Mayo Clinic Proceedings Home

Twenty-First Century Precision Medicine in Oncology: Genomic Profiling in Patients With Cancer

  • Mitesh J. Borad
    Correspondence
    Correspondence: Address to Mitesh J. Borad, MD, Division of Hematology and Oncology, Mayo Clinic, 13400 E Shea Blvd, Scottsdale, AZ 85259.
    Affiliations
    Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ

    Mayo Clinic Comprehensive Cancer Center, Scottsdale, AZ

    Department of Molecular Medicine, Mayo Clinic, Rochester, MN

    Center for Individualized Medicine, Mayo Clinic, Rochester, MN
    Search for articles by this author
  • Patricia M. LoRusso
    Affiliations
    Yale Cancer Center, Yale School of Medicine, New Haven, CT
    Search for articles by this author

      Abstract

      The advent of next-generation sequencing has accelerated the implementation of genomic profiling in the care and management of patients with cancer. Initial efforts have focused on target identification in patients with advanced cancer. Prognostication, resistance detection, disease monitoring, and early detection efforts are also underway. This review highlights some of the challenges in this evolving space. This includes choosing between gene-panel and comprehensive approaches, DNA and transcriptome data integration, reduction of false-positive variants, addressing tumor heterogeneity, establishment of workflows to address unsolicited findings, and data sharing and privacy concerns.

      Abbreviations and Acronyms:

      ct-DNA (circulating tumor DNA), MSI (microsatellite instability), NCI (National Cancer Institute), NGP (next-generation panel), NGS (next-generation sequencing), WES (whole exome sequencing), WGS (whole genome sequencing)
      CME Activity
      Target Audience: The target audience for Mayo Clinic Proceedings is primarily internal medicine physicians and other clinicians who wish to advance their current knowledge of clinical medicine and who wish to stay abreast of advances in medical research.
      Statement of Need: General internists and primary care physicians must maintain an extensive knowledge base on a wide variety of topics covering all body systems as well as common and uncommon disorders. Mayo Clinic Proceedings aims to leverage the expertise of its authors to help physicians understand best practices in diagnosis and management of conditions encountered in the clinical setting.
      Accreditation: Mayo Clinic College of Medicine is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.
      Credit Statement: Mayo Clinic College of Medicine designates this journal-based CME activity for a maximum of 1.0 AMA PRA Category 1 Credit(s).™ Physicians should claim only the credit commensurate with the extent of their participation in the activity.
      Credit Statement: Successful completion of this CME activity, which includes participation in the evaluation component, enables the participant to earn up to 1 MOC point in the American Board of Internal Medicine's (ABIM) Maintenance of Certification (MOC) program. Participants will earn MOC points equivalent to the amount of CME credits claimed for the activity. It is the CME activity provider's responsibility to submit participant completion information to ACCME for the purpose of granting ABIM MOC credit.
      Learning Objectives: On completion of this article, you should be able to (1) discern benefits and drawbacks of panel vs comprehensive genomic profiling approaches in the care of patients with cancer, (2) assess the effect of false-positive findings when using tumor-only assessment strategies, (3) account for tumor heterogeneity in genomic data interpretation, (4) identify settings where integrated DNA/RNA data analysis would be appropriate, and (5) identify appropriate workflows for return of genomic profiling results in the context of data sharing and privacy concerns.
      Disclosures: As a provider accredited by ACCME, Mayo Clinic College of Medicine (Mayo School of Continuous Professional Development) must ensure balance, independence, objectivity, and scientific rigor in its educational activities. Course Director(s), Planning Committee members, Faculty, and all others who are in a position to control the content of this educational activity are required to disclose all relevant financial relationships with any commercial interest related to the subject matter of the educational activity. Safeguards against commercial bias have been put in place. Faculty also will disclose any off-label and/or investigational use of pharmaceuticals or instruments discussed in their presentation. Disclosure of this information will be published in course materials so that those participants in the activity may formulate their own judgments regarding the presentation.
      In their editorial and administrative roles, Karl A. Nath, MBChB, Terry L. Jopke, Kimberly D. Sankey, and Nicki M. Smith, MPA, have control of the content of this program but have no relevant financial relationship(s) with industry.
      The authors report no competing interests.
      Method of Participation: In order to claim credit, participants must complete the following:
      • 1.
        Read the activity.
      • 2.
        Complete the online CME Test and Evaluation. Participants must achieve a score of 80% on the CME Test. One retake is allowed.
      Visit www.mayoclinicproceedings.org, select CME, and then select CME articles to locate this article online to access the online process. On successful completion of the online test and evaluation, you can instantly download and print your certificate of credit.
      Estimated Time: The estimated time to complete each article is approximately 1 hour.
      Hardware/Software: PC or MAC with Internet access.
      Date of Release: 10/1/2017
      Expiration Date: 9/30/2019 (Credit can no longer be offered after it has passed the expiration date.)
      Questions? Contact [email protected] .
      The announcement of several large initiatives including the US Cancer Moonshot Initiative
      • Aelion C.M.
      • Airhihenbuwa C.O.
      • Alemagno S.
      • et al.
      The US Cancer Moonshot initiative.
      and the Genomics England Initiative
      • Marx V.
      The DNA of a nation.
      have reinvigorated the precision medicine space. Given the genetic basis for cancer, the application of precision medicine to oncology has proven to be a natural evolution in this area. The initial foray has been in the context of biomarker-guided therapy selection. However, given technological improvements in sequencing technologies and more thorough evaluation of genotype-phenotype relationships, applications to prognostication and early detection are growing increasingly common.

