Supplemental Table 1: Lung Cancer Mutation Consortium Participating Institutions
Dana Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA*
H. Lee Moffitt Cancer Center, Tampa, FL
Hollings Cancer Center at the Medical University of South Carolina, Charleston, SC
Jonsson Cancer Center at the University of California, Los Angeles, Los Angeles, CA
Massachusetts General Hospital Cancer Center, Boston, MA*
MD Anderson Cancer Center, Houston, TX
Memorial Sloan Kettering Cancer Center, New York, NY*
National Cancer Institute intramural program, Bethesda, MD*
University of Pittsburgh Cancer Institute, Pittsburg, PA
Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Center,
Baltimore, MD
Simmons Cancer Center at the University of Texas Southwestern, Dallas, TX
University of Colorado Cancer Center, Aurora, CO*
Vanderbilt-Ingram Medical Center, Nashville, TN
Winship Cancer Institute at Emory University, Atlanta, GE*
* Centers performing FISH testing. Their respective testing facilities are as follows: Colorado Molecular Correlates at the University
of Colorado, Department of Pathology at the Memorial Sloan-Kettering Cancer Center, Molecular Diagnostic Laboratory at the
Massachusetts General Hospital, Department of Pathology at the Brigham and Women's Hospital, Oncology Cytogenetics of the
Department of Pathology and Laboratory Medicine at Emory University Hospital, and the Chromosome Pathology Unit (CPU) of the
Laboratory of Pathology (CCR) at the National Cancer Institute.
Supplemental Table 2. List of the 97 small mutations evaluated in LCMC.
Variant
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
AKT1_c.49G.A
Yes
Yes
Yes
Yes
Yes
Yes
BRAF_c.1397G.T
Yes
Yes
No
Yes
Yes
Yes
BRAF_c.1406G.A
Yes
Yes
Yes
Yes
No
Yes
BRAF_c.1406G.C
Yes
Yes
Yes
Yes
Yes
Yes
BRAF_c.1406G.T
Yes
Yes
Yes
Yes
Yes
Yes
BRAF_c.1781A.G
No
No
Yes
Yes
No
No
BRAF_c.1781A.T
No
No
Yes
Yes
No
No
BRAF_c.1789C.G
Yes
Yes
No
Yes
Yes
Yes
BRAF_c.1790T.G
No
No
No
Yes
No
No
BRAF_c.1798G.A
Yes
Yes
Yes
Yes
No
No
BRAF_c.1799T.A
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2125_2127GAA.CAT
Yes
No
Yes
Yes
Yes
No
EGFR_c.2125G.A
Yes
No
Yes
Yes
Yes
No
EGFR_c.2126A.C
Yes
No
Yes
Yes
Yes
No
EGFR_c.2126A.G
Yes
No
Yes
Yes
Yes
No
EGFR_c.2126A.T
Yes
No
Yes
Yes
Yes
No
EGFR_c.2155G.A
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2155G.T
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2156G.A
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2156G.C
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2281G.T
Yes
No
Yes
Yes
Yes
No
EGFR_c.2303G.T
Yes
No
Yes
Yes
Yes
No
EGFR_c.2326C.T
Yes
No
Yes
Yes
Yes
No
EGFR_c.2327G.A
Yes
No
Yes
Yes
Yes
No
EGFR_c.2369C.T
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_c.2560A.G
Yes
No
Yes
Yes
Yes
No
EGFR_c.2572C.A
Yes
No
Yes
Yes
Yes
No
EGFR_c.2573T.G
Yes
Yes
Yes
Yes
Yes
Yes
Variant
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
EGFR_c.2582T.A
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_exon.19.del
Yes
Yes
Yes
Yes
Yes
Yes
EGFR_exon.20.ins
Yes
Yes
Yes
Yes
Yes
Yes
ERBB2_c.2264T.C
No
No
Yes
Yes
No
No
ERBB2_c.2305G.C
No
No
Yes
Yes
No
No
ERBB2_c.2329G.A
No
No
Yes
Yes
No
No
ERBB2_c.2329G.T
No
No
Yes
Yes
No
No
ERBB2_ins.A775
