Genomic Medicine in Clinical Practice

Introduction

The latest evidence suggests that personalized treatments in oncology (across all cancer types) lead to higher response rates, longer PFS and OS and fewer deaths related to the toxicities of treatment. In the face of a rapidly evolving field, the oncology team is tasked with implementing appropriate management of each patient with cancer throughout the continuum of care. Regardless of practice settings (e.g., academia or community), the oncology team is bound by health care costs and practice/network guidelines. This module is intended to review the application of genomics in everyday clinical practice, with an emphasis on the therapeutic phase of the continuum of care.

Clinical Settings for Genomic Testing

Next-generation sequencing (NGS) technologies are advancing, leading to reduced costs and quicker turnaround; thus, access to NGS platforms is increasing. However, at this time, genomic testing is not appropriate for all patients with cancer. Instead, application of genomic testing guided by current clinical principles falls into three basic clinical settings: hereditary screening, early stages and advanced stages (Figure 1-23). Furthermore, with the availability of many testing platforms, it is important to consider platforms/panels that are consistent with the clinical setting. The number of genes tested, types of alterations measured and type of sample needed will vary based on the goal for testing.

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Hereditary Genomic Testing 

Hereditary genomic testing is performed when hereditary predisposition for cancer is suggested by family history and/or age of diagnosis.

Which patients?

• Approximately 5% to 10% of all cancers result from inheritance of a mutation.
• Asymptomatic patients with strong family history of cancer often proactively seek testing, usually through their primary care physician.
• Patients younger than 50 years of age who receive a diagnosis of cancer and who may or may not have a strong family history are strongly encouraged to have hereditary genomic testing performed.

Which testing platforms?

• Testing includes genes associated with cancer syndromes. Some of the most commonly detected cancer syndromes and genes associated with these diseases are shown in Table 1; however, at least 50 cancer syndromes have been described.
• Hereditary testing may include single gene tests or multigene cancer panels.
• Testing usually requires a single blood specimen, clinical questionnaire and results interpretation that follows American College of Medical Genetics guidelines. Positive results prompt services of genetic counseling, and follow-up may include recommendations for further testing in the family.
• For a list of commercially available platforms for hereditary testing, visit The Genetic Testing Registry at https://www.ncbi.nlm.nih.gov/gtr.

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Genomic Testing for Early Stages of Cancer

Genomic testing for early stages of cancer  is currently only routinely performed for breast cancer; however prognostic assays are being investigated for their role in many other cancer types.

Which patients?

• Genomic testing is used to identify more aggressive cases that have higher likelihood of recurrence and to guide selection of patients who would benefit most from adjuvant chemotherapy.
• Prognostic tools for risk stratification of early stages of cancer are currently only approved by the FDA for breast cancer.

Which testing platforms?

• Oncotype Dx (Genomic Health) is used for estrogen receptor–positive breast cancers and is covered by most insurance plans. This assay is used to determine which patients have a high risk for recurrence and, therefore, are predicted to benefit most from adjuvant chemotherapy.
• Mammaprint (Agendia), is FDA-approved and also covered by many insurance plans, is used in early-stage breast cancers regardless of estrogen receptor status to determine risk for recurrence and identification of patients who would benefit from adjuvant chemotherapy.
• Both breast prognostic assays use formalin-fixed paraffin-embedded tissue specimens for analysis.
• Patient selection tools that incorporate risk modeling based on genomic profiles are under investigation for early stages of several types of cancer, including melanoma, lung, colon and prostate cancers.

Genomic Testing for Advanced Stages 

Genomic testing for advanced stages of disease is used to guide selection of targeted therapies, monitor response and identify clinical trials for refractory disease after standard of care has been exhausted.

Which patients?

• Genomic testing for targeted therapies considered standard of care is dependent on tumor type, and assessment of one or several genes may guide selection of appropriate therapy.
• As novel receptor tyrosine kinase inhibitors targeting acquired resistance mechanisms are becoming available, real-time monitoring for the appearance of resistance mutations through noninvasive techniques are being used to prompt switching of agents. This currently is only applicable for the treatment of epidermal growth factor receptor–mutated non–small cell lung cancer.
• Patients with cancers lacking targeted therapy options (eg, sarcoma, cancer of unknown primary) or patients whose targeted therapies lack predictive markers (eg, erlotinib for pancreatic cancer, cetuximab for head and neck cancer) are assayed by genomic tests only after failure of standard of care or when failure of standard of care is anticipated (eg, aggressive clinical behavior) to identify potential clinical trial options.

