This document discusses precision medicine in oncology and molecular monitoring of cancer patients. It describes how molecular characterization of tumors can guide treatment decisions and help develop targeted therapies. Next-generation DNA sequencing is allowing large amounts of tumor DNA to be analyzed to identify molecular targets and guide clinical trials matching treatments to tumor mutations. Challenges include limiting sequencing to known targets, accounting for germline variants, incidental findings, and integrating sequencing results into clinical decision making. Repeated biopsies during treatment can provide insights into drug sensitivity and resistance mechanisms in individual patients.

1. Dr. AVR @ TMH
15 Precision Medicine in Oncology
James H. Doroshow
INTRODUCTION
Novel insights into the biology of cancer have been translated into improvements in clinical care at an accelerating
pace over the past 15 to 20 years.1 The introduction of increasingly sophisticated molecular tools with which to
interrogate both individual cancers and populations of patients with cancer has led to a steady stream of new
diagnostic and therapeutic interventions that have altered the natural history of several solid tumors and
hematopoietic malignancies.2,3 From the concurrent approval of trastuzumab and a companion diagnostic for
breast cancer patients whose tumors overexpress the HER2 gene in 19984 to the recent (May 2017) approval by
the U.S. Food and Drug Administration (FDA) of the anti–programmed cell death protein 1 (anti-PD-1) antibody
pembrolizumab for the treatment of adults and children with solid tumors that demonstrate high microsatellite
instability or mismatch repair deficiency independent of cancer histology,5 the application of molecular tumor
characterization in the clinic has facilitated introduction into oncologic practice of novel small molecules and
immunotherapies applicable to a variety of malignancies without substantive prior therapeutic options, effectively
ending the development of nonspecific cytotoxic agents.6,7
The approach to precision cancer medicine exemplified by these recent developments, and described in a recent
National Academy of Medicine report,8 can be defined as follows: an intervention to prevent, diagnose, or treat
cancer that is based on a molecular and/or mechanistic understanding of the causes, pathogenesis, and/or
pathology of the disease. Where the individual characteristics of the patient are sufficiently distinct, interventions
can be concentrated on those who will benefit, sparing expense and side effects for those who will not. The first
generation of clinical trials evaluating the feasibility of matching a range of treatments to specific molecular
features that can be measured in an individual patient’s malignancy has provided some notable successes as well
as demonstrated certain limitations of this approach that will require improvements in preclinical modeling,
diagnostic assay development, and clinical trial design to overcome.9,10 However, viewed from the perspective of
the therapeutics discovery model prevalent during the last half of the 20th century,11 reorientation of that
paradigm to focus on the need to develop innovative tools and molecules for translating modern cancer biology
into the clinic for individual patients (“precision oncology”) has already paid substantive dividends.12 This
dramatic change in the development of cancer therapeutics is, perhaps, best exemplified by the fact that of the
more than 50 new systemic treatments for cancer approved by the FDA in the past 5 years (2013 to 2017) that
were not formulation variants, only 2 were cytotoxic agents, and these possessed pleiotropic mechanisms of
action.
APPROACH TO PRECISION MEDICINE IN ONCOLOGY
The overall approach to the development of novel diagnostics and therapeutics for one patient at a time, as
outlined in Figure 15.1, depends on the interrogation of improved preclinical models that can be used to validate
molecular targets at a functional level and permit the evaluation of mechanism(s) of action in vivo by assays that
can be definitively transferred from the preclinical to the clinical setting. In this way, tumor tissues obtained prior
to treatment can be used to assign specific patients to clinical trial arms based on the molecular characteristics of
their disease. Patients could then be monitored both clinically and radiographically to determine drug exposure
levels and the efficacy of treatment, while subsequently undergoing posttreatment molecular analyses of
specimens of tumor or the tumor microenvironment (obtained either by direct biopsy or by monitoring circulating
tumor cells [CTCs], circulating tumor DNA, or circulating endothelial cells [CECs]), and by functional molecular
imaging to demonstrate engagement of essential therapeutic targets.