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.34G.A
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.34G.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.34G.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.35G.A
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.35G.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.35G.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.37G.A
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.37G.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.37G.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.38G.A
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.38G.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.38G.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c180.181TC.CA
Yes
No
Yes
Yes
Yes
No
KRAS_c.181C.A
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.181C.G
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.182A.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.182A.G
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.182A.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.183A.C
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.183A.T
Yes
Yes
Yes
Yes
Yes
Yes
KRAS_c.436G.A
Yes
No
Yes
Yes
No
No
Variant
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
KRAS_c.436G.C
Yes
No
Yes
Yes
No
No
KRAS_c.437C.T
Yes
No
Yes
Yes
No
No
MEK1_c.167A.C
Yes
Yes
Yes
Yes
Yes
Yes
MEK1_c.171G.T
Yes
Yes
Yes
Yes
Yes
Yes
MEK1_c.199G.A
Yes
Yes
Yes
Yes
Yes
Yes
NRAS_c.34G.A
Yes
Yes
Yes
Yes
No
No
NRAS_c.34G.C
Yes
Yes
Yes
Yes
No
No
NRAS_c.34G.T
Yes
Yes
Yes
Yes
No
No
NRAS_c.35G.A
Yes
Yes
Yes
Yes
No
No
NRAS_c.35G.C
Yes
Yes
Yes
Yes
No
No
NRAS_c.35G.T
Yes
Yes
Yes
Yes
No
No
NRAS_c.37G.A
Yes
Yes
Yes
Yes
No
No
NRAS_c.37G.C
Yes
Yes
Yes
Yes
No
No
NRAS_c.37G.T
Yes
Yes
Yes
Yes
No
No
NRAS_c.38G.A
Yes
Yes
Yes
Yes
No
No
NRAS_c.38G.C
Yes
Yes
Yes
Yes
No
No
NRAS_c.38G.T
Yes
Yes
Yes
Yes
No
No
NRAS_c.181C.A
Yes
Yes
Yes
Yes
Yes
Yes
NRAS_c.181C.G
Yes
Yes
Yes
Yes
No
Yes
NRAS_c.182A.C
Yes
Yes
Yes
Yes
No
Yes
NRAS_c.182A.G
Yes
Yes
Yes
Yes
Yes
Yes
NRAS_c.182A.T
Yes
Yes
Yes
Yes
Yes
Yes
NRAS_c.183A.C
Yes
Yes
Yes
Yes
No
No
NRAS_c.183A.G
Yes
Yes
Yes
Yes
No
No
NRAS_c.183A.T
Yes
Yes
Yes
Yes
No
No
PIK3CA_c.263G.A
Yes
Yes
Yes
Yes
No
No
PIK3CA_c.1035T.A
No
No
Yes
Yes
No
No
PIK3CA_c.1035T.G
No
No
Yes
Yes
No
No
PIK3CA_c.1258T.C
No
No
Yes
Yes
No
No
Variant
Site 1
Site 2
Site 3
Site 4
Site 5
Site 6
PIK3CA_c.1624G.A
Yes
Yes
Yes
Yes
Yes
Yes
PIK3CA_c.1624G.C
Yes
Yes
Yes
Yes
No
Yes
PIK3CA_c.1633G.A
Yes
Yes
Yes
Yes
Yes
Yes
PIK3CA_c.1633G.C
Yes
Yes
Yes
Yes
Yes
Yes
PIK3CA_c.1634A.C
No
No
Yes
Yes
No
No
PIK3CA_c.1634A.G
No
No
Yes
Yes
No
No
PIK3CA_c.1635G.T
No
No
Yes
Yes
No
No
PIK3CA_c.3129G.T
No
No
Yes
Yes
No
No
PIK3CA_c.3139C.T
Yes
Yes
Yes
Yes
No
No
PIK3CA_c.3140A.G
Yes
Yes
Yes
Yes
Yes
Yes
PIK3CA_c.3140A.T
Yes
Yes
Yes
Yes
Yes
Yes
Total evaluated per site
83
68
94
97
58
50
Supplemental Table 3. Genomic alterations in the validation cohort
Validation Samples
Genetic Change(s)
Cell line samples
22 RVI
PIK3CA c.1637A>G (p.Q546R)
A549
KRAS c.34G>A (p.G12S)
BFTC 905
NRAS c.182A>T (p.Q61L)
BFTC 909
PIK3CA c.1633G>A (p.E545K)
CAL-51
PIK3CA c.1624G>A (p.E542K)
CAL 62
KRAS c.34G>C (p.G12R)
