Supplemental Materials Individualized Molecular Analyses Guide

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Supplemental Materials Individualized Molecular Analyses Guide
Supplemental Materials
Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling
of Tissue and Blood in Metastatic Triple Negative Breast Cancer
Heather A. Parsons, MD MPH*1,#; Julia A. Beaver, MD*1; Ashley Cimino-Mathews, MD1; Siraj M. Ali, MD
PhD2; Jennifer Axilbund, MS, CGC1; David Chu1, Roisin M. Connolly, MBBS1; Rory L. Cochran, PhD1; Sarah
Croessmann, PhD1; Travis Clark, PhD2; Christopher Gocke, MD1; Stacie Jeter1; Mark Kennedy, PhD2; Josh
Lauring, MD, PhD1; Justin Lee1; Doron Lipson, PhD2; Vincent A. Miller, MD2; Geoff A. Otto, PhD2; Gary L.
Rosner, ScD1; Jeffrey S. Ross, MD2, Shannon Slater1; Phil J. Stephens, PhD2; Dustin A. VanDenBerg1;
Antonio C. Wolff, MD1; Lauren E. Young, MS2; Daniel J. Zabransky1; Zhe Zhang, MS1; Jane Zorzi, RN, BSN1;
Vered Stearns, MD1&; and Ben H. Park, MD, PhD1& (*These authors contributed equally to this study, &These
authors contributed equally to this study)
1
The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore,
MD; 2Foundation Medicine Inc., Cambridge, MA. #Current Affiliation: Susan F. Smith Center for Women’s
Cancers, Breast Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.
Corresponding authors: Ben H. Park and Vered Stearns, The Sidney Kimmel Comprehensive Cancer Center at
Johns Hopkins, 1650 Orleans Street, Baltimore, MD 21287, e-mail: [email protected], [email protected]
Supplemental Figure 1
Figure S1. Oncoprint of Somatic Genomic Alterations in Metastatic
Biopsies of 20 Triple Negative Breast Cancers. Shown are the
frequencies of genetic alterations identified by NGS in the 20 metastatic
lesions from triple negative breast cancer patients. Alterations include
point mutations and copy number alterations as shown in the key below.
Table S1. Characteristics of genomic alterations from metastatic tumor biopsies
Patient
1
1
1
1
1
1
1
2
2
2
2
2
3
3
3
3
3
5
5
5
5
6
6
6
6
6
6
7
7
7
8
8
9
9
9
9
9
9
9
10
13
13
13
Gene
TP53
FGFR1
CCNE1
MYC
FGFR2
MLL2
ZNF703
TP53
FGFR1
MCL1
ATRX
MYST3
TP53
RET
MYC
ZNF217
MYST3
TP53
PTEN
PTEN
NF1
TP53
FGFR1
AKT1
RB1
ZNF703
MYST3
TP53
MCL1
MYC
TP53
CCNE1
TP53
PIK3CA
CCND1
NOTCH1
FGF3
FGF4
FGF19
TP53
TP53
MCL1
NOTCH1
Alteration
R342*
AMP
