Coi 160031

Research
Original Investigation
The Molecular Landscape of Recurrent and Metastatic

Head and Neck Cancers
Insights From a Precision Oncology Sequencing Platform
Luc G. T. Morris, MD, MSc; Raghu Chandramohan, MSc; Lyndsay West, BA; Ahmet Zehir, PhD; Debyani Chakravarty, PhD;
David G. Pfister, MD; Richard J. Wong, MD; Nancy Y. Lee, MD; Eric J. Sherman, MD; Shrujal S. Baxi, MD; Ian Ganly, MD;
Bhuvanesh Singh, MD; Jatin P. Shah, MD; Ashok R. Shaha, MD; Jay O. Boyle, MD; Snehal G. Patel, MD; Benjamin R. Roman, MD;
Christopher A. Barker, MD; Sean M. McBride, MD; Timothy A. Chan, MD, PhD; Snjezana Dogan, MD; David M. Hyman, MD;
Michael F. Berger, PhD; David B. Solit, MD; Nadeem Riaz, MD; Alan L. Ho, MD, PhD
IMPORTANCE Recurrent and/or metastatic head and neck cancer is usually incurable.
Supplemental content at
jamaoncology.com
Implementation of precision oncology for these patients has been limited by incomplete
understanding of the molecular alterations underlying advanced disease. At the same time,
the molecular profiles of many rare head and neck cancer types are unknown. These
significant gaps in knowledge need to be addressed to rationally devise new therapies.
OBJECTIVE To illuminate the distinct biology of recurrent and metastatic head and neck
cancers and review implementation of precision oncology for patients with advanced disease.
DESIGN, SETTING, AND PARTICIPANTS After exclusions, 151 patients with advanced,
treatment-resistant head and neck tumors, including squamous cell carcinoma (HNSCC),
adenoid cystic carcinoma (ACC), and other salivary and cutaneous cancers, whose tumors were
sequenced between January 2014 and July 2015 at Memorial Sloan Kettering were recruited.
Next-generation sequencing of tumors as part of clinical care included high-depth (median
600) exonic coverage of 410 cancer genes and whole-genome copy number analysis.
INTERVENTIONS Next-generation sequencing of tumors and matched normal DNA.
MAIN OUTCOMES AND MEASURES Feasibility, the frequency of actionable molecular
alterations, the effect on decision making, and identification of alterations associated with
recurrent and metastatic disease.
RESULTS Overall, 151 patients (95 men and 56 women; mean [range] age, 61.8 [17-100] years)
were included in the study. Next-generation sequencing ultimately guided therapy in 21 of 151
patients (14%) (13 of 53 [25%] of patients with HNSCC) by refining diagnoses and matching
patients to specific therapies, in some cases with dramatic responses on basket studies.
Molecular alterations were potentially actionable in 28 of 135 patients (21%). The genetic profiles
of recurrent and metastatic tumors were often distinct from primary tumors. Compared to
primary human papillomavirus (HPV)-positive tumors, many recurrent and metastatic HPVpositive tumors exhibited a molecular profile more similar to HPV-negative tumors, including
enriched frequencies of TP53 mutation (3 of 20 tumors [15%]), whole genome duplication
(5 of 20 tumors [25%]), and 3p deletion (11 of 20 tumors [55%]). There were high rates of TERT
promoter mutation in recurrent and metastatic HPV-negative HNSCC (13 of 30 tumors [43%]),
cutaneous SCC (11 of 21 tumors [52%]), basal cell carcinoma (3 of 4 tumors [75%]), and ACC (5 of
36 tumors [14%]). Activating NOTCH1 mutations were enriched in metastatic ACCs (8 of 36
tumors [22%]).
CONCLUSIONS AND RELEVANCE These findings reveal the molecular landscape of advanced
disease and rare cancer subtypes, both predominant challenges in head and neck oncology.
To understand the repertoire of targetable alterations in advanced cancers, it is necessary to
sequence recurrent and metastatic tumors. These data are important first steps toward
implementation of precision head and neck oncology.
JAMA Oncol. doi:10.1001/jamaoncol.2016.1790
Published online July 21, 2016.
Author Affiliations: Author

affiliations are listed at the end of this
article.
Corresponding Author: Luc G. T.
Morris, MD, MSc, Department of
Surgery, Memorial Sloan Kettering
Cancer Center, 1275 York Ave,
New York, NY 10065
(morrisl@mskcc.org).
(Reprinted) E1
Copyright 2016 American Medical Association. All rights reserved.
Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016
Research Original Investigation
Next-Generation Sequencing in Difficult Head and Neck Cancers
recision oncology is a clinical approach that seeks to

match every patients tumor with the best drug, based
on molecular alterations. This approach also expands
our knowledge of cancer biology, by revealing the molecular
landscape of tumor types in which existing knowledge is
limited: recurrent, metastatic, and rare cancers.
Head and neck cancers are the sixth most common cancer worldwide, and arise from the upper aerodigestive
mucosa, salivary glands, and skin.1 Despite differences in
histology and biology across cancer types, most treatment
protocols are extrapolated from head and neck squamous
cell carcinoma (HNSCC)the most common histology.
Recurrent and metastatic disease is usually incurable. There
are significant gaps in knowledge. Unlike other cancer types,
there are no predictive biomarkers, and no new targeted
therapies have been approved for HNSCC other than cetuximab in 2006. Currently, our understanding of the molecular
landscape of head and neck cancer is drawn from exome
studies of primary tumors representing the more common
histologic subtypes.2-10
Genetic profiles of the most clinically challenging tumors
incurable, recurrent and metastatic diseaseremain poorly
defined. Less common cancer types have not heretofore been
molecularly profiled. Here, we describe our multidisciplinary head and neck cancer teams implementation of a precision oncology approach, review therapeutic successes and
limitations for patients, and analyze sequencing data to glean
new insights into the alterations that define recurrent and
metastatic head and neck cancer.
Key Points
Question Can clinical implementation of next-generation
sequencing of tumors help guide treatment and expand our
understanding of the biology of advanced head and neck cancer?
Findings Molecular profiling of advanced (nearly all recurrent and
metastatic) head and neck cancers was able to identify actionable
alterations and guide treatment in a portion of patients, refine
diagnoses in certain rare cancers, and discover unique genetic
findings that are enriched in advanced cancers.
Meaning Implementation of precision oncology is beginning to
guide treatment and improve our knowledge of molecular
alterations relevant to advanced, treatment-resistant head and
neck cancers.
Mutational signatures (APOBEC, tobacco, ultraviolet light

carcinogenesis) were analyzed using definitions previously
described.15,16
Somatic alterations in HNSCC were examined using a support vector machine algorithm to classify human papillomavirus (HPV) status, and using enrichment analysis for comparison to primary tumors in the The Cancer Genome Atlas
(TCGA) cohort.3 Germline sequencing from matched normal
blood was analyzed using a previously described pipeline.13
Additional technical details of the assay, variant calling, support vector machine algorithm, bioinformatic and biostatistical analyses are in the eAppendix in Supplement 1.
Results
Methods
The MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) assay is a targeted next-generation sequencing (NGS) assay approved
through Clinical Laboratory Improvement Amendments.11 The
assay is optimized for DNA from formalin-fixed, paraffinembedded samples, and targets single nucleotide variants, indels, and structural variants in 410 genes functionally relevant to cancer or clinically actionable targets (eTable 1 in
Supplement 2), and genome-wide copy number.12,13
After receiving institutional review board approval from
the Memorial Sloan Kettering Cancer Center, we reviewed patients treated by our multidisciplinary head and neck oncology team whose tumors were sequenced after informed written consent to an institutional review boardapproved protocol
(NCT01775072). Of 224 patients enrolled, 151 with minimum
6-month follow-up, whose tumors were sequenced between
January 2014 and July 2015, were included. Treatment(s)
initiated after NGS were considered guided by molecular data
if results led to, or justified continuation with, specific
treatments. Molecular alterations were classified by evidence
indicating standard or investigational therapies (eTable 2 in
Supplement 2).
Copy number analyses with FACETS14 were performed to
identify whole-genome duplication, 3p deletion (eFigures 1 and
2 in Supplement 1), and subclonal population structure.
E2
MSK-IMPACT was used to sequence 151 head and neck tumors,

including 53 HNSCC, 56 salivary carcinomas, 27 cutaneous carcinomas, 8 nasopharyngeal carcinomas, 3 neuroendocrine carcinomas, 2 odontogenic carcinomas, and 2 olfactory neuroblastomas (eFigure 11 in Supplement 1), in 95 men and 56 women;
66 patients had locoregional recurrence, 106 had distant metastases, and 6 had locally advanced tumors that were surgically unresectable. Clinical data are summarized in eTable 3 in
Supplement 2. Median (range) depth of sequencing was
600 (82 1165 ). Survival and genomic data are summarized in Figure 1 and eFigures 12 and 13 in Supplement 1.
Actionable Alterations
There are no standard-of-care biomarkers in head and neck
cancer, but 28 of 135 patients (21%) with tumors harboring alterations had findings with potential investigational implications7 patients (5%) with a US Food and Drug Administration (FDA)-approved biomarker and drug in another indication,
and 21 patients (16%) with clinical evidence linking the alteration to drug response (Figure 1) (eTable 2 in Supplement 2).
Ultimately, next-generation sequencing data guided therapy
in 21 of 151 patients (14%).
Landscape of HNSCC
The most frequent single nucleotide variants and copy number variants in HNSCC are depicted in Figure 2 and eTable 4
JAMA Oncology Published online July 21, 2016 (Reprinted)
jamaoncology.com
Original Investigation Research
Figure 1. Overall Survival for Patients Undergoing Clinical Tumor Sequencing

A 3-Year overall survival
HNSCC
All sites
1.0
1.0
ACC (94.1%)
NPC (83.3%)
0.8
0.6
Overall Survival
Overall Survival
0.8
HPV+ (70.9%)
0.4
HPV (60.5%)
0.2
Cutaneous SCC (79.4%)

0.6
Other salivary (66.5%)
HNSCC (64.3%)
0.4
0.2
P=.06
P=.58
0
0
0
Time From Diagnosis, y

No. at risk
HPV+
20
HPV
30
18
26
9
14
6
10
2
7
No. at risk
ACC
NPC
Skin SCC
Other salivary
HNSCC
1
6
36
7
19
18
51
33
7
14
13
44
30
4
8
9
23
0.8
0.8
HPV+ (50.5%)
0.4
HPV (29.4%)
0.2
25
2
7
7
14
21
2
6
4
9
18
0
5
3
7
ACC (83.7%)
NPC (80.0%)
Cutaneous SCC (76.2%)
Other salivary (67.5%)
0.6
0.4
HNSCC (37.4%)
0.2
P=.008
P=.53
0
0
0
Time From Recurrence, y

No. at risk
HPV+
20
HPV
28
All sites
1.0
Overall Survival
Overall Survival
HNSCC
1.0
0.6
Time From Diagnosis, y
6
7
3
3
7
0
5
1
1
4
0
4
1
0
Time From Recurrence, y
1
1
0
1
0
0
No. at risk
ACC
NPC
Skin SCC
Other salivary
HNSCC
34
7
19
18
49
22
4
12
10
13
14
2
7
3
6
10
0
6
2
2
Actionability of molecular alterations

FDA-approved in this indication
Standard of care but not FDA approved

FDA-approved in another indication
Clinical evidence in this indication
Clinical evidence in another indication
No clinical evidence
0
20
40
60
80
Patients, %
A, Overall survival from time of index treatment and time of disease recurrence
and/or metastasis, for selected tumor types. Survival probabilities were
calculated with the Kaplan-Meier method, and tumor types were compared
using the log-rank test. B, Distribution of molecular alterations, classified by
levels of evidence for actionability. HNSCC, head and neck squamous cell
carcinoma. ACC, adenoid cystic carcinoma; HPV, human papillomavirus;
NPC, nasopharyngeal carcinoma; Other salivary, other salivary cancer types;
SCC, squamous cell carcinoma.
in Supplement 2. Whole-genome duplication was present in