HEC-1
KRAS c.35G>A (p.G12D); PIK3CA c.3145G>C (p.G1049R)
HMV-II
NRAS c.181C>A (p.Q61K)
KYSE-410
KRAS c.34G>T (p.G12C)
LoVo
KRAS c.38G>A (p.G13D)
MFE-280
PIK3CA c.3139C>T (p.H1047Y)
NCI-H1437
MAP2K1 (MEK1) c.167A>C (p.Q56P)
NCI-H1666
BRAF c.1397G>T (p.G466V)
NCI-H1734
KRAS c.37G>T (p.G13C)
NCI-H1975
EGFR c.2369C>T (p.T790M); EGFR c.2573T>G (p.L858R)
PC-9*
EGFR c.2235_2249del15 (p.E746_A750del)
SNG-M
KRAS c.35G>T (p.G12V); PIK3CA c.263G>A (p.R88Q)
SW48
EGFR c.2155G>A (p.G719S)
Patient samples from
FFPE
DNA 1
AKT1 c.49G>A (p.E17K)
DNA 7
BRAF c.1799T>A (p.V600E)
DNA 8
EGFR c.2236_50del15 (p.E746_A750del)
DNA 17
EGFR Exon 19, 15 bp deletion
DNA 19
EGFR Exon 20, 9 bp insertion
DNA 24
ERBB2 exon 20, 12bp insertion
DNA 26
PIK3CA c.1636C>A (p.Q546K)
DNA 31
DNA 32
Patient samples for
FISH
ALK A
PIK3CA c.3140A>G (p.H1047R)
PIK3CA c.3140A>T (p.H1047L)
ALK C
Positive for ALK rearrangement
ALK D
Positive for ALK rearrangement
ALK E
Positive for ALK rearrangement
ALK F
Negative for ALK rearrangement
ALK G
Negative for ALK rearrangement
ALK J
Negative for ALK rearrangement
ALK L
Negative for ALK rearrangement
ALK M
Negative for ALK rearrangement
MET A
Negative for MET amplification
MET E
Negative for MET amplification
*Previous name: PC-14
Positive for ALK rearrangement
Supplemental Table 4. Analysis of mutation frequency for EGFR and KRAS, according to specimen type.
Subset
Biopsy
Cytology
Surgical p-value
KRAS genotyping completed (n=981)
n= 297
n= 143
n= 391
KRAS positive call rate
23% (68) 22% (31) 30% (117)
0.05
(proportion of cases detected with KRAS mutation)
EGFR genotyping completed (n=987)
n= 299
n= 142
n= 394
EGFR positive call rate
24% (73) 29% (41) 20% (79)
0.08
(proportion of cases detected with EGFR mutation)
Note that a number of specimens were of unspecified type, and are not included here.
Supplemental Table 5. Proficiency Testing Summary. The site that coordinated testing was excluded from analyses.
Proficiency Samples
M
U
T
A
T
I
O
N
F
I
S
H
Expected Result
1
2
3*
4**
5
NA
NA
NA
NA
NA
DNA 36
No consensus
DNA 53
PIK3CA c.1624G>A
Pass
Pass
NT
Pass
Pass
DNA 54
PIK3CA c.1633G>A
Pass
Pass
NT
Pass
Pass
DNA 56
KRAS c.34G>C
PIK3CA c.3140A>G
Pass
Pass
NT
Pass
Pass
DNA 59
KRAS c.38G>A
Pass
Pass
NT
Pass
Pass
ALK B
Positive
Pass
Pass
Pass
NT
Pass
ALK H
Negative
Pass
Pass
Pass
NT
Pass
MET C
Negative
Pass
Pass
Pass
NT
Pass
MET G
Negative
Pass
Pass
Pass
NT
Pass
*Site 3 was unable to process the mutation proficiency samples due to insufficient material;
**Site 4 did not participate in FISH testing and therefore was not assessed for FISH proficiency
NA: not applicable; NT: not tested
Supplemental Table 7. Association between mutations and histologic subtype in surgical specimens.
Mutation Status
Predominant histological subtype
Acinar
Lepidic
EGFR*
n=199
n=4
Negative
75% (149)
100% (4)
Positive
25% (50)
0% (0)
KRAS**
n=196
n=4
Negative
68% (133)
25% (1)
Positive
32% (63)
75% (3)
* In specimens assayed for EGFR mutation
** In specimens assayed for KRAS mutation
p-value
Micropapillary.
Papillary
Solid
n=3
100% (3)
0% (0)
n=3
67% (2)
33% (1)
n=17
71% (12)
29% (5)
n=17
88% (15)
12% (2)
n=165
86% (142)
14% (23)
n=165
72% (118)
28% (47)
0.05
0.13