      Background on Molecular Profiling in Cancer

      Molecular profiling–directed treatment of cancer traces its origins to paradigms such as the use of estrogen receptor and progesterone receptor
      • Jensen E.V.
      • Block G.E.
      • Smith S.
      • Kyser K.
      • DeSombre E.R.
      Estrogen receptors and breast cancer response to adrenalectomy.
      and Erb-B2 receptor tyrosine kinase 2 (ERBB2)/human epidermal growth factor receptor 2 (HER2) assessment in breast cancer.
      • Slamon D.J.
      • Leyland-Jones B.
      • Shak S.
      • et al.
      Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2.
      A study conducted by Von Hoff et al
      • Von Hoff D.D.
      • Stephenson Jr., J.J.
      • Rosen P.
      • et al.
      Pilot study using molecular profiling of patients' tumors to find potential targets and select treatments for their refractory cancers.
      using oligonucleotide microarrays for gene expression, fluorescent in situ hybridization, and immunohistochemistry for tumor profiling followed by treatment assignment provided a conceptual framework for current efforts. Since the sequencing of an individual human genome in 2007,
      • Levy S.
      • Sutton G.
      • Ng P.C.
      • et al.
      The diploid genome sequence of an individual human.
      massively parallel next-generation sequencing (NGS) has revolutionized most facets of scientific discovery and made major inroads into application in human health, particularly in the field of oncology, with potential utility encompassing the spectrum of early detection, diagnosis, prognosis ascertainment, recurrence detection, risk assessment, and treatment selection.

      Studies of Clinical Application of NGS and Areas of Controversy and Contention in Cancer