It is important to point out that molecular monitoring in this fashion is not exclusively performed using

2. genomic analyses; rather, conceptually, a variety of molecular characterization methodologies (transcriptomic,
proteomic, immunohistologic, epigenetic, or image-guided), in addition to somatic and germline genomics, are
used based on the disease and biologic contexts under examination.13,14 In fact, it is likely that with technologic
advances over time dynamic/functional tumor profiling may allow the type of biochemical pathway analysis that
is required for optimal therapeutic decision making.15
Next-Generation DNA Sequencing for Precision Oncology
The rapid improvement in massively parallel DNA sequencing capacity over the past decade has made it possible
to acquire enormous amounts of tumor DNA sequence data at rapidly declining cost over shorter time frames; this
remarkable advance has occurred together with the development of improved bioinformatic tools for analysis of
an increasing body of genomic information.16 With this capacity, the somatic mutational frequencies (at the >2%
level) of the most common human tumors have now been characterized in the primary disease setting,17 and
studies of the mutational landscape in metastatic cancers have recently become available.18,19
In this context, the use of pretreatment multigene profiling to direct therapeutic choice has progressed rapidly
over the past 5 years.20 There are multiple clinical programs at major U.S. and international medical centers that
use gene panels measuring defined mutational variants to assist clinical decision making. Some sites apply locked-
down algorithms, and others use expert tumor boards to guide the choice of specific targeted agents for individual
patients based on their mutational profiles.21,22 Currently, most commercially available and academic sequencing
efforts focus on panels of genes and mutations that can be examined at great depth of coverage within a less-than-
2-week time frame using both fresh and formalin-fixed, paraffin-embedded specimens to examine from 20 to
many hundreds of genes (with much larger numbers of variants).23 However, one of the major current limitations
of next-generation sequencing (NGS) panels is that the range of genes examined is, for the most part, limited to
genomic alterations that may underlie the efficacy of specific, known targeted therapeutic agents, so-called
“actionable” mutations of interest.21 Furthermore, the level of evidence used to support the potential clinical utility
of a specific mutation determined by NGS that is assessed in a particular gene panel often varies widely, not only
from gene to gene but also by disease context. It is also clear that an ongoing, major effort is required to assure the
accuracy and reproducibility of any mutational profile, including the concordance of results from laboratory to
laboratory,24 as well as to provide the decision support necessary to facilitate the use of this information by busy
clinicians.25 Another important issue that can affect the utility of NGS panels is that tumor tissues are often
sequenced without concomitant normal tissue controls. Unfortunately, even using the most sophisticated
algorithms, not correcting for germline variants can increase the false-positive variant call rate.26 Germline
sequencing may produce findings that can have a direct impact on the choice of a specific treatment (e.g.,
discovery of alterations in BRCA1/2) or unexpected results that are incidental to cancer treatment but could
provoke the need for timely genetic counseling for the patient’s family.20,27 As genomic testing becomes more
common and more broadly based, there is a growing need to clarify how and in what context incidental findings
should be disclosed.28
Figure 15.1 Molecular monitoring of patients treated with “precision” therapeutics to demonstrate

3. Dr. AVR @ TMH
proof-of-mechanism in vivo. The current approach to the development of targeted therapeutic
agents focuses on the use of preclinical models to validate biomarkers that can subsequently be used
with tissues obtained from patients for molecular tumor characterization and proof-of-mechanism
pharmacodynamic studies. Repeated tissue acquisition during therapy and at the time of disease
progression, correlated with clinical assessment of efficacy and toxicity, facilitates understanding of
the specific mechanisms of drug sensitivity and resistance operating in each individual patient.
FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; PK, pharmacokinetics; PD,
pharmacodynamics; CTCs, circulating tumor cells; CECs, circulating endothelial cells.
(Reproduced from Doroshow JH, Kummar S. Translational research in oncology—10 years of
progress and future prospects. Nature Rev Clin Oncology 2014;11:649–662, with permission.)
Although NGS panels provide broad mutational coverage and can be performed and interpreted on time scales
consistent with oncologic practice, whole exome sequencing (WES; ≈20,000 genes) provides greater breadth (at
less depth) of coverage than NGS panels with the opportunity for analysis of signaling pathways, in addition to
specific gene mutations, of importance for understanding drug resistance mechanisms and the potential role of
tumor heterogeneity in treatment response.29 However, the added information obtained from WES requires a
longer time frame and greater cost for both the genetic testing and bioinformatic analysis—a time frame and cost
that is not currently consistent with routine clinical requirements. In addition, the use of WES has led to the
discovery of large numbers of mutational variants of unknown biologic or clinical significance (VUS).30
Substantial effort to develop international, open-access databases to catalog the presence and functional
significance of mutational variants across disease histologies is currently under way to address this burgeoning
