Download Supplementary Table 1

Supplementary Table 1: Next-generation sequencing (MSK-IMPACT) gene panel - 241 genes*
(*241 genes represent shared genes across MSK-IMPACT V5 (300 genes) and V6 (341 genes), both of which were utilized in
this study)
Gene_Symbol
ABL1
AKT1
AKT2
AKT3
HGNC_ID
76
391
392
393
ALK
ALOX12B
AMER1
(FAM123B)
APC
AR
ARAF
ARID1A
ARID1B
ARID2
ASXL1
ATM
ATR
ATRX
AURKA
BAP1
427
430
26837
BCL2L1
BCL2L11
BCL6
BCOR
BRAF
BRCA1
BRCA2
CARD11
CBL
CCND1
CCND2
CCND3
CCNE1
CD79B
CDC73
992
994
1001
20893
1097
1100
1101
16393
1541
1582
1583
1585
1589
1699
16783
CDH1
CDK12
CDK4
CDK6
CDK8
1748
24224
1773
1777
1779
583
644
646
11110
18040
18037
18318
795
882
886
11393
950
Description
c-abl oncogene 1, non-receptor tyrosine kinase
v-akt murine thymoma viral oncogene homolog 1
v-akt murine thymoma viral oncogene homolog 2
v-akt murine thymoma viral oncogene homolog 3 (protein
kinase B, gamma)
anaplastic lymphoma receptor tyrosine kinase
arachidonate 12-lipoxygenase, 12R type
family with sequence similarity 123B
Location
9q34.1
14q32.32-q32.33
19q13.1-q13.2
1q44
adenomatous polyposis coli
androgen receptor
v-raf murine sarcoma 3611 viral oncogene homolog
AT rich interactive domain 1A (SWI-like)
AT rich interactive domain 1B (SWI1-like)
AT rich interactive domain 2 (ARID, RFX-like)
additional sex combs like 1 (Drosophila)
ataxia telangiectasia mutated
ataxia telangiectasia and Rad3 related
alpha thalassemia/mental retardation syndrome X-linked
aurora kinase A
BRCA1 associated protein-1 (ubiquitin carboxy-terminal
hydrolase)
BCL2-like 1
BCL2-like 11 (apoptosis facilitator)
B-cell CLL/lymphoma 6
BCL6 corepressor
v-raf murine sarcoma viral oncogene homolog B1
breast cancer 1, early onset
breast cancer 2, early onset
caspase recruitment domain family, member 11
Cas-Br-M (murine) ecotropic retroviral transforming sequence
cyclin D1
cyclin D2
cyclin D3
cyclin E1
CD79b molecule, immunoglobulin-associated beta
cell division cycle 73, Paf1/RNA polymerase II complex
component, homolog (S. cerevisiae)
cadherin 1, type 1, E-cadherin (epithelial)
cyclin-dependent kinase 12
cyclin-dependent kinase 4
cyclin-dependent kinase 6
cyclin-dependent kinase 8
5q21-q22
Xq12
Xp11.3-p11.23
1p36.1-p35
6q25.3
12q13.11
20q11
11q22-q23
3q22-q24
Xq21.1
20q13
3p21.31-p21.2
2p23
17p13.1
Xq11.1
20q11.21
2q13
3q27
Xp11.4
7q34
17q21-q24
13q12-q13
7p22
11q23.3-qter
11q13
12p13
6p21
19q12
17q23
1q25
16q22.1
17q12
12q13
7q21-q22
13q12
CDKN1A
CDKN2A
1784
1787
CDKN2B
CDKN2C
CHEK1
CHEK2
CIC
CREBBP
CRKL
CRLF2
1788
1789
1925
16627
14214
2348
2363
14281
CSF1R
CTCF
CTNNB1
DAXX
DDR2
DICER1
DIS3
DNMT1
DNMT3A
DNMT3B
E2F3
EGFR
EP300
EPHA3
EPHA5
EPHB1
ERBB2
2433
13723
2514
2681
2731
17098
20604
2976
2978
2979
3115
3236
3373
3387
3389
3392
3430
ERBB3
3431
ERBB4
3432
ERCC2
3434
ERCC5
3437
ERG
ESR1
ETV1
ETV6
EZH2
FAM46C
FAT1
FBXW7
FGFR1
FGFR2
FGFR3
3446
3467
3490
3495
3527
3595