12 of 48 cases (25%) with complete copy number data (Figure 2)
(eFigures 1 and 2 in Supplement 1).17
The promoter region of TERT harbored mutations in 16 of
30 HPV-negative tumors (53%) (Figure 3). In this recurrent and
metastatic population, mutations in the TERT promoter were
significantly more frequent than rates reported in primary HPVnegative HNSCCs18 (12 of 70 [17%]) (odds ratio (OR), 5.5;
P < .001), indicating enrichment for this mutation in advanced cancers, although we note that deep sequencing may
be more sensitive for single nucleotide variants. Remarkably,
10 of 11 (91%) HPV-negative tongue SCCs had TERT muta-
jamaoncology.com
(Reprinted) JAMA Oncology Published online July 21, 2016
E3
Figure 2. The Molecular Landscape of Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma
50
Mutation Count
40
30
20
10
Nonsynonymous
Synonymous
HPV status
HPV Negative
HPV Positive
Unknown
Tumor location
Hypopharynx
Larynx
Oral cavity
Oropharynx
Chr3p loss
Yes
No
Whole genome duplication
Yes
No
Sinonasal
Unknown
Unknown
Smoking status
Current
Former
Never
Site sequenced
Index primary
Distant metastasis
Local recurrence
Regional recurrence
Yes
No
Distant metastasis
100
Fraction of genome with log2 copy number

value >0.2 or <0.2
1
3
5
Unknown
2
4
6
Altered genome, %
0
Clones, No.
TP53 49.1%
TERT 32.1%
FAT1 15.1%
NOTCH1 17.0%
Mutation type
PIK3CA 24.5%
Missense
3q26.3 10.4%
Nonsense
Truncating
CDKN2A 24.5%
In-frame
CDKN2B 11.3%
Promoter
EGFR 13.2%
SCNA type
Amplification
ATR 13.2%
Deletion
KMT2D/MLL2 11.3%
KMT2C/MLL3 9.4%
NSD1 9.4%
11q13 10.4%
E4
Genetic alterations and clinical data for 53 recurrent and/or metastatic head and
neck squamous cell carcinomas. Copy number values are based on 48 cases
with informative copy number data; 11q13 includes CCND1, FGF3, FGF4, and
FGF19; 3q26.3 includes PIK3CA, SOX2, and DCUN1D1. Clones indicates number
of subclonal populations per tumor; HPV, human papillomavirus; SCNA, somatic
copy number alterations.
tions. TERT promoter mutations have been linked with poorer

survival.19 There were no TERT promoter mutations in HPVpositive HNSCC, consistent with the ability of the E6 oncoprotein to activate telomerase.20 Therefore, TERT mutation and
HPV infection may represent parallel mechanisms of
telomerase activation in HNSCC.
Four tumors had mutations in mismatch repair genes, including 1 truncating mutation in MLH1 (in the highly mutated
HPV-positive case) and missense mutations in MSH2, MSH6,
and POLD1 (HPV-negative cases). The average mutation count
in these tumors was significantly elevated (17.3 vs 4.5; P < .001).
After NGS, 17 of 53 patients with HNSCC (32%) were

enrolled in clinical trials. Treatment was guided by molecular data in 13 patients (25%). In 7 patients (13%), NGS nominated targeted therapies, similar to the rate in another
recent HNSCC precision oncology study (10%). 21 Four
patients with alterations in PIK3CA or PTEN were treated on
PI3K inhibitor trials, 1 HRAS mutation on a farnesyl transferase inhibitor trial, 1 MAPK1 mutation with an ERK inhibitor
on a single-patient IND (Investigational New Drug) application, and 1 SMARCB1 deletion on an EZH2 inhibitor trial. In
6 patients (12%), the lack of actionable alterations on
jamaoncology.com
MSK-IMPACT prompted the decision to instead enroll on

immunotherapy trials.
HPV-Positive and HPV-Negative HNSCC

Comparing HPV-positive tumors (n = 21 [39.6%]) with HPVnegative tumors (n = 30), current and former tobacco use was
slightly more common in the HPV-negative population (18 patients [60%] vs 10 patients [48%]) (eTable 3 in Supplement 2).
In contrast to prior studies of primary tumors,2,3,6 recurrent
and metastatic HPV-positive and HPV-negative tumors had
similar mutation counts (4.4 vs 5.9; P = .42) and copy number
altered fraction of genome (0.19 vs 0.18; P = .78) (Figure 2).
Several genes were more frequently altered in recurrent
or metastatic HPV-negative tumors compared with HPVpositive tumors, including TP53 (21 [72%] vs 3 [15%]; P < .001),
TERT promoter (16 [55%] vs 0 [0%]; P = 9 105), and CDKN2A
mutation and deletion (11 [37%] vs 1 [5%]; P = .016). A correlation network of altered genes revealed clusters altered primarily in HPV-positive or HPV-negative tumors (eFigure 14 in
Supplement 1). Gene ontology annotations of the HPVpositive clusters were strongly enriched for tyrosine kinase
signaling (P = 3 109) (eTable 5 in Supplement 2).
We used FACETS to infer levels of intratumor
heterogeneity. 14 In multivariable analyses, HPV-positive
tumors had fewer subclonal populations (P = .03). Recurrent
and metastatic sites trended toward having more subclonal mutations than primary sites (P = .08) (eTables 6 and 7 in the
Supplement 2) .
Alterations Enriched in Recurrent and Metastatic

HPV-Positive HNSCC
The vast majority of HPV-positive HNSCCs are cured with standard therapy.22 The genetic alterations in the minority of these
tumors developing recurrence and/or metastasis are largely undefined. We examined alterations that were enriched in recurrent and metastatic HPV-positive HNSCC sequenced with
MSK-IMPACT, in comparison to primary HPV-positive tumors sequenced by TCGA.3 These 2 cohorts had similar clinical and demographic profiles, including smoking history (50%
vs 61%; P = .57).
We first examined variant profiles and determined the degree of similarity between each advanced HPV-positive tumor sequenced with MSK-IMPACT compared with HPVpositive and HPV-negative primary tumors sequenced by
TCGA. We used a support vector machine algorithm to categorize tumors as more similar to HPV-positive or HPVnegative profiles based on mutations and copy number variants. The classifier was first trained and cross-validated in the
TCGA cohort, then applied to 53 sequenced MSK-IMPACT
samples in 51 patients with known HPV status. The classifier
correctly categorized 29 of 31 (91%) HPV-negative MSKIMPACT cases, but only 12 of 21 (57%) HPV-positive cases
(P = .007) (eFigure 15 in Supplement 1). The classifier had significantly higher confidence probabilities for HPV-negative tumors (P = 4.4 105) (eFigure 3A in Supplement 1). Therefore, in this cohort, 43% of advanced HPV-positive HNSCC
tumors had genotypes that resembled primary HPV-negative
tumors (eFigure 3B in Supplement 1). These HPV-negativejamaoncology.com
like HPV-positive tumors trended toward poorer survival (hazard ratio [HR], 2.3; P = .19) although this comparison was limited by small sample size (eFigure 3C in Supplement 1).
The mutational profile of recurrent and metastatic HPVpositive tumors sequenced by MSK-IMPACT appeared intermediate between the HPV-positive and HPV-negative primary tumors in the TCGA. In comparison, the mutational
profile of HPV-negative recurrent and metastatic tumors closely
matched the primary HPV-negative cohort (P = 1.3 104)
(eFigure 4 and eFigure 16 in Supplement 1).
We examined enrichment for specific genetic alterations,
focusing on the most frequent: whole-genome duplication, 3p
deletion, TP53 mutation, and PIK3CA mutation. To allow for
potential differences between platforms, we determined enrichment by comparing HPV-negative:HPV-positive ORs between data sets (Figure 4A) (eTable 8 in Supplement 2). In the
recurrent and metastatic HPV-positive tumors, there was significant enrichment for whole-genome duplication (6.7-fold;
P = .024), 3p deletion (9.1-fold; P = .002), and 3p deletionTP53 mutation (7.6-fold; P = .03). Compared with primary HPVpositive tumors, recurrent and metastatic HPV-positive tumors had higher rates of TP53 mutation (3 of 20 tumors [15%]
vs 1 of 36 tumors [3%]; enrichment 4.6; P = .11) and lower rates
of PIK3CA mutation (2 of 20 tumors [10%] vs 13 of 36 tumors
[36%]; enrichment 0.21, P = .06).
We sought to confirm these findings in additional data sets
of recurrent and metastatic HPV-positive HNSCC. While there
are no comparable cohorts limited to recurrent and metastatic disease, the data sets of Chung et al23 and Chau et al21
included mutational data for HPV-positive tumors, a proportion of which were recurrent or metastatic. Consistent with our
data, each of the HPV-positive cohorts in the studies by Chung
et al and Chau et al exhibited higher frequencies of TP53 mutation (5%-13%) and lower frequencies of PIK3CA mutation
(13%-20%), compared with observed rates in HPV-positive primary tumors.2,3,5,6 For additional confirmation, we analyzed
TP53 status in primary uterine cervical cancers (TCGA, n = 170)
and recurrent and metastatic HPV-positive cervical cancers
(MSK-IMPACT, n = 16). The frequency of TP53 mutation was
markedly higher in metastatic cases than primary cases (4 of
16 tumors [25%] vs 5 of 170 [3%] tumors; OR, 8.3; P = .008)
(eTable 9 in Supplement 2).
TP53 mutations are uncommon (0%-3%) in HPV-positive
primary HNSCC.2,3,5,6 All TP53 mutations were truncating
(eTable 4 in Supplement 2). One patient was a current smoker
(35 pack-year), and 2 were former oligosmokers (1 and 5 packyear). Although p53 is inactivated by the HPV E6 oncoprotein,24
in vitro data reveal that complete inactivation of p53 in HPVpositive HNSCC cell lines induces resistance to radiotherapy and
more aggressive tumor behavior.25 Interestingly, TP53 mutations in HPV-positive tumors were much more likely to be subclonal than in HPV-negative tumors (3 of 4 mutations [75%] vs
4 of 27 mutations [15%]; P = .03) (eTable 7 in Supplement 2). Our
hypothesis generating data suggest that TP53 mutation in a subset of HPV-positive tumors may be associated with tobacco use,
occur later in tumor evolution, and reflect poorer prognosis.
Similarly, alterations (mutations or deletions) in RB1 were
present in 3 of 20 (15%) recurrent and metastatic HPV-positive
E5
Figure 3. Mutation Distributions in PIK3CA, NOTCH1, TP53 and TERT in Head and Neck
Squamous Cell Carcinomas
No. of Mutations
PIK3CA
E545K
3
2
1
0
PI3..
0
PI3K_rbd
100
200
PI3K_C2
300
400
PI3Ka
500
PI3_PI4_kinase
600
700
800
900
1000 1068 aa
No. of Mutations
NOTCH1
HD-N domain
PEST domain
2
1
0
200
400
600
800
1000
1200
1400
1600
1800
2000
2200
2400 2555 aa
No. of Mutations
TP53
3
2
1
0
P53..
0
P53
50
100
150
P53..
200
250
300
350
393 aa
TERT
1 295 250
1 295 228
1 295 162
1 295 104
TERT
TERT promoter
TSS
C250T
3 cases
ATG
C228T
11 cases
C228A
2 cases
Green circles indicate missense

mutations; red, truncating;
black, in-frame insertions or
deletions.
Figure 4. Genetic Alterations Enriched in Recurrent and/or Metastatic HPV-Positive HNSCC