      As genomic profiling has become more ubiquitous in clinical practice, a number of retrospective institutional evaluations provided impetus for ongoing exploration of this approach, albeit with variable levels of success.
      • Schwaederle M.
      • Parker B.A.
      • Schwab R.B.
      • et al.
      Precision oncology: the UC San Diego Moores Cancer Center PREDICT Experience.
      • Wheler J.J.
      • Janku F.
      • Naing A.
      • et al.
      Cancer therapy directed by comprehensive genomic profiling: a single center study.
      Although these efforts should be lauded for helping lay out an appropriate structural framework for the application of precision medicine to oncology, they carry a number of inherent limitations. These include selection bias present in single-cohort studies lacking a control arm, ascription of success to alterations being identified simply as actionable (instead of more rigorous criteria that would classify alterations as useful or not on the basis of strength as a predictive marker for therapeutic efficacy), or leading to change in therapy (irrespective of such a change producing a favorable outcome), heterogeneity of histologic tumor types, and inflation of value of broad-based NGS profiling in the setting of inclusion of patients with well-characterized alterations (eg, patients with BRAF V600E melanoma) in reported studies.
      Pursuant to these initiatives, a number of prospective efforts are ongoing in both tumor-specific and tumor-agnostic settings (Tables 1 and 2). These trials are using an array of designs ranging from nonrandomized single-cohort to randomized/adaptively randomized trials.
      Table 1Selected Prospective Tumor-Specific Trials of Molecular Profiling–Directed Therapy
      ProgramLead organizationTrial designTumor typeIndicationClinicalTrials.gov identifier
      Lung-MAPSWOG/NCTNRSquamous cell lung cancerTreatment selectionNCT02154490
      SAFIR-02 LungUNICANCERRLung cancerTreatment selectionNCT02117167
      SAFIR-02 BreastUNICANCERRNon-HER2 advanced breast cancerTreatment selectionNCT02299999
      I-SPY2UCSF/MD Anderson Cancer CenterARNeoadjuvant breast cancerTreatment selectionNCT01042379
      SU2C Melanoma/GEMMYale/TGenRNon-V600E melanomaTreatment selectionNCT02094872
      FOCUS-4Cancer Research UKRColon cancerTreatment selectionNA
      SPECTAEORTCNRColon cancerTreatment selectionNA
      AR = adaptively randomized; EORTC = European Organisation for Research and Treatment of Cancer; GEMM = Genomics-Enabled Medicine for Melanoma; HER2 = human epidermal growth factor receptor 2; I-SPY2 = Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging And Molecular Analysis 2; LUNG-MAP = Lung Master Protocol; NA = not applicable; NR = nonrandomized; R = randomized; SPECTA = Screening Patients for Efficient Clinical Trial Access; SU2C = Stand Up to Cancer; SWOG/NCTN = Southwest Oncology Group/National Clinical Trials Network; TGen =Translational Genomics Research Institute; UCSF = University of California San Francisco.
      Table 2Selected Prospective Tumor-Agnostic Trials of Molecular Profiling–Directed Therapy
      IHC = immunohistochemistry; ITT = intent-to-treat; MALDI-TOF MS = matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; NA = not available; NGS = next-generation panel; NR = nonrandomized, single-arm design; PFS = progression-free survival; R = randomized.
      ProgramLead organizationTrial designTumor typeIndicationAssays usedNo. of patientsResponse rate – ITT (%)Response rate – genotype-directed treatment (%)Other outcomeStudy
      IMPACT/COMPACTPrincess Margaret HospitalNRAdvanced solid tumorsTreatment selectionNGS panel or MALDI-TOF MS hotspot panel18930.85
      Based on response rate observed in genotype-directed therapy applied to the initial cohort.
      19Stockley et al,
      • Stockley T.L.
      • Oza A.M.
      • Berman H.K.
      • et al.
      Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial.
      2016
      NCI/MATCH
      Based on preliminary analysis provided by study investigators.
      NCI and ECOG-ACRINNRAdvanced solid tumorsTreatment selectionNGS panel795<2
      Based on patients eventually enrolled in genotype-directed treatment.
      NAClinicalTrials.gov identifier: NCT02465060
      NCI/MPACTNCIRAdvanced solid tumorsTreatment selectionNGS panel700ClinicalTrials.gov identifier: NCT01827384
      NEXT-1Samsung Medical CenterNRAdvanced solid tumorsTreatment selectionNGS panel, cytoscan and IHC4281242.6Kim,
      • Kim S.T.
      • Lee J.
      • Hong M.
      • et al.
      The NEXT-1 (Next generation pErsonalized tX with mulTi-omics and preclinical model) trial: prospective molecular screening trial of metastatic solid cancer patients, a feasibility analysis.
      2015
      SHIVAInstitut CurieRAdvanced solid tumorsTreatment selectionNGS panel741Experimental vs control: 2.3 vs 2.0 PFS (P=.41)Le Tourneau et al,
      • Le Tourneau C.
      • Delord J.P.
      • Gonçalves A.
      • et al.
      SHIVA Investigators
      Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.
      2015
      My PathwayGenentechNRAdvanced solid tumorsTreatment selectionPlatform agnostic500ClinicalTrials.gov identifier: NCT02091141
      SIGNATURENovartisNRAdvanced solid tumorsTreatment selectionNGS panel1000ClinicalTrials.gov identifier: NCT01981187
      a IHC = immunohistochemistry; ITT = intent-to-treat; MALDI-TOF MS = matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; NA = not available; NGS = next-generation panel; NR = nonrandomized, single-arm design; PFS = progression-free survival; R = randomized.
      b Based on response rate observed in genotype-directed therapy applied to the initial cohort.
      c Based on preliminary analysis provided by study investigators.
      d Based on patients eventually enrolled in genotype-directed treatment.
      The SHIVA trial conducted by the Institut Curie
      • Le Tourneau C.
      • Delord J.P.
      • Gonçalves A.
      • et al.
      SHIVA Investigators
      Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.
      highlighted the challenges of the application of precision medicine. In this randomized controlled trial evaluating genomic profiling–directed therapy vs use of clinically available agents, no difference was noted between the experimental and control arms (progression-free survival, 2.3 months vs 2.0 months; P=.41). In an interim analysis in the NCI-MATCH trial, of the initial 795 patients, only 33 (4.2%) matched to a treatment arm and only 16 (2.0%) went on to receive genotype-directed therapy. A large effort by the Princess Margaret Hospital in the IMPACT/COMPACT program reported that of an initial 1893 patients, less than 1% eventually derived a treatment response from genotype-directed therapy.
      • Kim S.T.
      • Lee J.
      • Hong M.
      • et al.
      The NEXT-1 (Next generation pErsonalized tX with mulTi-omics and preclinical model) trial: prospective molecular screening trial of metastatic solid cancer patients, a feasibility analysis.
      Although at initial glance these data may suggest tempering enthusiasm for precision medicine–based approaches, it should be pointed out that many of the purported biomarkers used in these trials had little to no efficacy data and were included largely on the basis of their actionability as opposed to preliminary utility. Future trials using precision medicine will want to take this important aspect into consideration. Additional factors that have contributed to the relatively modest success include attrition of patients awaiting therapy due to time to result reporting, suboptimal specimen quality of performance of assays, and inability to access therapies in a timely manner. Consideration of these factors will need to be included in future trials in this space to increase the chances of success.
      As the precision medicine space evolves, a number of areas of controversy/contention and evolution will deserve special attention and are discussed in the sections that follow. These include (1) use of NGS panels vs more comprehensive methods such as whole exome sequencing (WES)/whole transcriptome sequencing, (2) tumor-only vs tumor/normal assessments, (3) effect of tumor heterogeneity and application of minimally invasive/noninvasive NGS testing methods, (4) incorporation of global/genome-scale markers in NGS testing, (5) return of results involving germline findings, and (6) data sharing and privacy concerns.