issue.31
Broadening the Spectrum of Molecular Characterization
Precision oncology has now become substantially more than an isolated NGS panel or WES testing of tumor or
germline DNA. Evaluating the mutational spectrum of the entire genome rather than individual genes has recently
been demonstrated to provide important clues to the underlying homologous recombination status of a tumor
(which is important for determining sensitivity to inhibitors of poly [ADP-ribose] polymerase); DNA sequencing
profiles can also be used to assess microsatellite instability (and enhanced presentation of neoantigens) by a
patient’s tumor, a predictive biomarker for response to anti–PD-1 antibodies.32,33 Combining simultaneous RNA
and DNA sequencing enhances molecular characterization by allowing comparison of expression profiling with
mutational analysis and permitting an understanding of the importance of the expression of specific alleles as well
as the ability to better define the presence of gene fusions, an increasingly important source of validated tumor
targets.23 It seems likely that in the near future clinical molecular characterization will employ a multidimensional
approach that combines genetic with epigenetic and proteomic analyses of malignant disease, especially important
to further our understanding of single nucleotide variants.13,34 Such multidimensional studies have begun to show
that gene expression at the mRNA level may not fully describe the expression of critical proteins in some tumors,
suggesting that an integrated genomic and proteomic perspective may be required for the most effective
development of targeted therapeutics.13,35
Because obtaining longitudinal tumor biopsy specimens for molecular characterization may entail substantial
difficulty,36 and because of the heterogeneity of the mutational spectra that occur across multiple sites of
disease,37 new technologies for molecular analysis of CTCs and circulating tumor DNA (ctDNA) (Fig. 15.2) offer
the possibility of repeating mutational or protein-based molecular profiles not only before (to determine a true
baseline) but also during treatment, including at the time of disease progression, using small volumes of
blood.38,39 In this fashion, it is possible that examination of the molecular characteristics of a tumor, derived from
multiple potential sites of disease, might provide a more comprehensive understanding of the heterogeneity of an
individual patient’s malignancy, facilitating treatment choice as well as understanding of the time- and therapy-
related development of resistance pathways.40,41 However, the concordance of NGS panel results from differing
ctDNA analysis platforms has not yet been widely established, suggesting that additional efforts to standardize
this approach will be required before it is widely adopted.42,43

4. Figure 15.2 Preclinical tumor models for precision oncology. Patient-derived xenografts (PDXs),
tumor organoids, and conditionally reprogrammed low-passage tumor cultures can be initiated by
transplantation of either surgical specimens or needle biopsies into severely immunocompromised
mice (PDXs), or disaggregation of tumors in carefully defined culture media that facilitates the
growth of tumor cells with stemlike qualities. These approaches provide low-passage tumor models
for molecular characterization, target validation, and drug screening; all three model systems
provide a closer approximation of in vivo tumor biology than previous large-scale cell line panels
and can be adapted for in vivo imaging, pharmacodynamic studies, and “preclinical” clinical trials
of novel targeted therapeutic agents or combinations. The techniques for separating large numbers
of circulating tumor cells (CTCs) and cell-free tumor DNA (cfDNA) have progressed rapidly and
now represent viable approaches for obtaining malignant tissue for DNA sequencing and/or
pharmacodynamics to supplement biopsies of metastatic disease or when biopsy sampling is not
practical. 2D, two-dimensional; 3D, three-dimensional.
PRECLINICAL MODELS TO INFORM PRECISION ONCOLOGY
Although useful for the evaluation of the therapeutic index of new anticancer drugs, mouse tumor xenografts
derived by transplanting long-established human tumor cell lines (that have been adapted to cell culture on plastic
for decades) into immunocompromised mice do not reproducibly predict the histologically specific efficacy of
anticancer agents.44 However, new in vivo models generated by transplantation of surgical or biopsy specimens of
human tumors into severely immunocompromised NOD/SCID/IL2Rγnull (NSG) mice, denoted as patient-derived
xenografts (PDXs) (see Fig. 15.2), have been developed over the past decade; altered natural killer cell maturation
in this mouse strain improves engraftment rates (now averaging 50% to 60%) for many common solid tumors.45,46
Importantly, early passage PDXs have been shown to retain histologic and genetic characteristics of the tumor of
origin as well as therapeutic profiles consistent with these expression patterns.47,48 Furthermore, recent studies
have demonstrated the ability of PDX models used at scale to both validate known therapeutic targets and to
confirm efficacy profiles appropriate for the drug classes investigated.49 The context of the prior treatment profiles
of the patients whose tumors were used to derive the PDXs can also be compared to results following exposure to
the same drugs in PDX models.50 DNA and RNA sequencing data from PDX tumors provide the opportunity to

5. Dr. AVR @ TMH
prospectively interrogate the role of specific mutational and expression profiles in the therapeutic activity of novel
targeted agents in a histology-agnostic fashion. In this way, “preclinical” clinical trials using PDX models could
accelerate the pace of cancer drug development.