A HPV-positive recurrent and/or metastatic tumors
HPV-positive HNSCC
vs HPV-positive primary tumors

0.5
3p deletion
9
8
3p- TP53
WGD
Chromosomal Instability
Enrichment (Ratio of Odds Ratios)
10
6
5
4
TP53 mutation
PIK3CA mutation
3
2
0.10
0.60
0.4
0.3
0.2
0.1
Frequency of alteration
0
0
0.5
1.0
1.5
2.0
2.5
3.0
log10 P value
A, Enrichment analysis for common alterations, comparing recurrent and/or

metastatic HPV-positive tumors to primary HPV-positive tumors. Red dots
indicate alterations enriched in recurrent and/or metastatic tumors, and blue
dots indicate alterations enriched in primary tumors. For these comparisons,
recurrent and/or metastatic tumors are MSK-IMPACT cases and primary tumors
are The Cancer Genome Atlas cases.3 B, Differences in chromosomal instability,
E6
P = .009
Mutant
Wild-type
TP53/RB1 Mutation Status
defined as proportion of genome copy number-altered, in TP53/RB1-mutated or

wild-type HPV-positive tumors in MSK-IMPACT (Memorial Sloan
Kettering-Integrated Mutation Profiling of Actionable Cancer Targets). Boxes
represent interquartile ranges and whiskers represent maxima and minima.
HPV indicates human papillomavirus. HNSCC, head and neck squamous cell
carcinoma.
jamaoncology.com
tumors. The degree of chromosomal instability in TP53 or RB1

mutated HPV-positive tumors was significantly higher than in
TP53/RB1 wildtype tumors (P = .009). This suggests that complete inactivation of p53 or RB has functional sequelae beyond
those resulting from incomplete degradation by E6/E7
(Figure 4B).
Mutational Signatures in HNSCC

The tobacco signature was strongest in current smokers and
was most evident in laryngeal cancers, similar to findings in
TCGA exome data.26 (eFigure 5 in Supplement 1) There was no
difference in APOBEC scores between HPV-positive and HPVnegative tumors (1.68 vs 1.36; P = .29), in contrast to data from
primary tumors, where the APOBEC signature is associated
with HPV-positivity.27 This is consistent with the overall trend
of molecular differences between HPV-positive and HPVnegative disease being attenuated in advanced cancers. The
tumors with the strongest APOBEC signatures were either sinonasal or oropharynx primaries, mostly HPV-positive
(eFigure 5 in Supplement 1).
Adenoid Cystic Carcinomas

Of 36 recurrent and metastatic ACCs, mutational load
(mean, 2.3) and fraction of copy number-altered genome
(mean, 0.12) were low. The most frequently altered gene
was NOTCH1 (12 of 33 [33%]). In 8 of 36 cases (22.2%), the
alterations (mutation or amplification) were consistent with
activating events (Figure 5) (eFigure 17 in Supplement 1).
Three samples had recurrent truncating alterations at serine
2467, which are activating mutations in leukemia. Comparing recurrent and metastatic ACCs to primary ACCs previously sequenced by our group,9 we identified significant
enrichment of NOTCH1 activating alterations (8 of 36
tumors [22.2%] vs 2 of 60 tumors [3.3%]; OR, 8.3; P = .005)
(eFigure 6 in Supplement 1), which have been linked to
aggressive tumor behavior in ACC. 28 Activating NOTCH1
mutations confer sensitivity to -secretase inhibitors, 29
nominating these drugs as potentially active in NOTCH1mutated ACCs. TERT promoter mutations were also identified in 5 ACCs (14%). TERT promoter mutations have not
been previously identified in salivary cancers (eFigure 17 in
Supplement 1 and eTable 4 in Supplement 2).
Twenty (56%) patients with ACCs were enrolled on clinical trials. In 4 patients (11%), protocol selection was guided by
NGS: 1 patient with FGFR3 mutation was treated with an FGFR
inhibitor, 1 patient with a PIK3CA mutation and 1 patient with
a PIK3R1 mutation were treated with a PI3K inhibitor, and 1 patient with MDM2 amplification was treated with an MDM2 inhibitor. Although not guided by NGS, 4 patients treated with
the multikinase inhibitor regorafenib were subsequently found
to have PDGFRA/KDR/KIT amplification, justifying the appropriateness of this protocol.
Other Salivary Cancers

There were 20 advanced salivary cancers of other histologies: 11 salivary duct carcinomas, 2 acinic cell carcinomas, 2
mammary analog secretory carcinomas (MASC), 2 mucoepidermoid carcinomas, 2 salivary adenocarcinomas, and
jamaoncology.com
1 epithelial-myoepithelial carcinoma (Figure 6) (eTable 4 in

Supplement 2).
Salivary duct carcinomas harbored numerous potentially actionable alterations (including PIK3CA, HRAS, ERBB2,
and AR) and several interesting structural variants in NF1 and
ROS1 (eTable 2) (eFigure 7 in Supplement 1). One mucoepidermoid tumor with an HRAS G13V mutation was enrolled on a
farnesyl transferase inhibitor trial.
One tumor was initially diagnosed as acinic cell carcinoma. Sequencing identified an ETV6-NTRK3 fusion (eFigure 8 in Supplement 1), changing the diagnosis to MASC.30
The patient was then enrolled on a TRK inhibitor basket
study, with a clinical near-complete response.31 A second
acinic cell c arcinoma was rediagnosed as MASC and
enrolled on a TRK inhibitor basket study, also with a similar
major response.
Cutaneous Carcinomas
Twenty-seven advanced nonmelanoma skin carcinomas of
the head and neck were sequenced: 21 squamous, 2 skin
adnexal, and 4 basal cell carcinomas (BCCs) (Figure 7) (eFigure 18 in Supplement 1 and eTable 4 in Supplement 2). A
predominating UV light mutational signature was evident in
18 of 21 (86%) cutaneous SCCs and was associated with
higher average mutation counts than the cutaneous SCCs
lacking a UV light mutational signature (37.9 mutations vs
4.3 mutations; P = .008). Deletion of 3p in combination with
TP53 mutation is a strong negative prognostic factor in
mucosal HNSCC,32 but these co-occurring alterations have
not been described in cutaneous SCC. We found 3p deletion
and TP53 mutation in 6 of 19 cases (32%).
Three of 4 advanced BCCs exhibited the UV light mutational signature, including 1 hypermutated tumor with 122 mutations. In this case, the finding of high mutational load led to
a decision to treat with immunotherapy.
One BCC lacking the UV light signature had only 2 nonsynonymous mutations: a patient who had scalp irradiation
in childhood. Three of four BCCs responded initially to hedgehog pathway inhibitors (prior to NGS) and were subsequently
confirmed to have PTCH1 mutations.
Nasopharyngeal Carcinomas
Eight recurrent and metastatic nasopharyngeal carcinomas
were sequenced (eFigure 19 in Supplement 1 and eTable 4 in
Supplement 2). Four patients with nasopharyngeal carcinoma (50%) were enrolled on clinical trials, of which one (13%)
was NGS-guided: a PIK3CA mutation led to enrollment on a
PI3K inhibitor trial.
Odontogenic Carcinomas
Two odontogenic carcinomas were profiled. Unexpectedly,
EWSR1 gene fusions were found in both (eFigure 9 in
Supplement 1). One case, initially diagnosed as ameloblastic carcinoma, had an EWSR1-FLI1 fusion, confirmed with a polymerase chain reaction assay. Fluorescence in situ hybridization analysis performed earlier had not identified rearrangement
of EWSR1, indicating the superior sensitivity of NGS in this case.
This changed the diagnosis to Ewing sarcoma with epithelial dif(Reprinted) JAMA Oncology Published online July 21, 2016
E7
Figure 5. Mutational Landscape of Recurrent and/or Metastatic Adenoid Cystic Carcinoma

7
Mutation Count
6
5
4
3
2
1
Nonsynonymous
Synonymous
Tumor location
Major salivary gland

Minor salivary gland
Histology
(growth pattern)
Cribiform or tubular
Solid
Unknown
Index primary
Distant metastasis
Site sequenced
Local recurrence
Regional recurrence
Index primary and

regional recurrence
Yes
No
Distant metastasis
Current
Former
Smoking status
Altered
genome, %
Tracheobronchial
100
Never

value >0.2 or <0.2
Present
Absent
Myb/NFIB staining
Not tested
NOTCH1 33.3%
KDM6A 19.4%
ARID1A 13.9%
Mutation type
TERT 13.9%
Missense
BCOR 11.1%
Nonsense
Truncating
MLL2 11.1%
In-frame
Promoter
4q12 11.1%
SCNA type
RASA1 8.3%
Amplification
Deletion
RUNX1 8.3%
TBX3 5.6%
YAP1 5.6%
CDKN2A/2B 5.6%
Genetic and clinical data for 36 recurrent and/or metastatic adenoid cystic carcinomas. SCNA indicates somatic copy number alterations.
ferentiation and ameloblastic morphology. This information was

used to guide chemotherapy with a sarcoma regimen.
The second case was a metastatic clear cell odontogenic
carcinoma of the maxilla, with an EWSR1-ATF1 fusion, which
has been seen in clear cell sarcomas and hyalinizing clear cell
carcinoma of salivary glands, but not in (morphologically similar) odontogenic tumors.
Other Rare Cancers

The findings in 2 olfactory neuroblastomas and 3 head and neck
neuroendocrine carcinomas are detailed in eTable 4 in
Supplement 2.
E8
Germline Analysis
One HNSCC patient had a germline heterozygous deletion in
FANCA (eFigure 10 in Supplement 1) and a tumor with a somatic
FANCA stopgain mutation. While homozygous loss of FANCA in
the germline causes Fanconi anemia, this double-hit affecting
FANCA is an interesting finding in HNSCC,33 similar to a report
in a prostate cancer, where it conferred sensitivity to cisplatin.34
The ability of NGS to profile both somatic and germline alterations is an additional source of potentially actionable data.
Complete genomic and clinical data from this study are
available in searchable form at http://www.cbioportal.org
/study?id=hnc_mskcc_2016.
jamaoncology.com
Figure 6. Mutational Landscape of Recurrent and/or Metastatic Other Salivary Carcinoma Types
30
Mutation Count
25
20
15
10
5
0
Histology
Location
Site sequenced
Distant metastasis
Smoking status
ETV6-NTRK3 fusion
Altered
genome, %
100
0
Nonsynonymous
Synonymous
Salivary duct carcinoma
Salivary ADC, NOS
Mucoepidermoid carcinoma
Acinic cell carcinoma
Epithelial-myoepithelial carcinoma
Mammary analog secretory carcinoma
Major salivary gland