      Next-Generation Panels vs Whole Genome/Transcriptome Approaches for Genomic Profiling

      Screening for drug targets/predictors of sensitivity to drugs in individual patients using genomic profiling has become a critical element in the discovery and translation of precision medicine. Both DNA and RNA assessment tools have made it to initial clinical application.
      Next-generation panels (NGPs) have garnered widespread clinical adoption, given the ability to use formalin-fixed paraffin embedded tissue samples in the context of routine pathology workflows, tumor-only assessments obviating the need for setup of a clinical workflow to deal with unsolicited but pathogenic germline variants, clinically relevant turnaround time (typically <2 weeks), and ability to achieve higher coverage of select events deemed to be “actionable” (or more aptly of potential therapeutic relevance and in some instances of biological significance but undruggable with currently available tools).
      • Frampton G.M.
      • Fichtenholtz A.
      • Otto G.A.
      • et al.
      Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
      • Hovelson D.H.
      • McDaniel A.S.
      • Cani A.K.
      • et al.
      Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors.
      Next-generation panels (Table 3) have been used in a number of efforts in a clinical/research setting including a large multicentered effort (MATCH trial) supported by the National Cancer Institute (NCI).
      • Tran B.
      • Brown A.M.
      • Bedard P.L.
      • et al.
      Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial.
      Table 3Selected Next-Generation Panel Assays in Clinical Use
      AssayManufacturerSettingNo. of genesSequencing depthSensitivity (%)Specificity (%)Study
      FoundationOneFoundation MedicineCentral laboratory287500×95-99>99Frampton et al,
      • Frampton G.M.
      • Fichtenholtz A.
      • Otto G.A.
      • et al.
      Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
      2013
      Ion Torrent-NCI/MPACTLeidos/NCI FrederickCentral laboratory201499×83.3-100100Lih,
      • Lih C.J.
      • Sims D.J.
      • Harrington R.D.
      • et al.
      Analytical validation and application of a targeted next-seneration sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial.
      2016
      WUCaMPUniversity of WashingtonLocal laboratory25≥1000×95.9-10099.6-100Cottrell,
      • Cottrell C.E.
      • Al-Kateb H.
      • Bredemeyer A.J.
      • et al.
      Validation of a next-generation sequencing assay for clinical molecular oncology.
      2014
      The limitations of NGPs can be overcome by approaches that provide greater coverage of the genome (WES and whole genome sequencing [WGS]). Whole exome sequencing/whole genome sequencing can serve as platforms for simultaneous assessment of known/established pathogenic alterations as well as discovery tools for novel events that may also have potential for application in an N=1 setting using heuristic logic-based methodologies.
      A more comprehensive assessment of alterations offered by WES/WGS also allows the ability to assess tumors from a pathway dysregulation perspective that can allow better prioritization among intervenable drug targets. Finally, WES/WGS would provide a mechanism for the detection of germline variants (including therapeutically relevant germline variants) in the same workflow as tumor analysis and, in the appropriate setup, for counseling of affected/at-risk family members in instances in which a pathogenic variant was identified in the proband. Current limitations of WES/WGS include uneven coverage across the genome, lower coverage of potential drug targets compared with NGPs, long turnaround time (typically >4 weeks), and need for more robust bioinformatics support. However, with the advent of more rapid sequencing, enhancements in big data informatics, and preanalytical methodologies increasing resolution of WES/WGS data, these limitations will likely be overcome and these approaches will garner more widespread adoption in the genomic profiling space. A number of early efforts in this regard have clearly highlighted the feasibility of applying WES/WGS to the clinical setting.
      • Beltran H.
      • Eng K.
      • Mosquera J.M.
      • et al.
      Whole-exome sequencing of metastatic cancer and biomarkers of treatment response.
      • Borad M.J.
      • Egan J.B.
      • Condjella R.M.
      • et al.
      Clinical implementation of integrated genomic profiling in patients with advanced cancers.
      Although approaches that incorporate both NGP and WES/WGS approaches in the same pipeline (with NGP used for rapid assessment and WES/WGS used for more comprehensive assessment), these have not been routinely applied, given the limitations that are imposed by the amount of tissue that can realistically be obtained in the clinical setting to use both approaches, notwithstanding the added cost that could make it practically prohibitive.
      Most of the ongoing efforts have had DNA analysis as the approach, whether they be NGP or WES/WGS. Transcriptome analysis provides an added dimension to genomic profiling. RNA-sequencing assesses gene fusions, expressed variants compared with nonexpressed ones (including allele-specific expression), and pathway analysis. Given that RNA-sequencing is already a genome-wide technology (and not a panel), it can be easily integrated into pipelines that use other broad-based approaches (WES/WGS). Pilot efforts of integrated exome, whole genome, and transcriptome in the clinical setting have already been implemented.
      • LoRusso P.M.
      • Boerner S.A.
      • Pilat M.J.
      • et al.
      Pilot trial of selecting molecularly guided therapy for patients with non-V600 BRAF-mutant metastatic melanoma: experience of the SU2C/MRA melanoma dream team.
      • Craig D.W.
      • O'Shaughnessy J.A.
      • Kiefer J.A.
      • et al.
      Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.
      • Mody R.J.
      • Wu Y.M.
      • Lonigro R.J.
      • et al.
      Integrative clinical sequencing in the management of refractory or relapsed cancer in youth.
      • Roychowdhury S.
      • Iyer M.K.
      • Robinson D.R.
      • et al.
      Personalized oncology through integrative high-throughput sequencing: a pilot study.
      Some of these have even led to the discovery of novel therapeutic targets despite their application in an N=1 setting.
      • Borad M.J.
      • Champion M.D.
      • Egan J.B.
      • et al.
      Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.
      Given the cost, bioinformatics support, and end-user (treating physician) comfort level needed to incorporate these efforts into a clinical context, despite their inherent advantages, for the near/intermediate term these will mostly be relegated to large academic/research centers.