Which testing platforms?

• Most major academic medical centers and large community health care systems have standardized approaches to genomic testing that may include two tiers of testing. Upon diagnosis, internal pathology laboratory services may provide many of the necessary tests to guide standard of care for some of the most common cancer types (eg, HER-2–positive breast or gastric cancer, or ALK- or EGFR-positive lung cancer, etc.). The second tier of testing that is usually reserved to identify expanded clinical options would include a multigene panel approach and may be performed internally as well, or submitted systematically to a preferred commercial vendor.
• Depending on treatment goal, three main categories of genomic testing are available for guidance of therapy selection (Figure 1-24).
  • Companion diagnostics are in vitro diagnostic tools that provide essential information for the safe and effective use of a corresponding therapeutic product, per the FDA’s definition. Used as enrichment tools (patients with positive results are enrolled) in the clinical trial, they are included in the drug’s labeling if co-approved by the FDA.
    • The single-analyte approach assesses specific alterations (e.g., mutations, amplifications, over-expression, rearrangement) in a specified gene or protein.
    • Results are easily interpreted, and the patient is deemed as responder or non responder.
  • Multigene NGS panels:
    • Targeted sequencing/hotspot NGS panels
      • Targeted sequencing panels usually include 30 to 50 genes and can detect multiple mutations within hotspot regions of genes (DNA only) associated with cancer.
      • The panels are designed to detect alterations, single nucleotide variants (SNVs) and small insertions/deletions (indels) in therapeutically relevant genes.
    • Comprehensive genomic profiling NGS panels
      • Hundreds (300 to 500) of genes are assessed.
      • The panels assess alterations in DNA and RNA (whole genome or whole exome).
      • The panels allow for simultaneous detection of SNVs, indels, genomic copy number variations and rearrangements/fusions.
      • Most data from comprehensive genomic profiling are exploratory, or for research purposes, or may lead to clinical trial options.
      • Multidisciplinary teams consisting of clinicians, cancer biologists, clinical geneticists, basic scientists, biostatisticians, bioinformaticians and others may collectively analyze and interpret data and discuss cases through institutional molecular tumor boards that meet to guide direction for patient care.
  • Several commercial assays have been validated in a Clinical Laboratory Improvement Amendments setting to detect therapeutically relevant genetic alterations and can be searched in The Genetic Testing Registry at https://www.ncbi.nlm.nih.gov/gtr.

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Considerations When Choosing a Genomic Testing Approach

In the community-based setting, where 80% to 85% of patients with cancer receive care, the choices may seem overwhelming. Before choosing a platform, test or vendor, the following factors may be considered:

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Health Status of Patient

• Invasive procedures are used to obtain biopsy material for genomic testing; therefore, the patient must be in sufficient health status to undergo such procedures.
• Planning for multiple lines of therapy may be expected for a patient in relatively good health status, whereas only a single line of therapy is to be expected for a patient who is rapidly progressing, both of which may impact the type of assay pursued.

Biopsy Material

• Is the biopsy a large surgical specimen, or small cytology sample?
• Specimen requirements vary widely by test; therefore, it is imperative to review these specifications to increase chance of successful testing.

Cost, Insurance Coverage and/or Financial Status

• A patient with cancer endures an increasing financial burden associated with his or her care; therefore, cost of the assay, which may be dependent on the depth of testing (single tests vs. multigene assays), should be evaluated.
• A portion of the costs associated with commercial assays are likely to be covered by most insurance carriers, but patients may incur out-of-pocket expenses.

Treatment Goal

• If genomic testing is required to guide selection of targeted therapies considered standard of care, then single tests such as companion diagnostics or targeted sequencing panels may be practical choices.
• If genomic testing is pursued to identify clinical trial options, then casting a wider net of genomic data may be preferred to maximize information output.