Minor salivary gland
Index primary
Distant metastasis
Local recurrence
Regional recurrence
Local and
regional recurrence
Yes
No
Current
Former
Unknown
Yes
No
value >0.2 or <0.2
TP53 50%
ERBB2 25%
PIK3CA 25%
Mutation type
HRAS 20%
Missense
Nonsense
CDKN2A 15%
Truncating
In-frame
FGFR1 10%
Promoter
MYC 15%
SCNA type
Amplification
NF1 15%
Deletion
CDK12 10%
FAT1 10%
MLL3 10%
Genetic and clinical data for 20 recurrent and/or metastatic other salivary carcinoma types. ADC indicates adenocarcinoma; SCNA, somatic copy number alterations.
Discussion
Critical gaps in knowledge must be addressed to rationally devise new therapies for head and neck cancers. To date, genomics studies have been limited to cohorts of primary tumors. The
molecular landscape of the most clinically challenging tumors
treatment-resistant, recurrent and metastatic diseasehas not
been defined. Furthermore, many uncommon cancer types
have not been molecularly profiled.
Here, we review our implementation of precision oncology for patients with advanced head and neck cancers. This
effort has been useful in 3 respects: (1) illuminating the unique
molecular landscape of advanced or understudied cancers;
jamaoncology.com
(2) refining diagnoses of rare cancers; and (3) guiding

treatment based on molecular alterations.
In the initial 2 years of this approach, NGS guided therapy
in 14% of patients (25% of HNSCC patients). A major limitation has been the low frequency (21%) of targetable alterations. This underscores the importance of profiling these tumors, and the potential benefits of basket studies for diseases
such as head and neck cancer. In several cases, such as the enrollment of metastatic MASC tumors on TRK inhibitor trials,
NGS facilitated dramatic therapeutic responses.
Focused analyses of recurrent and metastatic tumors can
provide valuable biologic insights, identifying alterations that
are associated with advanced cancers.35 For example, we identified a high rate of activating NOTCH1 mutations in meta(Reprinted) JAMA Oncology Published online July 21, 2016
E9
Figure 7. Mutational Landscape of Advanced Cutaneous Carcinomas of the Head and Neck
Mutation Count
1000
100
10
Nonsynonymous
Synonymous
Squamous cell carcinoma
Basal cell carcinoma
Skin adnexal carcinoma
Yes
Unknown
No
Yes
Unknown
No
Yes
No
Index primary
Local recurrence
Local and
Distant metastasis
Regional recurrence regional
recurrence
Yes
Histology
Ultraviolet light
signature
Chr3p loss
Immunosuppressed
Site sequenced
Distant metastasis
Altered
genome, %
No
value >0.2 or <0.2
100
0
TP53 85.2%
TERT 51.9%
Mutation type
NOTCH1 48.1%
Missense
CDKN2A 55.6%
Nonsense
Truncating
NOTCH2 48.1%
In-frame
FAT1 44.4%
Promoter
MLL2 37%
SCNA type
Amplification
NOTCH3 33.3%
Deletion
ROS1 33.3%
Genetic and clinical data for 27

advanced cutaneous head and neck
cancers. SCNA indicates somatic copy
number alterations
ASXL1 29.6%
static ACC. We also identified genetic alterations defining recurrent and metastatic HPV-positive cancers: many tumors had
genetic profiles closer to HPV-negative tumors, a finding that
has potential significance to current studies of targeted therapies and chemoradiotherapy deintensification in this population. An important caveat is that these findings are based on a
small cohort, and when comparing results to other data sets,
it is possible that differences in patient characteristics, prior
therapy, sequencing or analytic methodologies may contribute to differences observed. These results require further
confirmation.
Many head and neck cancers are understudied due to
their rarity. We report the first molecular data in mucoepidermoid carcinomas, acinic cell carcinomas, epithelialmyoepithelial carcinomas, MASC, salivary adenocarcinoma,
skin adnexal carcinomas, odontogenic carcinomas, and
head and neck neuroendocrine carcinomas. While sample
sizes were too limited to draw broad conclusions, many
potentially actionable findings were identified and several
uncommon diagnoses refined.
Finally, this analysis demonstrated the potential of targeted NGS to measure intratumor heterogeneity and identify
certain mutational signatures: those of carcinogenesis driven
by UV light, tobacco, AP OBEC, and mismatch repair
E10
deficiency.15,36,37 Emerging data implicate each of these features as potential predictive biomarkers for immunotherapy:
ITH, mutational load, and the tobacco and UV light mutational signatures have each been associated with response to
immune checkpoint inhibitors in lung, skin, and colorectal
cancers.38-42
Conclusions
To advance precision head and neck oncology, a necessary first
step is describing the complete catalog of molecular alterations in incurable and rare cancers. As demonstrated here, the
molecular profile of recurrent and metastatic tumors is quite
distinct from primary tumors. In these understudied diseases, no single institution will be able to profile a large number of patients. Pooling genomic data will be critical to devising rational therapies. Finally, a major therapeutic limitation
in head and neck cancer has been the lack of matched trial options. This shows the value of basket studies, which accounted for half of clinical trial enrollments in this cohort. As
understanding of molecular drivers and biomarkers expands, we anticipate the clinical value added by routine NGS
will continue to increase.
jamaoncology.com
ARTICLE INFORMATION
REFERENCES
Accepted for Publication: April 7, 2016.
1. Duvvuri U, Myers JN. Cancer of the head and

neck is the sixth most common cancer worldwide.
Curr Probl Surg. 2009;46(2):114-117.
Published Online: July 21, 2016.

doi:10.1001/jamaoncol.2016.1790.
Author Affiliations: Human Oncology and
Pathogenesis Program, Memorial Sloan Kettering
Cancer Center, New York, New York (Morris, Chan);
Head and Neck Surgical Oncology Service,
Department of Surgery, Memorial Sloan Kettering
Cancer Center, New York, New York (Morris, West,
Wong, Ganly, Singh, Shah, Shaha, Boyle, Patel,
Roman); Marie-Jose and Henry R. Kravis Center for
Molecular Oncology, Memorial Sloan Kettering
Cancer Center, New York, New York
(Chandramohan, Zehir, Chakravarty, Hyman,
Berger, Solit); Department of Pathology, Memorial
Sloan Kettering Cancer Center, New York, New York
(Zehir, Dogan, Berger); Head and Neck Oncology
Service, Department of Medicine, Memorial Sloan
Kettering Cancer Center, New York, New York
(Pfister, Sherman, Baxi, Ho); Department of
Radiation Oncology, Memorial Sloan Kettering
Cancer Center, New York, New York (Lee, Barker,
McBride, Chan, Riaz).
Author Contributions: Dr Morris had full access to
all the data in the study and takes responsibility for
the integrity of the data and the accuracy of the
data analysis.
Concept and design: Morris, Chan, Hyman, Solit, Ho.
Acquisition, analysis, or interpretation of data:
Morris, Chandramohan, West, Zehir, Chakravarty,
Pfister, Wong, Sherman, Baxi, Ganly, Singh, Shah,
Shaha, Patel, Roman, Barker, McBride, Chan,
Dogan, Hyman, Berger, Solit, Riaz, Ho.
Drafting of the manuscript: Morris, Chan, Solit.
Critical revision of the manuscript for important
intellectual content: Morris, Chandramohan, West,
Zehir, Chakravarty, Pfister, Wong, Sherman, Baxi,
Ganly, Singh, Shah, Shaha, Boyle, Patel, Roman,
Barker, McBride, Chan, Dogan, Hyman, Berger,
Solit, Riaz, Ho.
Statistical analysis: Morris, Chandramohan, Berger,
Riaz.
Obtaining funding: Morris, Chan, Solit.
Administrative, technical, or material support:
Morris, Sherman, Baxi, Singh, Shaha, Roman,
Barker, Chan, Hyman, Solit, Ho.
Study supervision: Morris, Chan, Dogan, Berger,
Solit, Ho.
Other: Morris, West.
Conflict of Interest Disclosures: None reported.
Funding/Support: This work was supported by NIH
P30 CA008748 (to the Memorial Sloan Kettering
Cancer Center), the Damon Runyon Cancer
Research Foundation, the National Institutes of
Health (grant No. NIH K08 DE024774), and the
Society of MSK (to Dr Morris).
Role of the Funder/Sponsor: The funders/
sponsors had no role in the design and conduct of
the study; collection, management, analysis, and
interpretation of the data; preparation, review, or
approval of the manuscript; and decision to submit
the manuscript for publication.
Additional Contributions: We thank our patients
and acknowledge our colleagues from the Head and
Neck Cancer Disease Management Team and the
Center for Molecular Oncology.
jamaoncology.com
2. Agrawal N, Frederick MJ, Pickering CR, et al.

Exome sequencing of head and neck squamous cell
carcinoma reveals inactivating mutations in
NOTCH1. Science. 2011;333(6046):1154-1157.
18. Killela PJ, Reitman ZJ, Jiao Y, et al. TERT

promoter mutations occur frequently in gliomas
and a subset of tumors derived from cells with low
rates of self-renewal. Proc Natl Acad Sci U S A. 2013;
110(15):6021-6026.
19. Qu Y, Dang S, Wu K, et al. TERT promoter
mutations predict worse survival in laryngeal cancer
patients. Int J Cancer. 2014;135(4):1008-1010.
3. Cancer Genome Atlas Network. Comprehensive

genomic characterization of head and neck
squamous cell carcinomas. Nature. 2015;517(7536):
576-582.
20. Liu X, Dakic A, Zhang Y, Dai Y, Chen R, Schlegel

R. HPV E6 protein interacts physically and
functionally with the cellular telomerase complex.
Proc Natl Acad Sci U S A. 2009;106(44):18780-18785.
4. India Project Team of the International Cancer

Genome Consortium. Mutational landscape of
gingivo-buccal oral squamous cell carcinoma
reveals new recurrently-mutated genes and
molecular subgroups. Nat Commun. 2013;4:2873.
21. Chau NG, Li YY, Jo VY, et al. Incorporation of

next-generation sequencing into routine clinical
care to direct treatment of head and neck
squamous cell carcinoma [published online January
13, 2016]. Clin Cancer Res. 2016. doi:10.1158
/1078-0432.CCR-15-2314.
5. Seiwert TY, Zuo Z, Keck MK, et al. Integrative and

comparative genomic analysis of HPV-positive and
HPV-negative head and neck squamous cell
carcinomas. Clin Cancer Res. 2015;21(3):632-641.
6. Stransky N, Egloff AM, Tward AD, et al. The
mutational landscape of head and neck squamous
cell carcinoma. Science. 2011;333(6046):1157-1160.
7. Lin DC, Meng X, Hazawa M, et al. The genomic
landscape of nasopharyngeal carcinoma. Nat Genet.
2014;46(8):866-871.
8. Pickering CR, Zhou JH, Lee JJ, et al. Mutational
landscape of aggressive cutaneous squamous cell
carcinoma. Clin Cancer Res. 2014;20(24):6582-6592.
9. Ho AS, Kannan K, Roy DM, et al. The mutational
landscape of adenoid cystic carcinoma. Nat Genet.
2013;45(7):791-798.
10. Stephens PJ, Davies HR, Mitani Y, et al. Whole
exome sequencing of adenoid cystic carcinoma.
J Clin Invest. 2013;123(7):2965-2968.
11. Hyman DM, Solit DB, Arcila ME, et al. Precision
medicine at Memorial Sloan Kettering Cancer
Center: clinical next-generation sequencing
enabling next-generation targeted therapy trials.
Drug Discov Today. 2015;20(12):1422-1428.
12. Cheng DT, Mitchell TN, Zehir A, et al. Memorial
Sloan Kettering-integrated mutation profiling of
actionable cancer targets (MSK-IMPACT):
a hybridization capture-based next-generation
sequencing clinical assay for solid tumor molecular
oncology. J Mol Diagn. 2015;17(3):251-264.
13. Schrader KA, Cheng DT, Joseph V, et al.
Germline Variants in Targeted Tumor Sequencing
Using Matched Normal DNA. JAMA Oncol. 2016;2
(1):104-111.
14. Shen R, Seshan V. FACETS: allele-specific copy
number and clonal heterogeneity analysis tool for
high-throughput DNA sequencing. Nucleic Acids Res.
2016;Jun 7:pii:gkw520.
15. Roberts SA, Lawrence MS, Klimczak LJ, et al. An
APOBEC cytidine deaminase mutagenesis pattern is
widespread in human cancers. Nat Genet. 2013;45
(9):970-976.
16. Pfeifer GP, You YH, Besaratinia A. Mutations
induced by ultraviolet light. Mutat Res. 2005;571(12):19-31.
17. Zack TI, Schumacher SE, Carter SL, et al.
Pan-cancer patterns of somatic copy number
alteration. Nat Genet. 2013;45(10):1134-1140.
22. Ang KK, Harris J, Wheeler R, et al. Human