      Tumor-Only vs Tumor/Normal Assessments for Clinical NGS Assays

      Most assays currently in clinical use have employed a strategy of analysis of tumor genome only followed by bioinformatics-guided annotation of variants as damaging vs benign. Although this strategy may allow accurate characterization of well-annotated alterations (eg, BRAF V600E sequence variations and KRAS sequence variations in codons 12 and 13), the misclassification rate has been unacceptably high for less well-characterized variants and poses a considerable problem with regard to potentially erroneous treatment decisions that could result based on these type of data. The primary impetus for tumor-only assays has been to reduce the complexity of testing for patients by eliminating the need to obtain a normal sample such as a buccal swab or buffy coat from blood and allowing operation in a framework in which formal genetic counseling for heritable disease-causing (cancer and noncancer) germline variants would not be required (as would be the case in tumor/normal analyses). Jones et al
      • Jones S.
      • Anagnostou V.
      • Lytle K.
      • et al.
      Personalized genomic analyses for cancer mutation discovery and interpretation.
      compared tumor-only approaches with tumor/germline sequencing approaches and found a 31% false-positive rate in NGP approaches and a 65% false-positive rate in tumor-only exome approach, highlighting the importance of transitioning to tumor/normal assays as the field moves forward. In contrast to these NGP tumor-only assays, WES/WGS pipelines typically use tumor/normal comparisons and as such are able to overcome this false-positive variant call issue.

      Tumor Heterogeneity, Multiregion Sequencing, and Minimally Invasive/Noninvasive NGS Assays

      Current clinical paradigms generally incorporate acquisition of tissue sample from a single discrete region (eg, a single metastatic liver lesion). As such, subsequent analyte extraction, sequencing, data interpretation, and, when relevant, therapeutic intervention are based on single-region sequencing as the starting point. It has been recognized widely now that tumor heterogeneity at a spatial (both intra- and interindividual) and temporal scale could contribute to an incomplete assessment of the tumor genome in an individual.
      • Gerlinger M.
      • Rowan A.J.
      • Horswell S.
      • et al.
      Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
      As costs for NGS-based approaches continue to decline, at least a subset of patients will likely have an opportunity to have genomic profiling that incorporates tumor heterogeneity, where multiregion biopsies can be undertaken without compromising patient safety. Along similar lines, sequential assessments of tumor genomes in the N=1 setting will become commonplace, given that it would be important to capture tumor/clonal evolution in the setting of emergence of resistant clones when therapeutic pressure is applied.
      Another exciting tool that provides not only a less invasive sample acquisition but also ability to encompass body-wide tumor heterogeneity is circulating tumor DNA (ct-DNA) assessment.
      • Diaz Jr., L.A.
      • Bardelli A.
      Liquid biopsies: genotyping circulating tumor DNA.
      It is anticipated that with improvements in technology, ct-DNA technologies will become a more widely used tool in genomic profiling of individual patients, including applications such as early detection of recurrence or de novo malignant tumors.
      • Bettegowda C.
      • Sausen M.
      • Leary R.J.
      • et al.
      Detection of circulating tumor DNA in early- and late-stage human malignancies.
      As precision medicine advances are made, a shift toward more comprehensive, more integrated (DNA/RNA and other platforms), and spatially/temporally frequent assessments and use of tools such as ct-DNA will allow harnessing its full potential.

      Global, Genome-Scale Biomarkers for Precision Medicine in Oncology

      Although most larger efforts have focused on reporting of alterations occurring at the single gene/variant level, several recent studies have exemplified the importance of assessing global, genome-scale perturbations such as microsatellite instability (MSI)/hypermutation status and homologous recombination deficiency signatures. In a study with patients with advanced ovarian cancer, the poly (ADP-ribose) polymerase (PARP) inhibitor rucaparib was found to have increased progression-free survival compared with placebo in a homologous recombination deficiency signature–positive cohort (hazard ratio, 0.62; 95% CI, 0.42-0.90; P=.011).
      • Swisher E.M.
      • Lin K.K.
      • Oza A.M.
      • et al.
      Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial.
      In a pilot evaluation, Le and colleagues evaluated patients with MSI/hypermutation and reported a high response rate (40% [4 of 10 patients]), with use of the programmed cell death protein-1 antibody pembrolizumab,
      • Le D.T.
      • Uram J.N.
      • Wang H.
      • et al.
      PD-1 blockade in tumors with mismatch-repair deficiency.
      and have also shown that a MSI/hypermutation signature can be inferred from NGPs in routine clinical use.
      • Lin E.I.
      • Tseng L.H.
      • Gocke C.D.
      • et al.
      Mutational profiling of colorectal cancers with microsatellite instability.