It is important to point out, however, that there are limitations associated with the use of PDX models to
support a precision approach to cancer therapeutics. The lack of human immune components in the PDX tumor
microenvironment not only limits the evaluation of immunotherapeutic agents in these models but also prohibits
examination of the role human microenvironmental elements play in the control of tumor growth by molecularly
targeted drugs. It is also clear that as the PDX passage number increases in vivo, clonal populations not
predominant in the original tumor may be selected for outgrowth, affecting gene copy number, mutational
spectrum, and the antiproliferative activity of therapy.50
In addition to the advent of PDX models to guide the use of molecular characterization of human tumors, new
methods for three-dimensional in vitro culture of malignant cells (from surgical or biopsy samples) have been
developed, facilitating tumor cell proliferation with a rich matrix of essential growth factors; such complex
organotypic (organoid) cultures retain many phenotypic and genotypic characteristics of cancer stem cells from
primary or metastatic tumors and thus may provide a closer approximation of human tumor biology than prior
two-dimensional cell culture approaches (see Fig. 15.2).51,52 Organoid cultures can also be used for drug screening
and for the propagation of PDX models, providing a means to rapidly move back and forth between low-passage
in vitro and in vivo models originating from the same clinically and molecularly annotated surgical or biopsy
specimen.53 As the range of tumors amenable to organoid culture expands (from colon, pancreatic, prostate, and
breast cancers) to other common malignancies, it is likely that these model systems will accelerate understanding
of the molecular interactions that underlie the spatial context of therapeutic response.
ROLE OF MOLECULAR PHARMACODYNAMICS AND DIAGNOSTICS IN
PRECISION ONCOLOGY
Human Biospecimens for Molecular Characterization
Molecular characterization of human tumors, whether it is for DNA or RNA sequencing, epigenetic studies,
proteomics, or immunohistochemistry, starts with the collection of biospecimens of high quality.54 Although
research biopsy techniques are improving, national standards for specimen acquisition, processing, fixation, and
storage have not been universally implemented, which hinders the comparability of results obtained across
multiple research sites.55 It is not infrequent, particularly for radiologically guided needle biopsies, that the
percentage of tumor in the specimen obtained may be <5%, possibly sufficient for pathologic diagnosis but often
inadequate for any protein-based molecular assay.36 Furthermore, the utility of the assay to be performed may be
diminished by insufficient attention to stabilizing the analyte of interest immediately after acquiring the specimen.
Unfortunately, techniques to stabilize biomarkers are infrequently examined before biomarker studies are
initiated.56,57 Attention to the details of tissue acquisition, either tumor or normal tissues, is fundamental to the
success of the molecular characterization efforts that are at the heart of a precision approach to oncology.
Molecular Pharmacodynamics in Precision Oncology
Evaluating therapeutic regimens for cancer based on the degree of their target engagement and the downstream
molecular events initiated by a drug-target interaction requires pharmacodynamic (PD) biomarkers: molecular
species that are altered in response to an oncologic drug or treatment and that, if measured, can be used to
establish the mechanism of action of the drug. A PD biomarker helps to define the drug-induced pharmacologic
effect associated with the therapeutic activity of the agent; however, a PD effect does not, by itself, ensure patient
benefit because biochemical events downstream of the drug target may impair tumor cell killing. Thus, PD
biomarkers may or may not be predictive of patient benefit (or toxicity) from a specific intervention. Although the
development of predictive biomarkers is a critical goal of precision oncology, the first step in the process is
establishing molecular proof-of-mechanism (PoM) in human tumors during early-phase clinical trials.58 It is in
later stage trials that definitive relationships between biomarker modulation and clinical response are established,
so-called proof-of-concept (PoC) studies.
Although the need to clarify the dose range and schedule that correlates with a molecular response in a tumor
(rather than simply with pharmacokinetics in the circulation or normal tissue toxicity) seems clear, the

6. development of robust assays for PD assessment has lagged behind the development of clinical DNA sequencing
for cancer.59 This may be due to the difficulties inherent in generating a variety of assays to examine a broad
range of biochemical targets using many different analytical platforms without the availability of high-quality
reagents.60 Developing novel, mechanistically based combination therapies targeting multiple signaling defects
has been enormously challenging in the absence of establishing the doses of the agents to be used in combination
that are needed to produce the degree of target inhibition required for optimal tumor cell killing.61 Furthermore,
failure to confirm PoM using appropriate PD assays in early-phase clinical studies has resulted in costly failures of
phase III clinical trials.62
If validated PD assays are available for characterization of specific molecular species, important insights into
drug action can be detailed from clinical trials that involve small numbers of patients; such studies can lead to the
confirmation (or rejection) of prevailing hypotheses regarding the PoM of specific drug classes.63 Recent
technologic improvements in microscopy, dye technology, and image processing now permit the quantitative
assessment of multiple aspects of pathway engagement following drug treatment across a spatial context using
formalin-fixed, paraffin-embedded biopsy tissues. Such quantitative immunofluorescence techniques are capable
of monitoring heterogeneous, individual cell-to-cell changes in tumoral DNA damage response following
exposure to DNA-damaging agents, for example.64 Improvements in proteomics now also support high-
throughput evaluation of reverse-phase protein arrays, permitting the development of proteomic response
signatures associated with drug treatment in vivo.65 It is likely that these new approaches will expand the use of
PD to a wider range of signaling pathways and will broadly enhance understanding of the molecular mechanisms
of drug action in patients.