Liquid Biopsies

Tissue biopsies remain the gold standard for genomic testing; however, alternative sources of tumor material, such as blood, saliva and urine, have been actively investigated in the past several years with the goal of providing biopsy surrogates that can provide rapid, accurate detection of genomic alterations through noninvasive procedures.

Liquid biopsies are based on the premise that tumor material is shed from a tumor in the form of circulating tumor cells or cell-free DNA (cfDNA) into the circulation of the patient. Studies have demonstrated genomic testing with advanced technology can detect the same genomic alterations in the shed material pulled out of bodily fluids as captured to sampling the actual tumor site.

Advantages

Several advantages of liquid biopsies exist:

• Liquid biopsies may provide a more complete assessment of the tumor landscape compared with single-site (traditional) tumor sampling, because tumor material shed into the bloodstream may be from the primary and/or metastatic sites.
• Serial sampling through liquid biopsies is a cost-effective approach to capture the acquisition of resistance mutations in real time, and studies have shown serial sampling may detect resistance mutations up to 16 weeks before finding progression through traditional monitoring platforms (CT/PET scans).
• Liquid biopsies provide a safe, noninvasive alternative to obtaining tumor material when the patient status or location of tumor limits feasibility of invasive procedures.
• EGFR-mutated lung cancer is currently the only tumor type in which monitoring treatment response through liquid or tumor biopsies is considered standard of care.
  • Appearance of the EGFR T790M mutation in patients with lung cancer, in either tumor or liquid biopsy, prompts the switching of therapies to osimertinib (Tagrisso, AstraZeneca), a targeted therapy developed to selectively inhibit T790M, the most common resistance mechanism in lung cancer patients treated with first-generation EGFR inhibitors (eg, erlotinib [Tarceva; Genentech, Astellas]).

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Liquid Biopsies in Clinical Practice

Status of liquid biopsies in clinical practice:

• Outside of lung cancer, liquid biopsies and genomic testing may be used as an alternative when tumor tissue is not available and selection of targeted therapy is dependent on genetic results.
  • The evidence for liquid biopsies demonstrates significant discordance between tissue- and liquid-based testing; therefore, currently, a negative result by liquid biopsy is not considered actionable, and retrieval of tissue sample is strongly encouraged.
• The use of genomic testing of liquid biopsies to monitor disease progression remains exploratory for other tumor types; however, several studies have shown quantitative measurement of mutations detected in cfDNA, particularly in patients receiving targeted therapies, may indicate disease progression and acquisition of resistance mutations.
  • BRCA1 reversions in ovarian cancers receiving platinum- or PARP-based treatment
  • ESR1 mutations in breast cancer patients receiving aromatase inhibitors
  • Presence of cfDNA may indicate manifestation of metastatic disease.

Frequently Discussed Topics

With the declining costs of comprehensive genomic profiling and NGS assays, access to large amounts of genomic information will continue to increase, and its application into clinical practice and guidance of personalized medicine will continue to expand. The following are commonly encountered issues or frequently discussed topics related to NGS testing and data.