papillomavirus and survival of patients with
oropharyngeal cancer. N Engl J Med. 2010;363(1):
24-35.
23. Chung CH, Guthrie VB, Masica DL, et al.
Genomic alterations in head and neck squamous
cell carcinoma determined by cancer gene-targeted
sequencing. Ann Oncol. 2015;26(6):1216-1223.
24. Werness BA, Levine AJ, Howley PM.
Association of human papillomavirus types 16 and
18 E6 proteins with p53. Science. 1990;248(4951):
76-79.
25. Kimple RJ, Smith MA, Blitzer GC, et al.
Enhanced radiation sensitivity in HPV-positive head
and neck cancer. Cancer Res. 2013;73(15):4791-4800.
26. Pickering CR, Zhang J, Neskey DM, et al.
Squamous cell carcinoma of the oral tongue in
young non-smokers is genomically similar to tumors
in older smokers. Clin Cancer Res. 2014;20(14):
3842-3848.
27. Henderson S, Chakravarthy A, Su X, Boshoff C,
Fenton TR. APOBEC-mediated cytosine
deamination links PIK3CA helical domain mutations
to human papillomavirus-driven tumor
development. Cell Rep. 2014;7(6):1833-1841.
28. Ferrarotto R, Mitani Y, Cai Y, Diao L. Notch1
mutations to define a subgroup of adenoid cystic
carcinoma (ACC): Tumor stage, propensity to bone
and liver metastasis, risk of relapse, and overall
survival. ASCO Annual Meeting Abstract 6081.
J Clin Oncol. 2015;33(Suppl):abstract 6081.
29. Stoeck A, Lejnine S, Truong A, et al. Discovery
of biomarkers predictive of GSI response in
triple-negative breast cancer and adenoid cystic
carcinoma. Cancer Discov. 2014;4(10):1154-1167.
30. Sklov A, Vanecek T, Sima R, et al. Mammary
analogue secretory carcinoma of salivary glands,
containing the ETV6-NTRK3 fusion gene: a hitherto
undescribed salivary gland tumor entity. Am J Surg
Pathol. 2010;34(5):599-608.
31. Drilon A, Li G, Dogan S, et al. What hides behind
the MASC: clinical response and acquired resistance
to entrectinib after ETV6-NTRK3 identification in a
mammary analogue secretory carcinoma (MASC).
Ann Oncol. 2016;27(5):920-926.
32. Gross AM, Orosco RK, Shen JP, et al.
Multi-tiered genomic analysis of head and neck
cancer ties TP53 mutation to 3p loss. Nat Genet.
2014;46(9):939-943.
E11
33. Mathew CG. Fanconi anaemia genes and

susceptibility to cancer. Oncogene. 2006;25(43):
5875-5884.
34. Beltran H, Eng K, Mosquera JM, et al.
Whole-Exome Sequencing of Metastatic Cancer and
Biomarkers of Treatment Response. JAMA Oncol.
2015;1(4):466-474.
35. Robinson D, Van Allen EM, Wu YM, et al.
Integrative clinical genomics of advanced prostate
cancer. Cell. 2015;161(5):1215-1228.
36. Alexandrov LB, Nik-Zainal S, Wedge DC, et al;
Australian Pancreatic Cancer Genome Initiative;
ICGC Breast Cancer Consortium; ICGC MMML-Seq
Consortium; ICGC PedBrain. Signatures of
E12
37. Cleaver JE, Crowley E. UV damage, DNA repair

and skin carcinogenesis. Front Biosci. 2002;7:
d1024-d1043.
therapy in patients with advanced Merkel cell

carcinoma (abstract). Paper presented at:
Proceedings of the European Cancer Congress
2015; September 25-29; Vienna, Austria.
2015:22LBA.
38. Rizvi NA, Hellmann MD, Snyder A, et al. Cancer

immunology. Mutational landscape determines
sensitivity to PD-1 blockade in non-small cell lung
cancer. Science. 2015;348(6230):124-128.
41. McGranahan N, Furness AJ, Rosenthal R, et al.

Clonal neoantigens elicit T cell immunoreactivity
and sensitivity to immune checkpoint blockade.
Science. 2016;351(6280):1463-1469.
39. Goh G, Walradt T, Markarov V, et al. Mutational

landscape of MCPyV-positive and MCPyV-negative
Merkel cell carcinomas with implications for
immunotherapy. Oncotarget. 2016;7(3):3403-3415.
42. Morris LG, Riaz N, Desrichard A, et al.

Pan-cancer analysis of intratumor heterogeneity as
a prognostic determinant of survival. Oncotarget.
2016;7(9):10051-10063.
mutational processes in human cancer. Nature.

2013;500(7463):415-421.
40. Nghiem P, Bhatia S, Daud A, et al. Activity of

PD-1 blockade with pembrolizumab as first systemic
jamaoncology.com
Supplementary Online Content
Morris LGT, Chandramohan R, West L, et al. The molecular landscape of

recurrent and metastatic head and neck cancers: insights from a precision
oncology sequencing platform. JAMA Oncol. Published online July 21, 2016.
doi:10.1001/jamaoncol.2016.1790
eAppendix.
Supplement 2 Table Legends.
eReferences.
eFigures 1-19.
This supplementary material has been provided by the authors to give readers
additional information about their work.
2016 American Medical Association. All rights reserved.

eAppendix
SUPPLEMENTARY METHODS
Patients and tumor samples
The MSK-IMPACT (Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer
Targets) assay is a next-generation sequencing (NGS) assay approved for clinical use through CLIA
(Clinical Laboratory Improvement Amendments) by the Centers for Medicare and Medicaid Services1.
The majority of patients have recurrent or metastatic disease but patients are otherwise unselected.
Since 2014, over 9,000 solid tumors have been profiled using MSK-IMPACT.
We reviewed all patients treated by the MSK multidisciplinary head and neck oncology team, whose
tumors were sequenced with MSK-IMPACT in the context of an Institutional Review Board (IRB)approved study (NCT01775072). Of 224 patients enrolled, 151 with a minimum of 6 month clinical
followup, whose tumors were sequenced between January 2014 and July 2015, were included. This
analysis was approved by the MSK IRB. Correlative clinical data are recorded prospectively in an IRBapproved database. Human papillomavirus (HPV) status was determined by p16 immunohistochemistry
and HPV in situ hybridization as part of routine care. Treatment(s) initiated after ordering NGS were
considered to be guided by molecular data if results led to, or justified continuation with, a specific
treatment.
Sequencing platform and variant calling
MSK-IMPACT is optimized for DNA extracted from low-input formalin-fixed, paraffin embedded (FFPE)
samples. The assay is designed to detect single nucleotide variants (SNVs), indels, copy number variants
(CNVs) and structural variants in genes that are functionally relevant to cancer and/or clinically
actionable targets. The current assay uses hybrid capture technology (Nimblegen SeqCap EZ library
custom oligo) to perform deep (>200x) sequencing (Illumina HiSeq 2500) of all 5781 exons and selected
introns of 410 cancer genes, including canonical and selected non-canonical transcripts, the TERT
promoter region, and 33 introns of 14 rearranged genes (eTable 1). The panel includes 1042 tiling
probes covering single nucleotide polymorphisms (SNPs), allowing genotyping to ensure tumor-normal
matching, identify contaminating DNA, and serve as a low-density SNP array for CNV analysis. MSKIMPACT has been extensively validated. Specific details of panel design, capture protocol, sequencing,
quality control, read alignment, and variant calling have been described2,3. Molecular alterations were
classified according to MSK levels of evidence that support standard or investigational therapeutic
indications (eTable 2).
Bioinformatic analyses
Additional copy number analyses were performed using FACETS4, which performs segmentation of total
and allelic copy ratio, and estimates allele-specific copy number, in targeted capture sequencing data.
We used FACETS to identify whole genome duplication (WGD) and deletion of 3p in SCC (eFigures 1-2).
The fraction of the genome with copy number alteration was defined with a log2 copy number ratio
threshold of .2 or -.2. For comparison, tumor ploidy and allele-specific copy number in The Cancer
Genome Atlas (TCGA) HNSCC cases5 were determined using SNP6 copy number data input into ASCAT6,
as previously described7.
Analyses of intratumor heterogeneity were also performed using FACETS, which estimates the cancer
cell fraction of somatic variants, by incorporating variant allelic fraction and adjusting for tumor purity
and underlying copy number4. The cancer cell fractions of somatic variants are expressed with intervals
representing full width at half maximum boundaries. Mutations with an upper boundary overlapping 1.0
were considered clonal; those with an upper boundary <0.95 were considered to be subclonal, similar to
the approach described by McGranahan et al8. Mutations with overlapping confidence intervals were
considered to comprise an individual subclonal or clonal population, and the total number of subclonal
populations, SNVs, and subclonal SNVs was determined for each sample. These parameters were
compared among subsets using stepwise logistic regression to control for HPV status, site sequenced,
purity, and ploidy.
Network analyses of SNVs were performed in Cytoscape 3.2.1 using CyniTools to infer significant
positive and negative correlations9. Functional annotations were analyzed by examining enrichment of
Gene Ontology terms with BINGO10.
Nonsynonymous and synonymous SNVs were used to delineate certain mutational signatures. The
APOBEC enrichment score, previously described, represents the enrichment of mutated C (or G) within
TCW (or WGA) motifs, in context of all mutated C (or G) 20 nucleotides upstream/downstream11. For the
tobacco signature, the number of transversions per tumor was calculated. The UV signature was based
on a predominance of C to T (or G to A) transitions in dipyrimidine contexts12.
Somatic alteration profiles of HNSCC were examined using a binary classifier to determine if profiles
most closely resembled HPV-positive or HPV-negative tumors. A support vector machine (SVM)
algorithm (in GenePattern13) maximizes the hyperplane separating HPV-positive and HPV-negative
samples14. The SVM model was first trained and cross-validated in the TCGA cohort of 298 cases with
somatic alteration (mutations and high-level CNVs in MSK-IMPACT genes) and HPV status information.
The model had 88% accuracy (p<10-6) in the validation set. The model was then applied to MSK-IMPACT
samples, and HPV status predicted for each case. A posterior probability (confidence) for each sample
classification represents distance from the hyperplane.
To determine if certain frequent genetic alterations were more common than expected in
recurrent/metastatic tumors, the MSK-IMPACT and TCGA cohorts were compared using enrichment
analysis. To allow for potential differences in sequencing platforms, enrichment was calculated as the
log-ratio of odds ratios: the odds ratio (OR) for alterations occurring in HPV-negative tumors, compared
to HPV-positive tumors, was calculated within each cohort, and ORs compared between cohorts.
Significance was tested with logistic regression using an interaction term:
logit (probability of variant) = E0 + E1(cohort) + E2(HPV status) + E3 (cohort x HPV status)
Where eE3 is the enrichment for an alteration in MSK-IMPACT HPV-positive tumors, compared to TCGA
tumors.
Germline variant analysis
After IRB approval for additional germline analyses, these were performed as previously described3.
Briefly, SNVs and indels identified in anonymized normal DNA were analyzed in Ingenuity Variant
Analysis software, categorizing variants by pathogenicity based on 2015 ACMG guidelines15. Pathogenic
and likely pathogenic variants were manually confirmed. We also included 93 genes in Online Mendelian
Inheritance in Man (OMIM) that have been associated with susceptibility to any cancer type3, and 26
genes recommended by the ACMG16.
SUPPLEMENT 2 TABLE LEGENDS
eTable 1. List of 410 genes (entire exonic regions included) and 36 additional intronic regions included in the MSKIMPACT next-generation sequencing panel.
eTable 2. Actionable molecular alterations, categorized by MSK levels of evidence.
eTable 3. Clinical and tumor characteristics of 151 patients with recurrent/metastatic and treatmentresistant head and neck cancers. HNSCC, head and neck squamous cell carcinoma. ACC, adenoid cystic
carcinoma. NPC, nasopharyngeal carcinoma. ONB, olfactory neuroblastoma. CT, chemotherapy. RT,
radiation therapy.
eTable 4. Matrix of clinical data and genetic alterations found in 151 advanced head and neck cancers,
subdivided by cancer type. Each alteration is described as: mutation genomic coordinates, nucleotide
variant, amino acid variant, variant allelic frequency, category of mutation | copy number alteration.
eTable 5. Gene ontology annotations enriched in the cluster of genes more frequently altered in HPVpositive HNSCC (clusters of green nodes in Figure 2D), with statistical testing corrected using BenjaminiHochberg false discovery rate.
eTable 6. FACETS estimates of tumor purity, ploidy, number of subclonal populations and number of
subclonal mutations (see Methods) for HNSCC cases.
eTable 7. Multivariable logistic regression models of the associations between intratumor heterogeneity
and (A) HPV status and (B) tumor site (primary vs. recurrence/metastasis); (C) (sub)clonal status of TP53
mutations in HPV-positive and HPV-negative HNSCC samples.
eTable 8. Odds ratios for common somatic alterations in HPV-negative compared to HPV-positive
tumors, in both recurrent/metastatic (MSK-IMPACT) and primary (TCGA) HNSCC datasets. Enrichment is
calculated as the ratio of odds ratios. Significance testing as indicated.
eTable 9. TP53 mutations in 16 recurrent/metastatic HPV-associated cervical carcinoma sequenced on MSK-IMPACT.
eTable 10. REMARK (Reporting recommendations for tumor marker studies) checklist.
REFERENCES (For Supplementary Methods)