Predictive Diagnostic Assays
Although PoM studies are critical first steps in the precision approach to cancer therapeutics, target engagement
does not necessarily confer therapeutic efficacy, in part because of the remarkable redundancy of growth-
controlling signal transduction pathways in human tumors.66 Furthermore, other than the predictive power of
mutational profiles, only a modest number of predictive biomarkers for cancer have been deployed successfully in
the clinic. Such biomarkers need to provide accurate correlations with a clinical outcome following specific
treatment interventions, unlike prognostic biomarkers that convey associations with clinical benefit, appropriate
for populations that are not unequivocally related to the treatment’s mechanism of action. Well-known predictive
biomarkers include the use of HER2 expression to select breast cancer patients who may benefit from
trastuzumab; the Oncotype DX and MammaPrint assays to establish the relative risk/benefit of adjuvant
chemotherapy in the setting of early-stage breast cancer67,68; and the detection of mutant KRAS, which predicts for
the lack of efficacy of cetuximab in colon cancer.69
In general, however, the successful transition from a molecular assay to a predictive biomarker remains
difficult. Problems that have slowed the field, but that have been appreciated to a greater degree recently, include
the requirement for standard operating procedures for both sample acquisition and assay validation, the need for
better statistical understanding of the sources of variability in the assay, the trial design features required to
qualify the assay in a clinical setting, and the necessity for a deep understanding of how the test will be used in the
appropriate clinical context.70 If these issues are carefully considered at the earliest stages of assay development,
the predictive tests needed to guide novel treatment programs and advance the field of precision oncology,
including immunotherapy, can be developed more effectively, and at an accelerated pace, facilitating the
successful application of targeted therapeutics for cancer.71
PRECISION ONCOLOGY CLINICAL TRIALS AND TRIAL DESIGNS
Application of the principles of precision medicine to oncology has progressed through several interrelated stages
over the past two decades. Beginning with the approval of trastuzumab for patients with HER2-expressing breast
cancers (defined by immunohistochemistry or fluorescence in situ hybridization)72 and the demonstration of the
efficacy of imatinib for patients with chronic myelogenous leukemia expressing the BCR-ABL oncogene,3
determination of therapeutic choice over this time frame by measurement of the expression of individual gene
variants has fostered dramatic changes in the treatment of patients with adenocarcinoma of the lung carrying
EGFR, ALK, and ROS1 mutations73–75 and patients with melanoma expressing mutant V600 BRAF species.76
With the initial research use of NGS, and continuing to the present, investigators have identified genotypes in

7. Dr. AVR @ TMH
single patients that appeared to explain an “exceptional” response or provided molecular insight into an unusual
disease that suggested a novel treatment program (Fig. 15.3).77 These and other such gratifying results stimulated
early attempts to define therapy based on a range of molecular tumor characteristics beyond those applied in
routine clinical practice.78,79 Although molecular aberrations could be detected in a substantial percentage of
patients enrolled on these trials, the degree to which the mutations detected in their tumors could be considered to
underlie the growth characteristics of their malignancies, as well as the strength of the data used to “match”
treatment to tumor, was limited. The nonrandomized nature of these initial clinical studies, as well as the
definitions used to define objective clinical responses, also limited interpretation of their results.9
A second phase of precision oncology trials (e.g., the BATTLE and SHIVA studies), some of which have been
reported,80,81 has provided important insights clarifying the feasibility, limitations, and requirements for
optimizing the principles of precision medicine in clinical oncology.10,82 The BATTLE study demonstrated the
feasibility of mandating tumor biopsies for molecular characterization as an entry criterion for patients with
advanced-stage non–small-cell lung cancer as well as the potential to apply adaptive randomization strategies in
the era of targeted therapy. The SHIVA trial provided important lessons that have guided the conduct of
subsequent, histology “agnostic” precision oncology trials; this trial was a prospective, randomized study in which
no difference in progression-free survival was demonstrated between the experimental arm (which used a therapy
targeting one of three molecular pathways) and physician’s choice of therapy for patients with advanced solid
tumors. However, for both of these trials, the level of evidence used to assign patients to a limited number of
specific pathway-driven treatments was based on potentially actionable biomarkers (or mutational variants of
unclear significance) rather than on strong evidence demonstrating that the specific mutation(s) of interest (or
other molecular characteristics) that were detected could drive tumor cell proliferation. Furthermore, only a
limited range of drugs was available for the targets under study in either investigation. It is also important to
