12q15
1.78E-15
67.48-68.02
8q24.21
9.06E-13
7p11.2
9.7
15 (12.1) 2
Yes8, 13, 14
8, 14, 82
NKX2-1 (this
34.64-36.2214
67.42-67.95
14
study)
MDM2
amp.
83
15 (4.0)
7 (5.6)
3
Yes
129.18-129.34 10.3
14 (3.8)
10 (8.1)
0
Yes 8, 13, 14, 84
128.77-129.00 8 MYC $$
amp., transl.30
9.97E-11
54.65-55.52
8.7
11 (3.0)
8 (6.5)
3
Yes 8, 13, 14, 85, 86
54.44-55.66 8
EGFR
amp., mut.29, 30
8q21.13
1.13E-07
80.66-82.55
10.4
9 (2.4)
6 (4.8)
8
Yes 8, 14
48.86-97.23 14
12q14.1
1.29E-07
56.23-56.54
10.4
11 (3.0)
5 (4.0)
15
Yes 8, 90
56.26-56.75 8
CDK4
mut. 29, 30
12p12.1
2.83E-07
24.99-25.78
10.4
8 (2.2)
5 (4.0)
6
Yes 14, 91
24.61-26.95 14
KRAS
mut. 29, 30
19q12
1.60E-06
34.79-35.42
6.7
7 (1.9)
5 (4.0)
5
Yes 8, 14
34.79-35.55 8
CCNE1
amp.93, 94
17q12
2.34E-05
34.80-35.18
16.1
5 (1.3)
1 (0.8)
12
Yes 8, 86
34.80-35.99 8
ERBB2
amp., mut.29, 30
11q13.3
5.17E-05
68.52-69.36
6.5
7 (1.9)
2 (1.6)
9
Yes 8, 13, 14, 96, 97
68.58-69.34 8
CCND1
transl. 30
5p15.33
0.000279
0.75-1.62
4.2
8 (2.2)
5 (4.0)
10
Yes 13, 14
1-4.50 13
TERT
mut.29
22q11.21
0.001461
19.06-20.13
6.6
6 (1.6)
3 (2.4)
15
Yes 8, 14
19.45-20.31 8
mut. 87-89
EGFR56
mut. 92
mut. 95
ERBB257
New candidate gene(s)
siRNA evidence
in lung adenocarcinoma
Genomic evidence in lung
adenocarcinoma$
Genomic evidence in cancer $
Known proto-oncogene in region*#
Minimal previously defined
regional boundary*
Region reported
in lung cancer?
23 (6.2)
# of genes *^
13.7
# of top tertile
(percentage) above threshold%
Peak region
35.61-36.09
# of samples (percentage)
above threshold%
2.26E-29
Max. inferred copy #
14q13.3
q value
Cytoband*
Supplementary table 10: Focal regions of amplification
NKX2-1, MBIP
5p15.31
0.007472
8.88-10.51
5.6
5 (1.3)
4 (3.2)
7
Yes 8
8.88-14.31 8
1q21.2
0.028766
143.48-149.41 4.6
5 (1.3)
4 (3.2)
86
No
20q13.32
0.0445
55.52-56.30
4.4
5 (1.3)
4 (3.2)
6
No
5p14.3
0.064673
19.72-23.09
3.8
5 (1.3)
3 (2.4)
2
No
6p21.1
0.078061
43.76-44.12
7.7
4 (1.1)
3 (2.4)
2
No
6p21.33
0.10468
30.24-30.53
6.2
3 (0.8)
3 (2.4)
5
No
2p15
0.12296
61.87-63.04
13.1
2 (0.5)
2 (1.6)
5
Yes 14
49.10-64.73 14
7q21.2
0.12296
91.38-92.69
7.7
3 (0.8)
3 (2.4)
11
Yes 8
90.81-92.22 8
3q26.2
0.12892
171.56-172.26 5.8
3 (0.8)
2 (1.6)
5
No
19q13.12
0.135
40.27-40.43
7.7
3 (0.8)
1 (0.8)
5
No
18q11.2
0.135
21.54-21.90
6.3
3 (0.8)
2 (1.6)
1
No
8p11.23
0.14247
38.16-40.88
8.1
4 (1.1)
4 (3.2)
16
Yes 8, 14
ARNT
transl., mut. 29, 30
VEGFA
38.24-38.45 14
CDK6
mut., transl., amp. 29, 30
SKIL
mut. 29
SS18
transl. 30
FGFR1
mut, transl. 29, 30
WHSC1L1 14
* based on hg17 human genome assembly, positions in Mb;
#
Known proto-oncogenes defined as found in either COSMIC
29,
CGP Census 30 or other evidence; if there is more than one known proto-oncogene in the region,
only one is listed (priority for listing is, in order: known lung adenocarcinoma mutation, known lung cancer mutation, other known mutation (by COSMIC frequency),
listing in CGP Census);
%
Most variable numbers and percentages refer to the top 1/3 least stromally contaminated samples, as assayed by standard deviation measurements;
^ RefSeq genes only;
$
Abbreviations are amp. = amplification, transl. = translocation and mut. = mutation;
$$
MYC is near, but not within the peak region.