AMP
AMP
FUSION
G2863fs*13
AMP
Y163C
AMP
AMP
R418*
AMP
M66fs*57
AMP
AMP
AMP
AMP
R209fs*6
T319fs*6
Y188fs*2
GAIN
R175H
AMP
E17K
SPLICE
AMP
AMP
R248Q
AMP
AMP
Y234C
AMP
P219fs*2
V344G
AMP
NOTCH1-SEC16A
AMP
AMP
AMP
R249W
Y163C
AMP
L2446fs*28
Tumor Allele
Type
Frequency(%)
TRUNCATION
63
CNA
NA
CNA
NA
CNA
NA
FUSION
NA
TRUNCATION
42
CNA
NA
MISSENSE
60
CNA
NA
CNA
NA
TRUNCATION
17
CNA
NA
TRUNCATION
77
CNA
NA
CNA
NA
CNA
NA
CNA
NA
TRUNCATION
21
TRUNCATION
7
TRUNCATION
15
CNA
NA
MISSENSE
43
CNA
NA
MISSENSE
42
SPLICE
36
CNA
NA
CNA
NA
MISSENSE
74
CNA
NA
CNA
NA
MISSENSE
18
CNA
NA
TRUNCATION
50
MISSENSE
63
CNA
NA
FUSION
NA
CNA
NA
CNA
NA
CNA
NA
MISSENSE
4
MISSENSE
72
CNA
NA
TRUNCATION
76
13
13
14
14
14
16
16
16
16
16
16
16
17
17
17
17
19
19
19
19
19
19
19
20
20
20
20
21
21
21
21
21
21
21
21
22
22
22
22
22
22
23
23
23
23
23
ARID1A
CTNNB1
TP53
IRS2
NPM1
TP53
MCL1
CCNE1
AKT3
MYC amp
NOTCH1
CTNNA1
TP53
EGFR
BAP1
BAP1
TP53
TP53
FANCA
IGF1R
FGF14
MAP3K1
RB1
TP53
FGFR4
MYC
NOTCH1
TP53
TP53
TP53
MAP2K1
CCNE1
MCL1
CREBBP
SETD2
TP53
PTEN
CCNE1
BRCA1
MYC
CEBPA
TP53
ERBB2
ERBB2
PIK3CA
GNAS
L1176fs*17
HOMDEL
T157_R158insRA
GAIN
ZNF573-NPM1
Y234DEL
AMP
AMP
GAIN
AMP
BARHL1-NOTCH1
SPLICE
A276G
R108K
E498fs*38
HOMDEL
P58fs*65
Y163C
T1161M
AMP
A236V
HOMDEL
HOMDEL
E221fs*4
D425N
AMP
ex 34
N247K
R175H
T253N
AMP
AMP
AMP
TRAP1-CREBBP
T2354A
P151R
HOMDEL
GAIN
E23fs*17
GAIN
GAIN
R273H
D769H
V777L
M1043V
GAIN
TRUNCATION
CNA
MISSENSE
CNA
FUSION
MISSENSE
CNA
CNA
CNA
CNA
FUSION
SPLICE
MISSENSE
MISSENSE
TRUNCATION
CNA
TRUNCATION
MISSENSE
MISSENSE
CNA
MISSENSE
CNA
CNA
TRUNCATION
MISSENSE
CNA
TRUNCATION
MISSENSE
MISSENSE
MISSENSE
CNA
CNA
CNA
FUSION
MISSENSE
MISSENSE
CNA
CNA
TRUNCATION
CNA
CNA
MISSENSE
MISSENSE
MISSENSE
MISSENSE
CNA
66
NA
11
NA
NA
64
NA
NA
NA
NA
NA
42
39
38
19
NA
13
12
12
NA
27
NA
NA
56
18
NA
NA
46
4
43
NA
NA
NA
NA
39
14
NA
NA
55
NA
NA
41
54
55
41
NA
23
23
23
23
25
25
25
25
26
26
26
26
26
26
26
AURKA
ARFRP1
EMSY
MUTYH
TP53
NF1
BRAF
CRKL
PIK3CA
PIK3CA
PTEN
FGFR2
MDM2
amp
MYC amp
RB1
GAIN
GAIN
AMP
G382D
V157F
S436*
G469R
AMP
M1043I
N1044K
C296fs*12
GAIN
CNA
CNA
CNA
MISSENSE
MISSENSE
TRUNCATION
MISSENSE
CNA
MISSENSE
MISSENSE
TRUNCATION
CNA
NA
NA
NA
55
30
22
12
NA
18
18
23
NA
GAIN
GAIN
1434_1498+49del114
CNA
CNA
SPLICE
NA
NA
6
CNA=copy number alteration, NA=not applicable

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