consider the contribution of tumor heterogeneity, the potential for suboptimal modulation of targeted pathways,
and upregulation of compensatory pathways to the modest or minimal single-agent activity demonstrated for
molecularly targeted drugs in these trials.10
The current generation of therapeutic precision oncology trials20 and recent reports of institutional experience
with NGS-selected treatment have attempted to address several of these critical considerations. Among the most
important is the strength of the treatment algorithm used for drug selection.83 The selection algorithm needs to
define how mutations are prioritized for defined therapies in the case of single or multiple targetable alterations
(Table 15.1), and specific prioritization rules must be developed prior to trial initiation. Contemporary
investigational studies also generally exclude patient entry based on known targets for FDA-approved drugs or
indications and prohibit “matching” drugs and targets where a solid base of clinical trial data already indicates that
the use of the agent in a specific disease context is unlikely to be effective (e.g., single-agent BRAF inhibitors for
patients with BRAFv600E-mutant advanced colon cancer). In a recent example of the use of molecular profiling for
the selection of a targeted drug, in a single-institution series of patients with metastatic adenocarcinoma of the
lung where tumors underwent NGS with a multigene panel, 69 of the 478 patients whose mutational profiles were
not associated with standard-of-care treatment options received matched therapy; clinical benefit was
demonstrated in 52% of these individuals.84
One of the major changes accompanying the implementation of molecular characterization assays to guide the
choice of oncologic therapy has been the application of novel clinical trial designs to optimize this approach.85,86
The overarching concept is to coordinate clinical studies so that more than a single treatment or disease can be
evaluated across a shared operational infrastructure, often focused on mechanism-based therapeutic
methodologies. Such “Master Protocols” offer the potential to examine several approaches in parallel using a
collective diagnostic or therapeutic platform that, although complex to organize and operate, offers the potential to
accelerate the entire clinical trials process.87 As shown in Figure 15.3, one type of master protocol design,
designated “basket” trials, generally focuses on a variety of malignant histologies and uses a single drug that
targets a single mutation. Such studies provide access to an investigational drug for a broad range of cancers that
may carry a specific mutation at low frequency. Although basket trials generally examine one drug/mutation pair
at a time, using a broad screening strategy may demonstrate clinical activity in patients carrying specific
mutations, leading to future clinical trials or possible FDA approval for the combination of drug and biomarker.
Several recent, successful, histology-agnostic basket trials have demonstrated substantive clinical benefit for pan-
HER2 inhibitors in patients carrying HER2 mutations in a wide range of solid tumors beyond breast cancer, for
larotrectinib in patients with various tumors expressing TRK fusion genes,88 and for patients with mismatch
repair–deficient tumors treated with a PD-1 inhibitor.32 These studies have clearly demonstrated that the

8. molecular background, as well as the histologic context, of solid tumors needs to be considered in the overall
paradigm of cancer drug development.
A different type of master protocol can be described as an “umbrella” trial (see Fig. 15.3). Umbrella studies can
take several different forms. Trials may be disease based, such as the Lung-MAP study sponsored by the National
Cancer Institute (NCI), supported by the Foundation for the National Institutes of Health (NIH), and directed by
the Southwest Oncology Group (SWOG) clinical trials group, in which patients with the same tumor type
(originally advanced squamous cell lung cancer in this case) are treated with multiple drugs targeting multiple
mutations. Such studies can be randomized or nonrandomized and frequently use a rules-based treatment
assignment. The trial is managed as series of substudies with an overarching administrative structure for
biomarker assessment and data acquisition; this allows for the addition of new substudies as accrual goals (or
futility boundaries) are reached. Disease-focused umbrella trials also frequently use shared control arms and
adaptive statistical end points.

9. Dr. AVR @ TMH
Figure 15.3 Clinical trial designs for precision oncology. Basket trials are histology-agnostic
studies that typically focus on a variety of tumors that carry a specific genetic mutation using a
single agent targeting that mutation. Umbrella trials use multiple drugs that target multiple
mutations in a range of tumor types in the context of a single study; they may be randomized or
nonrandomized. Exceptional responders are N-of-1 clinical experiences in which any patient with a
tumor type that is unlikely to undergo an objectively defined response demonstrates robust clinical

10. benefit from therapy; characterization of the tumors from such patients can define unique molecular
signatures that can be tested for their predictive power in subsequent clinical trials for defined
patient populations. (Reproduced from Kummar S, Williams PM, Lih CJ, et al. Application of
molecular profiling in clinical trials for advanced metastatic cancers. J Natl Cancer Inst
2015;107[4]:djv003.)