      Return of Results Involving Germline Findings

      Approaches that do not involve reporting of germline findings have primarily found favor, given that these approaches do not require setup of workflows for return of germline results and associated counseling. However, even with tumor-only approaches, there remains the possibility of uncovering unsolicited findings that could suggest a germline basis for pathogenesis.
      • Catenacci D.V.
      • Amico A.L.
      • Nielsen S.M.
      • et al.
      Tumor genome analysis includes germline genome: are we ready for surprises?.
      Disparate views on reporting incidental/unsolicited findings have resulted in equivocal guidance on this issue.
      • Green R.C.
      • Berg J.S.
      • Grody W.W.
      • et al.
      American College of Medical Genetics and Genomics
      ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
      • Berg J.S.
      • Amendola L.M.
      • Eng C.
      • et al.
      Members of the CSER Actionability and Return of Results Working Group
      Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
      A pilot study that assessed the attitudes of patients with cancer toward precision medicine found that a proportion of patients did not harbor significant concern over unsolicited/incidental findings.
      • Gray S.W.
      • Hicks-Courant K.
      • Lathan C.S.
      • Garraway L.
      • Park E.R.
      • Weeks J.C.
      Attitudes of patients with cancer about personalized medicine and somatic genetic testing.
      As genome-wide approaches are used in the clinical setting, greater attention to ethical, legal, and social implications of NGS testing will need to be considered to ensure success. Issues pertaining to responsibilities of physicians ordering tests with regard to timely disclosure of incidental findings will need to be addressed. Clarity will also need to be achieved in how to deal with disclosure of incidental findings that may affect individuals other than the patient (eg, siblings, children, and parents). A balance between patient privacy laws and information provision to at-risk individuals will need to be achieved to address the welfare of at-risk individuals other than the patient. It will also be important to closely integrate disclosure of incidental findings with data and privacy sharing concerns. These types of issues are likely to arise in the context of required disclosures to third parties such as applicants applying coverage to life insurance companies. Data sharing and privacy concerns are addressed in additional detail below.

      Data Sharing and Privacy Concerns

      The rapid evolution of NGS testing as a clinical tool has resulted in much of such testing done at a single institutional level or under the auspices of commercial vendors in which data sharing could represent a competitive barrier. These caveats of NGS testing have resulted in the development of “data silos.” These data include not only the genetic alterations uncovered by NGS testing but more importantly the outcomes such as response to therapy (and equally important, the lack of response) in the context of specific putative biomarker-driven interventions. Some of these silos are being overcome through the conduct of collaborative multicentered efforts such as the MATCH trial, which is an initiative of the NCI using a multiarm evaluation of targeted therapies in a tumor-agnostic fashion with profiling-based assignment to specific arms. As the field evolves, regulations and legislation may also impose requirements for data sharing, especially for government-funded efforts such as those by the National Institutes of Health/NCI. From an individual patient's perspective, the concern for data privacy is a real one and should not be taken lightly. Legislation such as the Genetic Information Nondiscrimination Act
      • Green R.C.
      • Lautenbach D.
      • McGuire A.L.
      GINA, genetic discrimination, and genomic medicine.
      has set the stage for privacy protection and nondiscrimination, which will further encourage the altruism of patients with cancer that has been instrumental toward advances occurring at a rapid pace.