1. Hyman DM, Solit DB, Arcila ME, et al. Precision medicine at Memorial Sloan Kettering Cancer
Center: clinical next-generation sequencing enabling next-generation targeted therapy trials.
Drug discovery today. Dec 2015;20(12):1422-1428.
2. Cheng DT, Mitchell TN, Zehir A, et al. Memorial Sloan Kettering-Integrated Mutation Profiling of
Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation
Sequencing Clinical Assay for Solid Tumor Molecular Oncology. The Journal of molecular
diagnostics : JMD. May 2015;17(3):251-264.
3. Schrader KA, Cheng DT, Joseph V, et al. Germline Variants in Targeted Tumor Sequencing Using
Matched Normal DNA. JAMA oncology. Jan 1 2016;2(1):104-111.
4. Shen R, Seshan V. FACETS: allele-specific copy number and clonal heterogeneity analysis
tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016;Jun 7:pii:gkw520.
Medline:27270079
5. Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous
cell carcinomas. Nature. Jan 29 2015;517(7536):576-582.
6. Van Loo P, Nordgard SH, Lingjaerde OC, et al. Allele-specific copy number analysis of tumors.
Proceedings of the National Academy of Sciences of the United States of America. Sep 28
2010;107(39):16910-16915.
7. Morris LG, Riaz N, Desrichard A, et al. Pan-cancer analysis of intratumor heterogeneity as a
prognostic determinant of survival. Oncotarget. Jan 28 2016.
8. McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of
actionable driver events and the timing of mutational processes in cancer evolution. Science
translational medicine. Apr 15 2015;7(283):283ra254.
9. Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models
of biomolecular interaction networks. Genome research. Nov 2003;13(11):2498-2504.
10. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene
ontology categories in biological networks. Bioinformatics. Aug 15 2005;21(16):3448-3449.
11. Roberts SA, Lawrence MS, Klimczak LJ, et al. An APOBEC cytidine deaminase mutagenesis
pattern is widespread in human cancers. Nature genetics. Sep 2013;45(9):970-976.
12.
Pfeifer GP, You YH, Besaratinia A. Mutations induced by ultraviolet light. Mutation research. Apr
1 2005;571(1-2):19-31.
13. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nature genetics.
May 2006;38(5):500-501.
Rifkin R, Mukherjee S, Tamayo P, et al. An Analytical Method for Multiclass Molecular Cancer
Classification. SIAM Review. 2003;45(4):706-723.
15. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence
variants: a joint consensus recommendation of the American College of Medical Genetics and
Genomics and the Association for Molecular Pathology. Genetics in medicine : official journal of
the American College of Medical Genetics. May 2015;17(5):405-424.
16. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical
exome and genome sequencing. Genetics in medicine : official journal of the American College of Medical
Genetics. Jul 2013;15(7):565-574.
14.
eFigure 1.
HNSCC tumor with single copy loss of 3p and single copy gain of 3q
eFigure 1. Analysis of whole-genome copy number via targeted capture next-generation

sequencing. The MSK-IMPACT platform includes exonic and intronic coverage of selected genes
as well as tiling probes across the genome. FACETS is used for segmentation and to determine
copy number based on SNP loci read counts. The top plot represents total copy number log-ratio,
corrected for library size and GC content. The middle plot represents allelic imbalance (similar to
B-allele frequency), using variant allele log-odds ratio, which includes both tumor and normal
allelic information. The bottom plot represents allele-specific integer copy number. The case
depicted is a tumor (HPV-negative HNSCC) with single copy loss of 3p and single copy gain of
3q.
eFigure 2A.
HNSCC tumor with whole genome duplication and copy-neutral loss of heterozygosity at 3p
eFigure 2. Analysis of whole-genome copy number via targeted capture next-generation sequencing, as
depicted in eFigure 1, showing whole genome duplication. (A) A representative case of a tumor (HPVnegative HNSCC) with whole genome duplication and copy-neutral loss of heterozygosity at 3p. (B) Ploidy
in HPV-positive and HPV-negative HNSCC tumors. (C) Whole genome duplication and 3p deletion in
HNSCC tumors.
eFigure 2B.
Ploidy and whole-genome duplication (WGD) in HPV-positive and HPV-negative HNSCC tumors
eFigure 2C.
Whole genome duplication (WGD) in 3p-deleted HNSCC tumors
WGD in 3p-deleted vs. 3p-normal tumors: p=.0001
Chromosome 3p deletion
eFigure 3.
TP53
p=4.4x10-5
TERT
NOTCH1
PIK3CA
3q26
CDKN2A
Overall survival
EGFR
ATR
SVM: HPV-positive
SVM: HPV-negative
MLL2
MLL3
NSD1
HR=2.3 (95%CI .37-14.1), p=.19
Months from recurrence
eFigure 3. (A) Posterior probabilities of Support Vector Machine (SVM) algorithm, used to
classify HPV status based on genetic alterations in MSK-IMPACT HNSCC cases. X-axis
reflects actual HPV status. Y-axis reflects the confidence level of the classification, described in
Methods. (B) Alterations present in the HPV-positive (MSK-IMPACT) HNSCC cases that
were classified as HPV-negative or HPV-positive by SVM. (C) Overall survival of HPVpositive HNSCC cases in MSK-IMPACT cohort, based on SVM categorization as HPVpositive or HPV-negative.
eFigure 4.
eFigure 4. Comparison of mutational frequencies in recurrent/metastatic HNSCC (MSK-IMPACT) and

primary HNSCC (TCGA) tumors, either HPV-positive (left bar graph) or HPV-negative (right bar
graph).
eFigure 5.
APOBEC signature
APOBEC enrichment score
Tobacco signature
eFigure 5. Distribution of tobacco signature (transversions per tumor) by HNSCC subsite, indicating that
transversion-high tumors were mostly laryngeal cancers.
HPV
HPV +
eFigure 6.
Enrichment in NOTCH1 mutations
eFigure 6. Comparison of mutational frequencies in recurrent/

metastatic ACC (MSK-IMPACT) and primary ACC tumors (Ho et al,
Nature Genetics 2013).
eFigure 7.
NF1 intragenic deletion
ROS1 intragenic deletion

Exons 32-42 (including kinase domain)
LATS1 intragenic inversion

Exon 5 (involving splice site)
eFigure 7. Structural variants observed in salivary duct carcinomas: Integrative Genomics Viewer (IGV) panels.
eFigure 8. ETV6-NTRK3 fusion
eFigure 8. ETV6-NTRK3 reciprocal fusion in a salivary carcinoma, leading to change in

diagnosis to mammary analog secretory carcinoma (MASC) of the salivary gland.
eFigure 9.
EWSR1-ATF1 reciprocal fusion

in a clear cell odontogenic carcinoma
t(22;12)(q12.2;q13.12)
EWSR1-FLI1 reciprocal fusion

in a mandibular cancer initially diagnosed as
ameloblastic carcinoma, rediagnosed as Ewing
sarcoma
EWSR1 exon 7 fused to FLI1 exon 6

t(22;11)(q12.2;q24.3)
eFigure 9. EWSR1 fusions in odontogenic carcinomas
eFigure 10.
Germline Copy Number

FANCA intragenic deletion in a case of HNSCC
FANCA exon 16-17 loss
eFigure 10. Deletion in FANCA observed in germline DNA.
eFigure 11
Odontogenic
Olfactory neuroblastoma
H&N neuroendocrine
Nasopharyngeal carcinoma
Other salivary
H&N cutaneous
Adenoid cystic carcinoma
H&N squamous cell carcinoma
2
2
3
8
20
27
36
53
H&N squamous cell carcinoma

Adenoid cystic carcinoma
H&N cutaneous
Other salivary
Nasopharyngeal carcinoma
H&N neuroendocrine
Olfactory neuroblastoma
Odontogenic
0
10
20
30
40
eFigure 11. Advanced head and neck cancers profiled using a

precision oncology sequencing platform
50
60
eFigure 12
eFigure 12. Scatterplot of log (mutation count) and fraction of genome with copy number alteration,
by tumor type
HNSCC, head and neck squamous cell carcinoma. ACC, adenoid cystic carcinoma. NPC,
nasopharyngeal carcinoma.
50
eFigure 13
Number of Mutations
40
30
Subgroup
HPVpos
HPVneg
20
10
0.00
0.25
0.50
% Genome Altered
0.75
1.00
eFigure 13. (Above) Scatterplot of mutation counts and percentage of genome with copy number alteration, by
human papillomavirus (HPV) status in head and neck squamous cell (HNSCC) samples.
eFigure 14
HPV
More frequent in
HPV+
eFigure 14. Correlation network of somatic alterations, where the color of

nodes represents relative predominance in HPV-positive or HPV-negative
tumors, the size of the nodes represents frequency of alteration, and edges
represent correlations or anti-correlations.
eFigure 15
HPV +
p=.007
HPV
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVpos
HPVneg
HPVneg
HPVneg
HPVneg
HPVpos
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVpos
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVpos
HPVpos
HPVneg
HPVpos
HPVpos
HPVpos
HPVneg
HPVneg
HPVneg
HPVpos
HPVneg
HPVneg
HPVpos
HPVneg
HPVneg
HPVpos
HPVpos
HPVneg
HPVpos
HPVpos
HPVpos
57% match
MSK-IMPACT
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVneg
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
HPVpos
91% match
Actual | Predicted
eFigure 15. A machine-learning algorithm was used to classify the genotypes of

recurrent/metastatic tumors as more similar to HPV-negative or HPV-positive primary tumors.
Similarity of IMPACT (HPV+) to TCGA (HPV+/-)
Similarity with TCGA HPV+ cohort
-1
Similarity of IMPACT (HPV-) to TCGA (HPV+/-)