16712
3688
3689
3690
cyclin-dependent kinase inhibitor 1A (p21, Cip1)
cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits
CDK4)
cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)
cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)
CHK1 checkpoint homolog (S. pombe)
CHK2 checkpoint homolog (S. pombe)
capicua homolog (Drosophila)
CREB binding protein
v-crk sarcoma virus CT10 oncogene homolog (avian)-like
cytokine receptor-like factor 2
colony stimulating factor 1 receptor
CCCTC-binding factor (zinc finger protein)
catenin (cadherin-associated protein), beta 1, 88kDa
death-domain associated protein
discoidin domain receptor tyrosine kinase 2
dicer 1, ribonuclease type III
DIS3 mitotic control homolog (S. cerevisiae)
DNA (cytosine-5-)-methyltransferase 1
DNA (cytosine-5-)-methyltransferase 3 alpha
DNA (cytosine-5-)-methyltransferase 3 beta
E2F transcription factor 3
epidermal growth factor receptor
E1A binding protein p300
EPH receptor A3
EPH receptor A5
EPH receptor B1
v-erb-b2 erythroblastic leukemia viral oncogene homolog 2,
neuro/glioblastoma derived oncogene homolog (avian)
v-erb-b2 erythroblastic leukemia viral oncogene homolog 3
(avian)
v-erb-a erythroblastic leukemia viral oncogene homolog 4
(avian)
excision repair cross-complementing rodent repair deficiency,
complementation group 2
excision repair cross-complementing rodent repair deficiency,
complementation group 5
v-ets erythroblastosis virus E26 oncogene homolog (avian)
estrogen receptor 1
ets variant 1
ets variant 6
enhancer of zeste homolog 2 (Drosophila)
family with sequence similarity 46, member C
FAT tumor suppressor homolog 1 (Drosophila)
F-box and WD repeat domain containing 7
fibroblast growth factor receptor 1
fibroblast growth factor receptor 2
fibroblast growth factor receptor 3
6p21.1
9p21
9p21
1p32.3
11q24.2
22q12.1
19q13.2
16p13.3
22q11.21
Xp22.3 and
Yp11.3
5q32
16q21-q22.3
3p21
6p21.3
1q12-q23
14q32.2
13q21.32
19p13.2
2p23
20q11.2
6p22
7p12
22q13.2
3p11.2
4q13.1
3q21-q23
17q11.2-q12
12q13
2q33.3-q34
19q13.3
13q22-q34
21q22.3
6q24-q27
7p22
12p13
7q35-q36
1p12
4q35.2
4q31.23
8p12
10q25.3-q26
4p16.3
FGFR4
FH
FLCN
FLT1
3691
3700
27310
3763
FLT3
FLT4
FOXL2
FUBP1
GATA1
GATA2
GATA3
GNA11
3765
3767
1092
4004
4170
4171
4172
4379
GNAQ
GNAS
GRIN2A
GSK3B
HNF1A
HRAS
IDH1
IDH2
IGF1R
IKBKE
4390
4392
4585
4617
11621
5173
5382
5383
5465
14552
IKZF1
IL7R
INPP4A
INPP4B
INSR
IRF4
IRS1
IRS2
JAK1
JAK2
JAK3
JUN
KDM5C
KDM5A
KDR
13176
6024
6074
6075
6091
6119
6125
6126
6190
6192
6193
6204
11114
9886
6307
KEAP1
KIT
23177
6342
KRAS
LMO1
MAP2K1
MAP2K2
MAP2K4
6407
6641
6840
6842
6844
fibroblast growth factor receptor 4
fumarate hydratase
folliculin
fms-related tyrosine kinase 1 (vascular endothelial growth
factor/vascular permeability factor receptor)
fms-related tyrosine kinase 3
fms-related tyrosine kinase 4
forkhead box L2
far upstream element (FUSE) binding protein 1