      Discussion and Future Perspectives

      The common challenges that prospective efforts have faced with regard to the high level of attrition of patients from an intent-to-treat time point to successful delivery of therapy include (1) time lost from consent to coordination of tissue sampling and from tissue sampling to shipment to a central laboratory, (2) delays attributable to batching of samples to ensure cost efficiencies of NGS, (3) inadequate/low-quality biospecimens requiring resampling or an inability to process further, (4) manual confirmation of bioinformatics results and regulatory requirement-driven report sign-offs, (5) interpretation of data by genomic tumor boards when used and variable endorsement and implementation by treating clinicians, (6) availability of therapies and ability to meet stringent eligibility criteria to receive investigational drugs, and (7) focus on single-agent therapies as opposed to targeting relevant pathways at an N=1 level. It is anticipated that a number of these barriers will be resolved over time as NGS testing is moved toward a local laboratory model compared with the current central laboratory model, that testing can be done on smaller biospecimens and reliably on samples such as plasma and urine, and that bioinformatics tools for whole genome analysis reach the robustness of analysis of panel sequencing.
      The rapid deployment of NGS panel assays into the clinical space has occurred in large part in the absence of rigorous clinical evaluation underscoring the relationship between specific genomic markers and response to targeted therapies. As such, the utility of most assays in use remains unproven and has been a source of ongoing controversy. This has led to variable reimbursement from payers, significant off-label use of targeted therapies, and confusion in the burgeoning precision medicine space. Although efforts such as the MATCH trial will serve as a rigorous platform to study clinical utility of genomic targets and help provide clarity to some of these issues, the N-of-1 (single subject clinical trial) context of an individual patient will remain an issue that cannot be ignored because of the somewhat ubiquitous availability of NGS assays. Notable negative trials such as the SHIVA trial have provided an element of caution in the precision medicine space and serve as a reminder that unbridled enthusiasm could indeed derail this promising field if not subjected to the same level of rigor required of other approaches in drug development, before embarking on larger-scale efforts. Another overlooked aspect in the solid tumor space that has been highlighted is the relatively delayed time point in a patient's care when genomic profiling is typically undertaken. Using the framework of chronic myelogenous leukemia, current timing of targeted therapy treatment of solid tumors is similar in concept to intervening in blast crisis as opposed to the chronic phase.
      • Westin J.R.
      • Kurzrock R.
      It's about time: lessons for solid tumors from chronic myelogenous leukemia therapy.
      As such, it is anticipated that testing will move earlier into the diagnostic and treatment paradigm in solid tumors, allowing earlier genotype-directed intervention and enhancement of the probability of the success of such efforts.
      Most of the emphasis thus far has been on the evaluation of single-agent therapies in the context of specified genetic markers. With the knowledge that most malignancies even at the level of individual patients comprise a combination of multiple genomic aberrations that collectively drive tumorigenesis, it is not entirely surprising that application of NGS-based interrogation of individual cancer genomes followed by single-agent therapy has resulted in only moderate success. There is clearly a need for multiagent targeted therapy evaluation as an extension to work done thus far. Although this represents an obvious conceptual advance that needs to be undertaken, some of the challenges foreseen in the implementation of this vision include achieving adequate safety when combining therapies, attaining necessary pharmacokinetic-pharmacodynamic thresholds with combinations, and maneuvering collaborations between multiple pharmaceuticals/biotechs when agents are manufactured by different entities.
      Although a bulk of the efforts for genomic profiling in cancer have been directed toward patients with advanced disease, the use of tools such as ct-DNA assessment have broadened the horizons toward application of these technologies to settings such as detection of recurrence,
      • Tie J.
      • Wang Y.
      • Tomasetti C.
      • et al.
      Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer.
      prognostication,
      • Eckel-Passow J.E.
      • Lachance D.H.
      • Molinaro A.M.
      • et al.
      Glioma Groups Based on 1p/19q, IDH, and TERT promoter mutations in tumors.
      and, the ultimate holy grail in this space, early detection in otherwise unaffected individuals. International collaboration, harmonization of quality standards, data sharing, and rapid communication of outcomes will constitute the sine qua non that will ensure ongoing success of the application of precision medicine in the 21st century.