2
-1
-2
eFigure 16
eFigure 16. Column graph representing the most frequent mutations in recurrent/metastatic
tumors, and the similarity of mutational frequencies to those in primary HPV-positive/negative
tumors. Similarity score is defined as: [ -log10(|TCGA%HPVsame -IMPACT%|) - -log10(|TCGA%
HPVdifferent - IMPACT%)], for all mutations with average frequency >.02.
eFigure 17
Adenoid Cystic Carcinoma
HD-N domain
PEST domain
TERT
eFigure 17. Mutation Distributions of NOTCH1 and TERT in ACC. Green

circles indicate missense mutations; red, truncating; black, inframe insertions
or deletions.
eFigure 18
TERT promoter mutations in cutaneous carcinomas

NOTCH1 mutations in cutaneous SCC
BCC (75%)
HD-N domain
PEST domain
SCC (43%)
eFigure 18. NOTCH1 and TERT Mutations in Cutaneous Squamous (SCC) and Basal
Cell (BCC) Carcinomas of the Head and Neck. Green circles indicate missense
mutations; red, truncating; black, inframe insertions or deletions.
Mutation Count
20
15
10
5
0
Viral Status
WHO Type
Site Sequenced
Distant Metastasis
100
% Altered Genome 50
0
MLL2 50%
MDC1 33.3%
ARID1A 16.7%
AXIN1 16.7%
BCL6 16.7%
BMPR1A 16.7%
CARD11 16.7%
ERCC4 16.7%
FBXW7 16.7%
FOXP1 16.7%
JAK1 16.7%
MAX 16.7%
MLL 16.7%
NFE2L2 16.7%
NRAS 16.7%
PIK3CA 16.7%
PTPRD 16.7%
TP53 16.7%
YAP1 16.7%
TGFBR2
16.7%
Downloaded
From: http://oncology.jamanetwork.com/
by a Texas A&M University User on 08/29/2016
eFigure 19
Non-synonymous
Synonymous
HPV+ve
EBV+ve
WHO III
WHO I
WHO II
Index Primary
Local Recurrence
Distant Metastasis
Regional Recurrence
Yes
No
Fraction of Genome with log2
Copy Number Value > 0.2 or < -0.2
eFigure 19. (Above) Mutational landscape of recurrent/metastatic nasopharyngeal carcinomas. EBV, EpsteinBarr virus; HPV, Human papillomavirus.
Supplementary Online Content

The Molecular Landscape of Recurrent and Metastatic Head and Neck Cancers: Insights From a Precision Oncology Sequencing Platform
JAMA Oncol . Published online July 21, 2016.
doi:10.1001/jamaoncol.2016.1790
eTable 1. List of genes and additional intronic regions included in MSK-IMPACT next-generation sequencing panel.
Gene Symbol
Gene Name
ABL1
ACVR1
AKT1
AKT2
AKT3
ALK
ALOX12B
ANKRD11
APC
AR
ARAF
ARID1A
ARID1B
ARID2
ARID5B
ASXL1
ASXL2
ATM
ATR
ATRX
AURKA
AURKB
AXIN1
AXIN2
AXL
B2M
BAP1
BARD1
BBC3
BCL10
BCL2
BCL2L1
BCL2L11
BCL6
BCOR
BIRC3
BLM
BMPR1A
BRAF
BRCA1
BRCA2
BRD4
BRIP1
BTK
CALR
CARD11
CASP8
CBFB
CBL
CCND1
CCND2
c-abl oncogene 1, non-receptor tyrosine kinase

activin A receptor, type I
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
ankyrin repeat domain 11
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)
AT rich interactive domain 5B (MRF1-like)
additional sex combs like 1 (Drosophila)
additional sex combs like 2 (Drosophila)
ataxia telangiectasia mutated
ataxia telangiectasia and Rad3 related
alpha thalassemia/mental retardation syndrome X-linked
aurora kinase A
aurora kinase B
axin 1
axin 2
AXL receptor tyrosine kinase
beta-2-microglobulin
BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)
BRCA1 associated RING domain 1
BCL2 binding component 3
B-cell CLL/lymphoma 10
BCL2-like 1
BCL2-like 11 (apoptosis facilitator)
BCL6 corepressor
baculoviral IAP repeat-containing 3
Bloom syndrome, RecQ helicase-like
bone morphogenetic protein receptor, type IA
v-raf murine sarcoma viral oncogene homolog B1
breast cancer 1, early onset
breast cancer 2, early onset
bromodomain containing 4
BRCA1 interacting protein C-terminal helicase 1
Bruton agammaglobulinemia tyrosine kinase
calreticulin
caspase recruitment domain family, member 11
caspase 8, apoptosis-related cysteine peptidase
core-binding factor, beta subunit
Cas-Br-M (murine) ecotropic retroviral transforming sequence
cyclin D1
cyclin D2
CCND3
CCNE1
CD274
CD276
CD79A
CD79B
CDC73
CDH1
CDK12
CDK4
CDK6
CDK8
CDKN1A
CDKN1B
CDKN2A
CDKN2B
CDKN2C
CEBPA
CENPA
CHEK1
CHEK2
CIC
CREBBP
CRKL
CRLF2
CSF1R
CSF3R
CTCF
CTLA4
CTNNB1
CUL3
CXCR4
DAXX
DCUN1D1
DDR2
DICER1
DIS3
DNAJB1
DNMT1
DNMT3A
DNMT3B
DOT1L
E2F3
EED
EGFL7
EGFR
EIF1AX
EIF4A2
EIF4E
EP300
EPCAM
EPHA3
EPHA5
EPHA7
EPHB1
ERBB2
ERBB3
ERBB4
cyclin D3
cyclin E1
CD274 molecule
CD276 molecule
CD79a molecule, immunoglobulin-associated alpha
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 inhibitor 1A (p21, Cip1)
cyclin-dependent kinase inhibitor 1B (p27, Kip1)
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)
CCAAT/enhancer binding protein (C/EBP), alpha
centromere protein A
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
colony stimulating factor 3 receptor (granulocyte)
CCCTC-binding factor (zinc finger protein)
cytotoxic T-lymphocyte-associated protein 4
catenin (cadherin-associated protein), beta 1, 88kDa
cullin 3
chemokine (C-X-C motif) receptor 4
death-domain associated protein
DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)
discoidin domain receptor tyrosine kinase 2
dicer 1, ribonuclease type III
DIS3 mitotic control homolog (S. cerevisiae)
DnaJ (Hsp40) homolog, subfamily B, member 1
DNA (cytosine-5-)-methyltransferase 1
DNA (cytosine-5-)-methyltransferase 3 alpha
DNA (cytosine-5-)-methyltransferase 3 beta
DOT1-like, histone H3 methyltransferase (S. cerevisiae)
E2F transcription factor 3
embryonic ectoderm development
EGF-like-domain, multiple 7
epidermal growth factor receptor
eukaryotic translation initiation factor 1A, X-linked
eukaryotic translation initiation factor 4A2
eukaryotic translation initiation factor 4E
E1A binding protein p300
epithelial cell adhesion molecule
EPH receptor A3
EPH receptor A5
EPH receptor A7
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)
ERCC2
ERCC3
ERCC4
ERCC5
ERG
ERRFI1
ESR1
ETV1
ETV6
EZH2
FAM123B
FAM175A
FAM46C
FANCA
FANCC
FAT1
FBXW7
FGF19
FGF3
FGF4
FGFR1
FGFR2
FGFR3
FGFR4
FH
FLCN
FLT1
FLT3
FLT4
FOXA1
FOXL2
FOXO1
FOXP1
FUBP1
FYN
GATA1
GATA2
GATA3
GLI1
GNA11
GNAQ
GNAS
GPS2
GREM1
GRIN2A
GSK3B
H3F3A
H3F3B
H3F3C
HGF
HIST1H1C
HIST1H2BD
HIST1H3A
HIST1H3B
HIST1H3C
HIST1H3D
HIST1H3E
HIST1H3F
excision repair cross-complementing rodent repair deficiency, complementation group 2

excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B com
v-ets erythroblastosis virus E26 oncogene homolog (avian)
ERBB receptor feedback inhibitor 1
estrogen receptor 1
ets variant 1
ets variant 6
enhancer of zeste homolog 2 (Drosophila)
family with sequence similarity 123B
family with sequence similarity 175, member A
family with sequence similarity 46, member C
Fanconi anemia, complementation group A
Fanconi anemia, complementation group C
FAT tumor suppressor homolog 1 (Drosophila)
F-box and WD repeat domain containing 7
fibroblast growth factor 19
fibroblast growth factor receptor 1
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 A1
forkhead box L2
forkhead box O1
forkhead box P1
far upstream element (FUSE) binding protein 1
FYN oncogene related to SRC, FGR, YES
GATA binding protein 1 (globin transcription factor 1)
GATA binding protein 2
GATA binding protein 3
GLI family zinc finger 1
guanine nucleotide binding protein (G protein), alpha 11 (Gq class)
guanine nucleotide binding protein (G protein), q polypeptide
GNAS complex locus
G protein pathway suppressor 2
gremlin 1
glutamate receptor, ionotropic, N-methyl D-aspartate 2A
glycogen synthase kinase 3 beta
H3 histone, family 3A
H3 histone, family 3B (H3.3B)
H3 histone, family 3C
hepatocyte growth factor (hepapoietin A; scatter factor)
histone cluster 1, H1c
histone cluster 1, H2bd
histone cluster 1, H3a
histone cluster 1, H3b
histone cluster 1, H3d
histone cluster 1, H3e
histone cluster 1, H3f
HIST1H3G
HIST1H3H
HIST1H3I
HIST1H3J
HIST2H3C
HIST2H3D
HIST3H3
HLA-A
HNF1A
HOXB13
HRAS
ICOSLG
ID3
IDH1
IDH2
IFNGR1
IGF1
IGF1R
IGF2
IKBKE
IKZF1
IL10
IL7R
INHA
INHBA
INPP4A
INPP4B
INSR
IRF4
IRS1
IRS2
JAK1
JAK2
JAK3
JUN
KDM5A
KDM5C
KDM6A
KDR
KEAP1
KIT
KLF4
KRAS
LATS1
LATS2
LMO1
MALT1
MAP2K1
MAP2K2
MAP2K4
MAP3K1
MAP3K13
MAP3K14
MAPK1
MAPK3
MAX
MCL1
MDC1
histone cluster 1, H3g