GATA binding protein 1 (globin transcription factor 1)
GATA binding protein 2
GATA binding protein 3
guanine nucleotide binding protein (G protein), alpha 11 (Gq
class)
guanine nucleotide binding protein (G protein), q polypeptide
GNAS complex locus
glutamate receptor, ionotropic, N-methyl D-aspartate 2A
glycogen synthase kinase 3 beta
HNF1 homeobox A
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
isocitrate dehydrogenase 1 (NADP+), soluble
isocitrate dehydrogenase 2 (NADP+), mitochondrial
insulin-like growth factor 1 receptor
inhibitor of kappa light polypeptide gene enhancer in B-cells,
kinase epsilon
IKAROS family zinc finger 1 (Ikaros)
interleukin 7 receptor
inositol polyphosphate-4-phosphatase, type I, 107kDa
inositol polyphosphate-4-phosphatase, type II, 105kDa
insulin receptor
interferon regulatory factor 4
insulin receptor substrate 1
insulin receptor substrate 2
Janus kinase 1
Janus kinase 2
Janus kinase 3
jun proto-oncogene
lysine (K)-specific demethylase 5C
lysine (K)-specific demethylase 5A
kinase insert domain receptor (a type III receptor tyrosine
kinase)
kelch-like ECH-associated protein 1
v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene
homolog
v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
LIM domain only 1 (rhombotin 1)
mitogen-activated protein kinase kinase 1
mitogen-activated protein kinase kinase 2
mitogen-activated protein kinase kinase 4
5q33-qter
1q42.1
17p11.2
13q12
13q12
5q34-q35
3q23
1p31.1
Xp11.23
3q21
10p15
19p13.3
9q21
20q13.2-q13.3
16p13.2
3q13.3
12q24.31
11p15.5
2q32-qter
15q21-qter
15q26.3
1q31
7pter-7qter
5p13
2q11.2
4q31.1
19p13.3-p13.2
6p25-p23
2q36
13q34
1p32.3-p31.3
9p24
19p13-p12
1p32-p31
Xp11.22-p11.21
12p11
4q11-q12
19p13.2
4q11-q12
12p12.1
11p15
15q22.1-q22.33
19p13.3
17p11.2
MAP3K1
MAPK1
MCL1
MDM2
MDM4
MED12
MEF2B
MEN1
MET
MITF
MLH1
MLL
6848
6871
6943
6973
6974
11957
6995
7010
7029
7105
7127
7132
MLL2
MLL3
MPL
MRE11A
MSH2
MSH6
MTOR
MYC
MYCL1
7133
13726
7217
7230
7325
7329
3942
7553
7555
MYCN
7559
MYD88
NBN
NF1
NF2
NFE2L2
NKX2-1
NOTCH1
NOTCH2
NOTCH3
NOTCH4
NPM1
NRAS
NTRK1
NTRK2
NTRK3
PAK7
PALB2
PARK2
PARP1
PAX5
PBRM1
PDGFRA
PDGFRB
PHOX2B
7562
7652
7765
7773
7782
11825
7881
7882
7883
7884
7910
7989
8031
8032
8033
15916
26144
8607
270
8619
30064
8803
8804
9143
mitogen-activated protein kinase kinase kinase 1
mitogen-activated protein kinase 1
myeloid cell leukemia sequence 1 (BCL2-related)
Mdm2 p53 binding protein homolog (mouse)
Mdm4 p53 binding protein homolog (mouse)
mediator complex subunit 12
myocyte enhancer factor 2B
multiple endocrine neoplasia I
met proto-oncogene (hepatocyte growth factor receptor)
microphthalmia-associated transcription factor
mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)
myeloid/lymphoid or mixed-lineage leukemia (trithorax
homolog, Drosophila)
myeloid/lymphoid or mixed-lineage leukemia 2
myeloid/lymphoid or mixed-lineage leukemia 3
