*
42%
809
P119
LCNEC
TP53
chr17:7577556
NM_000546
c.725G>A
p.C242Y
11%
849
P185
SCLC
TP53
chr17:7577570
NM_000546
c.711G>T
p.M237I
37%
1,626
P122
LCNEC
TP53
chr17:7577605
NM_000546
c.676G>A
p.G226S
16%
199
P081
LCNEC
TP53
chr17:7578195
NM_000546
c.654_655insGTT
p.V218_P219insV
23%
206
P007
SCLC
TP53
chr17:7578206
NM_000546
c.643A>G
p.S215G
41%
188
P184
SCLC
TP53
chr17:7578206
NM_000546
c.643A>G
p.S215G
92%
1,204
P196
SCLC
TP53
chr17:7578211
NM_000546
c.638G>T
p.R213L
41%
465
P113
LCNEC
8
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
TP53
chr17:7578239
NM_000546
c.610G>T
p.E204*
45%
636
P161
LCNEC
TP53
chr17:7578395
NM_000546
c.535C>T
p.H179Y
27%
403
P005
SCLC
TP53
chr17:7578431
NM_000546
c.499C>T
p.Q167*
31%
153
P185
SCLC
TP53
chr17:7578455
NM_000546
c.475G>C
p.A159P
20%
296
P105
LCNEC
TP53
chr17:7578455
NM_000546
c.470_475delTCCGCG
p.V157_R158del
20%
938
P115
LCNEC
TP53
chr17:7578456
NM_000546
c.469_474delGTCCGC
p.V157_R158del
62%
834
P115
LCNEC
TP53
chr17:7578461
NM_000546
c.469G>T
p.V157F
81%
355
P091
LCNEC
TP53
chr17:7578461
NM_000546
c.464_469delCCCGCG
p.T155_V157delinsI
11%
401
P115
LCNEC
TP53
chr17:7578464
NM_000546
c.466_467insC
p.R156fs
43%
241
P180
LCNEC
TP53
chr17:7578464
NM_000546
c.466_467insC
p.R156fs
50%
211
P183
SCLC
TP53
chr17:7578464
NM_000546
c.466_467insC
p.R156fs
86%
526
P186
SCLC
TP53
chr17:7578465
NM_000546
c.463_465delinsCTT
p.T155L
14%
262
P180
LCNEC
TP53
chr17:7578467
NM_000546
c.463A>C
p.T155P
74%
206
P183
SCLC
TP53
chr17:7578467
NM_000546
c.463A>C
p.T155P
76%
548
P186
SCLC
TP53
chr17:7578468
NM_000546
c.462_463insC
p.T155fs
30%
208
P183
SCLC
9
Allelic
Gene
Start Position
Transcript ID
cDNA Change
Change_Protein
Tumor
Cov.
Patient
Freq.
Type
TP53
chr17:7578469
NM_000546
c.461G>T
p.G154V
89%
138
P190
SCLC
TP53
chr17:7578469
NM_000546
c.461G>T
p.G154V
93%
283
P191
SCLC
TP53
chr17:7578469
NM_000546
c.461G>T
p.G154V
68%
191
P193
SCLC
TP53
chr17:7578475
NM_000546
c.455delC
p.P152fs
25%
132
P185
SCLC
TP53
chr17:7579463
NM_000546
c.224delC
p.P75fs
57%
89
P195
SCLC
VHL
chr3:10191497
NM_000551
c.490C>T
p.Q164*
13%
305
P185
SCLC
10
1
Table S3. Overview of significant results and statistical tests.
Variable
Gene
p-Value
ATM
0.022
TP53
<0.001
ATM
0.008
TP53
<0.001
PIK3CA
0.031
ATM
0.005
TP53
<0.001
ATM
0.013
TP53
<0.001
PIK3CA
0.029
Overall Survival (OS)
PIK3CA
0.040
Progression Free Survival
ATM
0.020
(PFS)
APC
0.020
Tumor Type
IASLC-Grade
Test
Pearson's Chi-squared test
Exact Wilcoxon Mann-Whitney
Rank Sum Test
N-Status
Metastasis
Fisher's Exact Test for Count Data
Fisher's Exact Test for Count Data
Score (logrank) test (COXPH)
Score (logrank) test (COXPH)
2
3
11