TABLE 15.1
Levels of Evidence for Prioritization of Actionable Molecular Abnormalities in the NCI-
MATCH Trial
Level 1: Gene variant credentialed for a U.S. Food and Drug Administration–approved drug
Level 2: Molecular characteristic is an eligibility criterion for an ongoing clinical trial utilizing that drug or the abnormality has been
identified in an N-of-1 clinical response
Level 3: Preclinical response: (1) models with variant respond while models without abnormality do not, (2) gain-of-function
mutation demonstrated in a preclinical model, (3) loss of function in a preclinical model (tumor suppressor gene or pathway
inhibitor)
NCI-MATCH, National Cancer Institute Molecular Analysis for Therapy Choice.
Adapted from Conley BA, Doroshow JH. Molecular Analysis for Therapy Choice: NCI MATCH. Semin Oncol 2014;41:297–299.
Umbrella trials may also be histology independent and focus on multiple drug targets across a broad array of
malignancies. Although such studies are most often signal-seeking/hypothesis-generating endeavors that are
unlikely, despite their large size, to facilitate FDA approval of a specific mutation/biomarker pair and are resource
intensive, they are a major avenue for evaluating the role of treating patients who harbor tumors that express low-
prevalence mutations with targeted therapeutics. Screening large numbers of patients to be treated for a broad
range of molecular targets with a large formulary of drugs also decreases the failure rate of mutational screening,
improving the chance that patients will receive treatment on study. The largest of such efforts is the NCI
Molecular Analysis for Therapy Choice (MATCH) trial, overseen for the NCI’s National Clinical Trials Network
by the Eastern Cooperative Oncology Group–American College of Radiology Imaging Network (ECOG-ACRIN)
group.21 This study, with the trial schema shown in Figure 15.4, has reached the goal of its initial phase of accrual;
approximately 6,400 patients were enrolled and had fresh biopsies of metastatic sites at over 1,000 participating
institutions in less than 2 years. Over 90% of the successful biopsies underwent NGS analysis with a validated
assay performed by a centralized laboratory network with a median turnaround time of 15 days; 1,004 patients
were assigned to treatment based on a rules-based algorithm, and 689 patients have been treated as of January
2018 on one of 30 different treatment arms. Therapeutic activity has been demonstrated on multiple trial arms.
Although the primary focus of the NCI-MATCH trial is hypothesis generation, it does demonstrate the possibility
of studying the utility of molecularly targeted therapy for low-prevalence mutations when the trial population and
the range of drug choices are both large. It has also clearly shown that the entire oncology community can be
enlisted to examine the feasibility of scaling the precision medicine paradigm if it provides novel treatment
options for patients across a broad geographic distribution.

11. Dr. AVR @ TMH
Figure 15.4 Schema for the National Cancer Institute Molecular Analysis for Therapy Choice
(NCI-MATCH) clinical trial. The NCI-MATCH clinical trial is an umbrella study to examine the
hypothesis that treating adult solid tumors and lymphomas with molecularly targeted therapies
independent of disease histology can be effective. Over 6,000 patients have been accrued at over
1,000 clinical trial sites; patients underwent fresh tumor biopsies for next-generation sequencing by
a centralized laboratory network. A formulary of over 30 drugs from a wide range of
pharmaceutical firms permitted accrual of patients with low-prevalence mutations to a series of
phase II investigations.
IMAGING AND PRECISION ONCOLOGY
Current functional molecular imaging techniques (such as positron emission tomography [PET], single-photon
emission computed tomography [SPECT], and dynamic contrast-enhanced magnetic resonance imaging [DCE-
MRI]) can provide a noninvasive approach to quantitating the presence in tumors of specific molecular targets, the
spatial heterogeneity of target expression, intratumoral drug pharmacokinetics, and target modulation following
treatment with a therapeutic agent.89,90 Examples of molecular targets and receptor occupancy that can be imaged
include epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), and
vascular endothelial growth factor (VEGF).89,91,92 Substantial progress has also been made in the use of [18F]-
fluoro-17-β-estradiol (FES) for PET scanning to demonstrate the presence of the estrogen receptor (ER) in breast
cancers and modulation of ER occupancy by tamoxifen (Fig. 15.5). Recent studies suggest that uptake of FES in
ER-positive breast cancers is correlated with objective response to antiestrogen therapy and that heterogeneous
ER expression, when detected, may indicate the development of resistance to hormonal therapy.93 Thus,
molecular imaging techniques provide an important means of defining patient populations that may benefit from
specific molecularly targeted treatments as well as delineating sites of clinical tumoral heterogeneity

12. noninvasively.
Recently, improved analytical processing capabilities for both anatomic and molecular imaging data have
allowed the quantitation of a range of phenotypic features from these images (e.g., tumor shape, texture, edge, and
intensity) and the subsequent development of image signatures (radiomics) as well as a better understanding of the
interaction of the tumor with its microenvironment (habitat imaging).94 These data can be used for prognostic
purposes and can be integrated with genetic features of tumors to provide better understanding of tumor
heterogeneity and biology in a spatial context (radiogenomics).95 The metrics developed by radiomic techniques
can assist in distinguishing benign from malignant lesions, in differentiating disease grades, and in improving
evaluation of treatment response. Ultimately, molecular tumor characterization efforts are likely to use both
invasive (tissue-based) and noninvasive features to develop a complete understanding of human tumors at both the
level of anatomic architecture and molecular infrastructure.