myeloproliferative leukemia virus oncogene
MRE11 meiotic recombination 11 homolog A (S. cerevisiae)
mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)
mutS homolog 6 (E. coli)
mechanistic target of rapamycin (serine/threonine kinase)
v-myc myelocytomatosis viral oncogene homolog (avian)
v-myc myelocytomatosis viral oncogene homolog 1, lung
carcinoma derived (avian)
v-myc myelocytomatosis viral related oncogene,
neuroblastoma derived (avian)
myeloid differentiation primary response gene (88)
nibrin
neurofibromin 1
neurofibromin 2 (merlin)
nuclear factor (erythroid-derived 2)-like 2
NK2 homeobox 1
notch 1
notch 2
notch 3
notch 4
nucleophosmin (nucleolar phosphoprotein B23, numatrin)
neuroblastoma RAS viral (v-ras) oncogene homolog
neurotrophic tyrosine kinase, receptor, type 1
neurotrophic tyrosine kinase, receptor, type 2
neurotrophic tyrosine kinase, receptor, type 3
p21 protein (Cdc42/Rac)-activated kinase 7
partner and localizer of BRCA2
parkinson protein 2, E3 ubiquitin protein ligase (parkin)
poly (ADP-ribose) polymerase 1
paired box 5
polybromo 1
platelet-derived growth factor receptor, alpha polypeptide
platelet-derived growth factor receptor, beta polypeptide
paired-like homeobox 2b
5q11.2
22q11.2
1q21
12q13-q14
1q32
Xq13
19p13.11
11q13
7q31
3p14.1-p12.3
3p22.3
11q23
12q12-q13
7q36
1p34
11q21
2p21
2p16
1p36
8q24
1p34.3
2p24.3
3p22
8q21-q24
17q11.2
22q12.2
2q31
14q13.3
9q34.3
1p13-p11
19p13.2-p13.1
6p21.3
5q35.1
1p13.2
1q21-q22
9q22.1
15q24-q25
20p12
16p12.1
6q25.2-q27
1q41-q42
9p13.2
3p21
4q12
5q33.1
4p13
PIK3C2G
PIK3CA
PIK3CB
PIK3CD
PIK3CG
PIK3R1
PIK3R2
PIK3R3
PLK2
PMS2
PNRC1
POLE
PPP2R1A
PRDM1
PRKAR1A
8973
8975
8976
8977
8978
8979
8980
8981
19699
9122
17278
9177
9302
9346
9388
PTCH1
PTEN
PTPN11
PTPRD
PTPRS
PTPRT
RAC1
9585
9588
9644
9668
9681
9682
9801
RAD50
RAF1
RARA
RB1
REL
RET
RICTOR
RNF43
ROS1
RPTOR
RUNX1
SDHA
SETD2
SF3B1
SHQ1
SMAD2
SMAD3
SMAD4
SMARCA4
9816
9829
9864
9884
9954
9967
28611
18505
10261
30287
10471
10680
18420
10768
25543
6768
6769
6770
11100
SMARCB1
11103
SMO
SOCS1
SOX2
11119
19383
11195
phosphoinositide-3-kinase, class 2, gamma polypeptide
phosphoinositide-3-kinase, catalytic, alpha polypeptide
phosphoinositide-3-kinase, catalytic, beta polypeptide
phosphoinositide-3-kinase, catalytic, delta polypeptide
phosphoinositide-3-kinase, catalytic, gamma polypeptide
phosphoinositide-3-kinase, regulatory subunit 1 (alpha)
phosphoinositide-3-kinase, regulatory subunit 2 (beta)
phosphoinositide-3-kinase, regulatory subunit 3 (gamma)
polo-like kinase 2
PMS2 postmeiotic segregation increased 2 (S. cerevisiae)
proline-rich nuclear receptor coactivator 1
polymerase (DNA directed), epsilon
protein phosphatase 2, regulatory subunit A, alpha
PR domain containing 1, with ZNF domain
protein kinase, cAMP-dependent, regulatory, type I, alpha
(tissue specific extinguisher 1)
patched 1
phosphatase and tensin homolog