      References

        • Aelion C.M.
        • Airhihenbuwa C.O.
        • Alemagno S.
        • et al.
        The US Cancer Moonshot initiative.
        Lancet Oncol. 2016; 17: e178-e180
        • Marx V.
        The DNA of a nation.
        Nature. 2015; 524: 503-505
        • Jensen E.V.
        • Block G.E.
        • Smith S.
        • Kyser K.
        • DeSombre E.R.
        Estrogen receptors and breast cancer response to adrenalectomy.
        Natl Cancer Inst Monogr. 1971; 34: 55-70
        • Slamon D.J.
        • Leyland-Jones B.
        • Shak S.
        • et al.
        Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2.
        N Engl J Med. 2001; 344: 783-792
        • Von Hoff D.D.
        • Stephenson Jr., J.J.
        • Rosen P.
        • et al.
        Pilot study using molecular profiling of patients' tumors to find potential targets and select treatments for their refractory cancers.
        J Clin Oncol. 2010; 28: 4877-4883
        • Levy S.
        • Sutton G.
        • Ng P.C.
        • et al.
        The diploid genome sequence of an individual human.
        PLoS Biol. 2007; 5: e254
        • Schwaederle M.
        • Parker B.A.
        • Schwab R.B.
        • et al.
        Precision oncology: the UC San Diego Moores Cancer Center PREDICT Experience.
        Mol Cancer Ther. 2016; 15: 743-752
        • Wheler J.J.
        • Janku F.
        • Naing A.
        • et al.
        Cancer therapy directed by comprehensive genomic profiling: a single center study.
        Cancer Res. 2016; 76: 3690-3701
        • Stockley T.L.
        • Oza A.M.
        • Berman H.K.
        • et al.
        Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial.
        Genome Med. 2016; 8: 109
        • Kim S.T.
        • Lee J.
        • Hong M.
        • et al.
        The NEXT-1 (Next generation pErsonalized tX with mulTi-omics and preclinical model) trial: prospective molecular screening trial of metastatic solid cancer patients, a feasibility analysis.
        Oncotarget. 2015; 6: 33358-33368
        • Le Tourneau C.
        • Delord J.P.
        • Gonçalves A.
        • et al.
        • SHIVA Investigators
        Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.
        Lancet Oncol. 2015; 16: 1324-1334
        • Frampton G.M.
        • Fichtenholtz A.
        • Otto G.A.
        • et al.
        Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
        Nat Biotechnol. 2013; 31: 1023-1031
        • Hovelson D.H.
        • McDaniel A.S.
        • Cani A.K.
        • et al.
        Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors.
        Neoplasia. 2015; 17: 385-399
        • Lih C.J.
        • Sims D.J.
        • Harrington R.D.
        • et al.
        Analytical validation and application of a targeted next-seneration sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial.
        J Mol Diagn. 2016; 18: 51-67
        • Cottrell C.E.
        • Al-Kateb H.
        • Bredemeyer A.J.
        • et al.
        Validation of a next-generation sequencing assay for clinical molecular oncology.
        J Mol Diagn. 2014; 16: 89-105
        • Tran B.
        • Brown A.M.
        • Bedard P.L.
        • et al.
        Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial.
        Int J Cancer. 2013; 132: 1547-1555
        • Beltran H.
        • Eng K.
        • Mosquera J.M.
        • et al.
        Whole-exome sequencing of metastatic cancer and biomarkers of treatment response.
        JAMA Oncol. 2015; 1: 466-474
        • Borad M.J.
        • Egan J.B.
        • Condjella R.M.
        • et al.
        Clinical implementation of integrated genomic profiling in patients with advanced cancers.
        Sci Rep. 2016; 6: 25
        • LoRusso P.M.
        • Boerner S.A.
        • Pilat M.J.
        • et al.
        Pilot trial of selecting molecularly guided therapy for patients with non-V600 BRAF-mutant metastatic melanoma: experience of the SU2C/MRA melanoma dream team.
        Mol Cancer Ther. 2015; 14: 1962-1971
        • Craig D.W.
        • O'Shaughnessy J.A.
        • Kiefer J.A.
        • et al.
        Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.
        Mol Cancer Ther. 2013; 12: 104-116
        • Mody R.J.
        • Wu Y.M.
        • Lonigro R.J.
        • et al.
        Integrative clinical sequencing in the management of refractory or relapsed cancer in youth.
        JAMA. 2015; 314: 913-925
        • Roychowdhury S.
        • Iyer M.K.
        • Robinson D.R.
        • et al.
        Personalized oncology through integrative high-throughput sequencing: a pilot study.
        Sci Transl Med. 2011; 3: 111ra121
        • Borad M.J.
        • Champion M.D.
        • Egan J.B.
        • et al.
        Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.
        PLoS Genet. 2014; 10: e1004135
        • Jones S.
        • Anagnostou V.
        • Lytle K.
        • et al.
        Personalized genomic analyses for cancer mutation discovery and interpretation.
        Sci Transl Med. 2015; 7: 283ra253
        • Gerlinger M.
        • Rowan A.J.
        • Horswell S.
        • et al.
        Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
        N Engl J Med. 2012; 366 ([published correction appears in N Engl J Med. 2012;367(10):976]): 883-892
        • Diaz Jr., L.A.
        • Bardelli A.
        Liquid biopsies: genotyping circulating tumor DNA.
        J Clin Oncol. 2014; 32: 579-586
        • Bettegowda C.
        • Sausen M.
        • Leary R.J.
        • et al.
        Detection of circulating tumor DNA in early- and late-stage human malignancies.
        Sci Transl Med. 2014; 6: 224ra224
        • Swisher E.M.
        • Lin K.K.
        • Oza A.M.
        • et al.
        Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial.
        Lancet Oncol. 2017; 18: 75-87
        • Le D.T.
        • Uram J.N.
        • Wang H.
        • et al.
        PD-1 blockade in tumors with mismatch-repair deficiency.
        N Engl J Med. 2015; 372: 2509-2520
        • Lin E.I.
        • Tseng L.H.
        • Gocke C.D.
        • et al.
        Mutational profiling of colorectal cancers with microsatellite instability.
        Oncotarget. 2015; 6: 42334-42344
        • Catenacci D.V.
        • Amico A.L.
        • Nielsen S.M.
        • et al.
        Tumor genome analysis includes germline genome: are we ready for surprises?.
        Int J Cancer. 2015; 136: 1559-1567
        • Green R.C.
        • Berg J.S.
        • Grody W.W.
        • et al.
        • American College of Medical Genetics and Genomics
        ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
        Genet Med. 2013; 15: 565-574
        • Berg J.S.
        • Amendola L.M.
        • Eng C.
        • et al.
        • Members of the CSER Actionability and Return of Results Working Group
        Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
        Genet Med. 2013; 15 ([published correction appears in Genet Med. 2014;16(2):203]): 860-867
        • Gray S.W.
        • Hicks-Courant K.
        • Lathan C.S.
        • Garraway L.
        • Park E.R.
        • Weeks J.C.
        Attitudes of patients with cancer about personalized medicine and somatic genetic testing.
        J Oncol Pract. 2012; 8 (322 p following 335): 329-335
        • Green R.C.
        • Lautenbach D.
        • McGuire A.L.
        GINA, genetic discrimination, and genomic medicine.
        N Engl J Med. 2015; 372: 397-399
        • Westin J.R.
        • Kurzrock R.
        It's about time: lessons for solid tumors from chronic myelogenous leukemia therapy.
        Mol Cancer Ther. 2012; 11: 2549-2555
        • Tie J.
        • Wang Y.
        • Tomasetti C.
        • et al.
        Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer.
        Sci Transl Med. 2016; 8: 346ra392
        • Eckel-Passow J.E.
        • Lachance D.H.
        • Molinaro A.M.
        • et al.
        Glioma Groups Based on 1p/19q, IDH, and TERT promoter mutations in tumors.
        N Engl J Med. 2015; 372: 2499-2508