histone cluster 1, H3h
histone cluster 1, H3i
histone cluster 1, H3j
histone cluster 2, H3d
histone cluster 3, H3
major histocompatibility complex, class I, A
HNF1 homeobox A
homeobox B13
v-Ha-ras Harvey rat sarcoma viral oncogene homolog
inducible T-cell co-stimulator ligand
inhibitor of DNA binding 3, dominant negative helix-loop-helix protein
isocitrate dehydrogenase 1 (NADP+), soluble
isocitrate dehydrogenase 2 (NADP+), mitochondrial
interferon gamma receptor 1
insulin-like growth factor 1 (somatomedin C)
insulin-like growth factor 1 receptor
insulin-like growth factor 2 (somatomedin A)
inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon
IKAROS family zinc finger 1 (Ikaros)
interleukin 10
interleukin 7 receptor
inhibin, alpha
inhibin, beta A
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 5A
lysine (K)-specific demethylase 5C
lysine (K)-specific demethylase 6A
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
Kruppel-like factor 4 (gut)
v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
LATS, large tumor suppressor, homolog 1 (Drosophila)
LATS, large tumor suppressor, homolog 2 (Drosophila)
LIM domain only 1 (rhombotin 1)
mucosa associated lymphoid tissue lymphoma translocation gene 1
mitogen-activated protein kinase kinase 1
mitogen-activated protein kinase kinase kinase 1
mitogen-activated protein kinase 1
mitogen-activated protein kinase 3
MYC associated factor X
myeloid cell leukemia sequence 1 (BCL2-related)
mediator of DNA-damage checkpoint 1
MDM2
MDM4
MED12
MEF2B
MEN1
MET
MGA
MITF
MLH1
MLL
MLL2
MLL3
MPL
MRE11A
MSH2
MSH6
MST1
MST1R
MTOR
MUTYH
MYC
MYCL1
MYCN
MYD88
MYOD1
NBN
NCOA3
NCOR1
NEGR1
NF1
NF2
NFE2L2
NFKBIA
NKX2-1
NKX3-1
NOTCH1
NOTCH2
NOTCH3
NOTCH4
NPM1
NRAS
NSD1
NTRK1
NTRK2
NTRK3
NUP93
PAK1
PAK7
PALB2
PARK2
PARP1
PAX5
PBRM1
PDCD1
PDGFRA
PDGFRB
PDPK1
PGR
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)
MAX gene associated
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)
macrophage stimulating 1 (hepatocyte growth factor-like)
macrophage stimulating 1 receptor (c-met-related tyrosine kinase)
mechanistic target of rapamycin (serine/threonine kinase)
mutY homolog (E. coli)
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)
myogenic differentiation 1
nibrin
nuclear receptor coactivator 3
nuclear receptor corepressor 1
neuronal growth regulator 1
neurofibromin 1
neurofibromin 2 (merlin)
nuclear factor (erythroid-derived 2)-like 2
nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha
NK2 homeobox 1
NK3 homeobox 1
notch 1
notch 2
notch 3
notch 4
nucleophosmin (nucleolar phosphoprotein B23, numatrin)
neuroblastoma RAS viral (v-ras) oncogene homolog
nuclear receptor binding SET domain protein 1
neurotrophic tyrosine kinase, receptor, type 1
nucleoporin 93kDa
p21 protein (Cdc42/Rac)-activated kinase 1
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
programmed cell death 1
platelet-derived growth factor receptor, alpha polypeptide
platelet-derived growth factor receptor, beta polypeptide
3-phosphoinositide dependent protein kinase-1
progesterone receptor
PHOX2B
PIK3C2G
PIK3C3
PIK3CA
PIK3CB
PIK3CD
PIK3CG
PIK3R1
PIK3R2
PIK3R3
PIM1
PLCG2
PLK2
PMAIP1
PMS1
PMS2
PNRC1
POLD1
POLE
PPM1D
PPP2R1A
PPP6C
PRDM1
PRKAR1A
PTCH1
PTEN
PTPN11
PTPRD
PTPRS
PTPRT
RAB35
RAC1
RAD21
RAD50
RAD51
RAD51C
RAD51L1
RAD51L3
RAD52
RAD54L
RAF1
RARA
RASA1
RB1
RBM10
RECQL4
REL
RET
RFWD2
RHEB
RHOA
RICTOR
RIT1
RNF43
ROS1
RPS6KA4
RPS6KB2
RPTOR
paired-like homeobox 2b
phosphoinositide-3-kinase, class 2, gamma polypeptide
phosphoinositide-3-kinase, class 3
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)
pim-1 oncogene
phospholipase C, gamma 2 (phosphatidylinositol-specific)
polo-like kinase 2
phorbol-12-myristate-13-acetate-induced protein 1
PMS1 postmeiotic segregation increased 1 (S. cerevisiae)
PMS2 postmeiotic segregation increased 2 (S. cerevisiae)
proline-rich nuclear receptor coactivator 1
polymerase (DNA directed), delta 1, catalytic subunit 125kDa
polymerase (DNA directed), epsilon
protein phosphatase, Mg2+/Mn2+ dependent, 1D
protein phosphatase 2, regulatory subunit A, alpha
protein phosphatase 6, catalytic subunit
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
RAB35, member RAS oncogene family
ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)
RAD21 homolog (S. pombe)
RAD50 homolog (S. cerevisiae)
RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)
RAD51 homolog C (S. cerevisiae)
RAD51-like 1 (S. cerevisiae)
RAD51-like 3 (S. cerevisiae)
RAD52 homolog (S. cerevisiae)
RAD54-like (S. cerevisiae)
v-raf-1 murine leukemia viral oncogene homolog 1
retinoic acid receptor, alpha
RAS p21 protein activator (GTPase activating protein) 1
retinoblastoma 1
RNA binding motif protein 10
RecQ protein-like 4
v-rel reticuloendotheliosis viral oncogene homolog (avian)
ret proto-oncogene
ring finger and WD repeat domain 2
Ras homolog enriched in brain
ras homolog gene family, member A
RPTOR independent companion of MTOR, complex 2
Ras-like without CAAX 1
ring finger protein 43
c-ros oncogene 1 , receptor tyrosine kinase
ribosomal protein S6 kinase, 90kDa, polypeptide 4
ribosomal protein S6 kinase, 70kDa, polypeptide 2
regulatory associated protein of MTOR, complex 1
RUNX1
RYBP
SDHA
SDHAF2
SDHB
SDHC
SDHD
SETD2
SF3B1
SH2B3
SH2D1A
SHQ1
SMAD2
SMAD3
SMAD4
SMARCA4
SMARCB1
SMARCD1
SMO
SOCS1
SOX17
SOX2
SOX9
SPEN
SPOP
SRC
SRSF2
STAG2
STAT3
STAT5A
STAT5B
STK11
STK40
SUFU
SUZ12
SYK
TBX3
TCEB1
TCF3
TCF7L2
TERT
TET1
TET2
TGFBR1
TGFBR2
TMEM127
TMPRSS2
TNFAIP3
TNFRSF14
TOP1
TP53
TP63
TRAF2
TRAF7
TSC1
TSC2
TSHR
U2AF1
runt-related transcription factor 1

RING1 and YY1 binding protein
succinate dehydrogenase complex, subunit A, flavoprotein (Fp)
succinate dehydrogenase complex assembly factor 2
succinate dehydrogenase complex, subunit B, iron sulfur (Ip)
succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa
succinate dehydrogenase complex, subunit D, integral membrane protein
SET domain containing 2
splicing factor 3b, subunit 1, 155kDa
SH2B adaptor protein 3
SH2 domain containing 1A
SHQ1 homolog (S. cerevisiae)
SMAD family member 2
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
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
smoothened homolog (Drosophila)
suppressor of cytokine signaling 1
SRY (sex determining region Y)-box 17
spen homolog, transcriptional regulator (Drosophila)
speckle-type POZ protein
v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)
serine/arginine-rich splicing factor 2
stromal antigen 2
signal transducer and activator of transcription 3 (acute-phase response factor)
signal transducer and activator of transcription 5A
signal transducer and activator of transcription 5B
serine/threonine kinase 11
serine/threonine kinase 40
suppressor of fused homolog (Drosophila)
suppressor of zeste 12 homolog (Drosophila)
spleen tyrosine kinase
T-box 3
transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)
transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)
transcription factor 7-like 2 (T-cell specific, HMG-box)
telomerase reverse transcriptase
tet oncogene 1
tet oncogene family member 2
transforming growth factor, beta receptor 1
transforming growth factor, beta receptor II (70/80kDa)
transmembrane protein 127
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
TNF receptor-associated factor 2
TNF receptor-associated factor 7
tuberous sclerosis 1
tuberous sclerosis 2
thyroid stimulating hormone receptor
U2 small nuclear RNA auxiliary factor 1
VEGFA
VHL
VTCN1
WT1
XIAP
XPO1
XRCC2
YAP1
YES1
ZFHX3
ZRSR2
Intron regions captured

NTRK1_intron_8
NTRK1_intron_9
NTRK1_intron_10
NTRK1_intron_11
NTRK1_intron_12
ALK_intron_19
BIM_intron_2
PAX8_intron_10
PAX8_intron_9
PAX8_intron_8
FGFR3_intron_18
CD74_intron_6
ROS_intron_35
ROS_intron_34
ROS_intron_33
ROS_intron_32
ROS_intron_31
EGFR_intron_7
BRAF_intron_10
BRAF_intron_9
BRAF_intron_8
BRAF_intron_7
RET_intron_9
RET_intron_10
RET_intron_11
FGFR2_intron_17
ETV6_intron_4
ETV6_intron_5
NAB2_intron_2to6
NUT_intron_1
DNAJB1_intron_2
DNAJB1_intron_1
TMPRSS2_intron_2
TMPRSS2_intron_1
EWSR1_intron_7to13
TFE3_intron_4to5
vascular endothelial growth factor A

von Hippel-Lindau tumor suppressor
V-set domain containing T cell activation inhibitor 1
Wilms tumor 1
X-linked inhibitor of apoptosis
exportin 1 (CRM1 homolog, yeast)
X-ray repair complementing defective repair in Chinese hamster cells 2
Yes-associated protein 1
v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
zinc finger homeobox 3
zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2

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Research

The Molecular Landscape of Recurrent and Metastatic

Author Affiliations: Author

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Research Original Investigation

Next-Generation Sequencing in Difficult Head and Neck Cancers

recision oncology is a clinical approach that seeks to

Mutational signatures (APOBEC, tobacco, ultraviolet light

MSK-IMPACT was used to sequence 151 head and neck tumors,

JAMA Oncology Published online July 21, 2016 (Reprinted)

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Next-Generation Sequencing in Difficult Head and Neck Cancers

Original Investigation Research

Figure 1. Overall Survival for Patients Undergoing Clinical Tumor Sequencing

Cutaneous SCC (79.4%)

Time From Diagnosis, y

Time From Recurrence, y

Time From Diagnosis, y

Time From Recurrence, y

Actionability of molecular alterations

Standard of care but not FDA approved

in Supplement 2. Whole-genome duplication was present in

(Reprinted) JAMA Oncology Published online July 21, 2016

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Research Original Investigation

Next-Generation Sequencing in Difficult Head and Neck Cancers

Whole genome duplication

Fraction of genome with log2 copy number

tions. TERT promoter mutations have been linked with poorer

After NGS, 17 of 53 patients with HNSCC (32%) were

JAMA Oncology Published online July 21, 2016 (Reprinted)

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Next-Generation Sequencing in Difficult Head and Neck Cancers

MSK-IMPACT prompted the decision to instead enroll on

HPV-Positive and HPV-Negative HNSCC

Alterations Enriched in Recurrent and Metastatic

Original Investigation Research

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Research Original Investigation

Next-Generation Sequencing in Difficult Head and Neck Cancers

Green circles indicate missense

Figure 4. Genetic Alterations Enriched in Recurrent and/or Metastatic HPV-Positive HNSCC

vs HPV-positive primary tumors

Enrichment (Ratio of Odds Ratios)

A, Enrichment analysis for common alterations, comparing recurrent and/or

TP53/RB1 Mutation Status

defined as proportion of genome copy number-altered, in TP53/RB1-mutated or

JAMA Oncology Published online July 21, 2016 (Reprinted)

Copyright 2016 American Medical Association. All rights reserved.

Downloaded From: http://oncology.jamanetwork.com/ by a Texas A&M University User on 08/29/2016

Next-Generation Sequencing in Difficult Head and Neck Cancers

tumors. The degree of chromosomal instability in TP53 or RB1

Mutational Signatures in HNSCC

Adenoid Cystic Carcinomas

Other Salivary Cancers

Original Investigation Research

1 epithelial-myoepithelial carcinoma (Figure 6) (eTable 4 in

Copyright 2016 American Medical Association. All rights reserved.