protein tyrosine phosphatase, non-receptor type 11
protein tyrosine phosphatase, receptor type, D
protein tyrosine phosphatase, receptor type, S
protein tyrosine phosphatase, receptor type, T
ras-related C3 botulinum toxin substrate 1 (rho family, small
GTP binding protein Rac1)
RAD50 homolog (S. cerevisiae)
v-raf-1 murine leukemia viral oncogene homolog 1
retinoic acid receptor, alpha
retinoblastoma 1
v-rel reticuloendotheliosis viral oncogene homolog (avian)
ret proto-oncogene
RPTOR independent companion of MTOR, complex 2
ring finger protein 43
c-ros oncogene 1 , receptor tyrosine kinase
regulatory associated protein of MTOR, complex 1
runt-related transcription factor 1
succinate dehydrogenase complex, subunit A, flavoprotein (Fp)
SET domain containing 2
splicing factor 3b, subunit 1, 155kDa
SHQ1 homolog (S. cerevisiae)
SMAD family member 2
SMAD family member 3
SMAD family member 4
SWI/SNF related, matrix associated, actin dependent regulator
of chromatin, subfamily a, member 4
SWI/SNF related, matrix associated, actin dependent regulator
of chromatin, subfamily b, member 1
smoothened homolog (Drosophila)
suppressor of cytokine signaling 1
SRY (sex determining region Y)-box 2
12p12
3q26.3
3q21-qter
1p36.2
7q22
5q13.1
19q13.2-q13.4
1p34.1
5q12.1-q13.2
7p22.1
6q16.1
12q24.3
19q13
6q21
17q23-q24
9q22.1-q31
10q23
12q24.1
9p24.1-p23
19p13.3
20q12-q13
7p22
5q23-q31
3p25
17q21.1
13q14.2
2p13-p12
10q11.2
5p13.1
17q23.2
6q21-q22
17q25.3
21q22.3
5p15
3p21.31
2q33.1
3p13
18q21
15q21-q22
18q21.1
19p13.3
22q11.23
7q32.1
16p13.13
3q26.3-q27
SPOP
SRC
11254
11283
STAG2
STK11
SUFU
SYK
TERT
TET1
TET2
TGFBR2
TMPRSS2
TNFAIP3
TNFRSF14
11355
11389
16466
11491
11730
29484
25941
11773
11876
11896
11912
TOP1
TP53
TP63
TSC1
TSC2
TSHR
U2AF1
VHL
WT1
XPO1
YAP1
YES1
11986
11998
15979
12362
12363
12373
12453
12687
12796
12825
16262
12841
speckle-type POZ protein
v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog
(avian)
stromal antigen 2
serine/threonine kinase 11
suppressor of fused homolog (Drosophila)
spleen tyrosine kinase
telomerase reverse transcriptase
tet oncogene 1
tet oncogene family member 2
transforming growth factor, beta receptor II (70/80kDa)
transmembrane protease, serine 2
tumor necrosis factor, alpha-induced protein 3
tumor necrosis factor receptor superfamily, member 14
(herpesvirus entry mediator)
topoisomerase (DNA) I
tumor protein p53
tumor protein p63
tuberous sclerosis 1
tuberous sclerosis 2
thyroid stimulating hormone receptor
U2 small nuclear RNA auxiliary factor 1
von Hippel-Lindau tumor suppressor
Wilms tumor 1
exportin 1 (CRM1 homolog, yeast)
Yes-associated protein 1
v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
17q21.33
20q12-q13
Xq25
19p13.3
10q24.32
9q22
5p15.33
10q21
4q24
3p22
21q22.3
6q23-q25
1p36.32
20q12-q13.1
17p13.1
3q27-q29
9q34
16p13.3
14q24-q31
21q22.3
3p25.3
11p13
2p15
11q13
18p11.31-p11.21