Figure 15.5 Functional imaging of the estrogen receptor in a patient with metastatic breast cancer
and receptor blockade by the tamoxifen metabolite endoxifen. A,C: [18F]-Fluoro-17-β-estradiol
(FES) scan of a patient with metastatic breast cancer in the pelvis; the metastatic site is shown
(circled) in C. B,D: When the patient underwent repeat positron emission tomography–computed
tomography (PET-CT) imaging on day 6 after 5 days of treatment with the active metabolite of
tamoxifen, endoxifen, uptake of FES at that site was substantially decreased. SUV, standardized
uptake value. (Reproduced from Doroshow JH, Kummar S. Translational research in oncology—10
years of progress and future prospects. Nature Rev Clin Oncol 2014;11:649–662, with permission.)
PRECISION PREVENTION
Although the concept of precision prevention in oncology has been defined (see earlier discussion), actual
interventions that can be applied today to prevent cancer based on a deep molecular understanding of the
pathogenesis of premalignant lesions are not as robust as those available for the treatment of established
malignancies. In part, this is because molecular profiling approaches have not yet been extensively applied in this

13. Dr. AVR @ TMH
arena.96 Limited knowledge of the biology of precancer, including the biology and immunology of populations at
high risk of developing cancer, has slowed progress toward developing a better understanding of the molecular
characteristics of individual subjects requiring preemptive interception.97
Effective preventive strategies have, most recently, taken advantage of a rapidly developing appreciation of the
pathobiology of inherited (germline) cancer susceptibilities. The importance of microsatellite instability and its
immune consequences have stimulated the growth of screening strategies for the Lynch syndrome, and a better
understanding of the role of BRCA1 in the control of replication stress and the hormonal milieu of the breast has
helped to explain the mechanistic basis for the utility of tamoxifen as a prevention strategy in BRCA1-mutant
breast cells (that are predominantly ER negative). In like manner, initial large genomic studies of premalignant
tissues have begun to develop mutational signatures of DNA repair pathways, the APOBEC family of deaminases,
and oxidative stress that will inform improved diagnostic and interventional strategies. Progress has been notable
for patients with Barrett esophagus; this progress has resulted from NGS and transcriptomic studies that have
described microbiota-related inflammatory changes and the mutational profile and molecular evolution of this
form of precancer.
Beyond the remarkable benefits of vaccination against HPV and hepatitis B, understanding of the epigenetics
and immune-oncology of premalignancy is at an early stage of development. It seems likely that an improved
comprehension of the microenvironment of premalignant pathologies, particularly inflammation-related
conditions such as inflammatory bowel disease, chronic pancreatitis, and hepatic and/or pulmonary fibrosis, will
be necessary to intervene on a patient-specific basis. However, recent studies implicating certain proinflammatory
cytokines in cancer etiology (e.g., interleukin-17 in colorectal adenomas and cancer, for which therapeutic
antibodies have recently reached the clinic) suggest that novel precision preventive approaches will be
forthcoming in the near future.98 NGS of premalignant tissues could also be used to identify potential neoantigens
amenable to vaccine or therapeutic antibody development.
Perhaps the most important focus for precision prevention efforts in the future is the development of a
“precancer atlas” in which systematic, clinically annotated collections of tissue and blood from patients with
premalignant conditions or those who are at high risk of developing cancer are built at scale and subjected to
intensive, multidimensional molecular characterization. It is the expectation that, in analogy to the NIH-supported
Cancer Genome Atlas project, such studies would provide substantively enhanced understanding of the biology of
precancer that would stimulate and sustain new approaches to the diagnosis and interdiction of the malignant
process.97,99
FUTURE PROSPECTS
The pace of implementation of precision approaches to cancer treatment and diagnosis has been dramatic over the
past 5 years. As genomic technical capabilities continue to improve, the application of multidimensional
approaches to elucidate the dynamics of tumor biology in vivo are likely to become routine components of the
therapeutic paradigm of the future. In this way, proteomic, epigenetic, and immunologic profiling of tumors and
the tumor microenvironment, as well as pathway molecular imaging, will support development of more precise
and more predictive biomarkers for both treatment and preventive interventions. Finally, novel insights into the
measurement of tumor heterogeneity in the clinic will permit the application of interventions to preempt
therapeutic resistance on a patient-by-patient basis, an essential component of long-term cancer control.
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