Supplemental Table 1: Lung Cancer Mutation Consortium Participating Institutions

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
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
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
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 / KRASc.34G>A (p.G12S)
BFTC 905 / NRASc.182A>T (p.Q61L)
BFTC 909 / PIK3CAc.1633G>A (p.E545K)
CAL-51 / PIK3CAc.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 / PIK3CA c.3140A>G (p.H1047R)
DNA 32 / PIK3CA c.3140A>T (p.H1047L)
Patient samples for FISH
ALK A / Positive for ALK rearrangement
ALK C / Positive for ALKrearrangement
ALK D / Positive for ALKrearrangement
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

Supplemental Table 4. Analysis of mutation frequency for EGFR andKRAS, 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
(proportion of cases detected with KRAS mutation) / 23% (68) / 22% (31) / 30% (117) / 0.05
EGFR genotyping completed (n=987) / n= 299 / n= 142 / n= 394
EGFR positive call rate
(proportion of cases detected with EGFR mutation) / 24% (73) / 29% (41) / 20% (79) / 0.08

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 / Expected Result
1 / 2 / 3* / 4** / 5
M
U
T
A
T
I
O
N / DNA 36 / No consensus / NA / NA / NA / NA / NA
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
F
I
S
H / 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 4did 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 / p-value
Acinar / Lepidic / Micropapillary. / Papillary / Solid
EGFR* / n=199 / n=4 / n=3 / n=17 / n=165 / 0.05
Negative / 75% (149) / 100% (4) / 100% (3) / 71% (12) / 86% (142)
Positive / 25% (50) / 0% (0) / 0% (0) / 29% (5) / 14% (23)
KRAS** / n=196 / n=4 / n=3 / n=17 / n=165 / 0.13
Negative / 68% (133) / 25% (1) / 67% (2) / 88% (15) / 72% (118)
Positive / 32% (63) / 75% (3) / 33% (1) / 12% (2) / 28% (47)

* In specimens assayed for EGFR mutation

** In specimens assayed for KRAS mutation