Companion Diagnostics and Standardization of Assays

• Many targeted therapies are being co-developed with companion diagnostics; however, many multigene NGS assays or other laboratory-developed tests provide the same genomic or protein results as a companion diagnostic.
• The use of genomic results from testing other than the FDA-approved companion diagnostic may be considered off-label by some health insurers, despite providing comparable results.
• Under certain circumstances, appealing an insurer’s decision may be possible given evidence to support the equal nature of the laboratory-developed test results.
• The appeal of a companion diagnostic is that the assay dichotomizes patient populations into two groups, responders and nonresponders, whereas laboratory-developed tests may provide layers of genomic information, some of which may not be interpretable in relation to the therapy in question.
• In addition to the potential issues regarding companion diagnostics, the following points may be factored into the clinician’s decision process in selecting a genomic testing approach:
  • There are countless options in clinical NGS testing platforms for clinicians to choose from, each designed and validated with unique bioinformatics frameworks, coverage bias, variant-calling algorithms and final clinical data reporting.
  • The pharmaceutical industry is pairing with diagnostic testing companies more frequently to co-develop unique companion diagnostics for targeted therapies, which presents a logistical challenge, considering what clinicians may face if individual companion diagnostics are paired to each new drug approval.
  • This is illustrated by the explosion of assays that have been developed to detect levels of PD-L1 for predicting response to immuno-oncology agents (eg, pembrolizumab [Keytruda, Merck], nivolumab [Opdivo, Bristol-Myers Squibb]). Currently, there are multiple antibody clones, thresholds and scoring conventions that differ by drug and tumor type.
  • A recent comparison of four PD-L1 assays (The Blueprint PD-L1 IHC Assay Comparison Project) demonstrated differences in staining performance, and the researchers concluded interchanging assays may lead to “misclassification” of PD-L1 status.
• Conclusion - There is a dire need for industry-wide standardization of clinical NGS and companion diagnostics testing platforms.
• Moving Forward – Industry, government and health care entities will likely have to merge efforts to standardize precision medicine standards.

Passenger and Driver mutations, Tumor Mutation Burden and Variant Annotation

• Cancer arises from an accumulation of genetic alterations that cooperatively transform normal cells. On average, sequencing with whole-exome or whole-genome platforms yields between 30 to 65 variants, for which distinguishing between the disease-causing and random mutations, or drivers and passengers, is critical for clinical interpretation.
• The first layer of assessing raw NGS data lies in the bioinformatics data filtering, variant calling algorithms and decision support processes developed for the NGS platform.
  • In a recent large-scale genome sequencing study, almost 95% of somatic variants were novel and not reported in public mutation databases (eg, Catalog of Somatic Mutations in Cancer), although a portion of variants did occur in therapeutically relevant genes.
• The second layer of assessing NGS data includes assigning variant annotation according to consensus guidelines endorsed by the American College of Medical Genetics and Genomics, Association for Molecular Pathology, ASCO and College of American Pathologists, where trained clinical molecular geneticists categorize somatic variants using a tiered system (eg, pathogenic, presumed pathogenic, variants of unknown clinical significance and benign variants) based on the strength of evidence and potential clinical impact.
• Some cancers exhibit very high mutational frequencies, also known as tumor mutation burden, in the range of >100/Mb (more than 100 mutations per megabase of DNA sequenced), which is often related to the underlying environmental exposures (eg, smoking).
  • In tumors with high tumor mutation burden, classification of drivers or passengers is not as clinically relevant, as it is suggested that the high number of mutations act as neo-antigens that facilitate tumor clearance through activation of the immune system.
• Conclusion - Robust variant filtering, decision support platforms and a team of clinical molecular geneticists to annotate mutations are basic approaches to filtering large amounts of genomic data. In cancers with high mutational frequencies, distinguishing drivers and passengers may not be necessary, as a high tumor mutation burden represents an alternate therapeutically relevant genomic finding.
• Moving Forward – Development of shared variant annotation databases may help standardize reporting of sequence variants, and/or providing free access to such resources would ease the interpretation of NGS reports for researchers and clinicians.

Genetic Heterogeneity and Allele Fraction

• Genetic heterogeneity describes a tumor comprised of a collection of mutations; some are important to survival (driver mutations), and some are bystanders (passengers).
  • Diversity of genomic alterations exist between patients, between tumors within a patient and even within an individual tumor (intratumor heterogeneity).
  • Subclonal evolution occurs during disease progression, in which genetic alterations that provide a survival advantage to the cells are selected, and variants that do not provide any survival advantage are lost. Treatment with targeted therapies applies a selective pressure on the tumor cells, where clonal evolution results in these changes (i.e., resistance mechanism).
  • Genetic heterogeneity presents the greatest clinical challenge in terms of treatment because, in theory, a tumor comprised of genetic diversity relies on multiple signaling nodes that can adapt to new environments, even those threatened with cancer therapeutics.
• Mutant allele fraction
  • NGS assesses millions of pieces of DNA, provides a count of the pieces of DNA covering a genomic region and calculates the proportion of those pieces that exhibit a mutated sequence.
  • The fraction of pieces exhibiting a mutation is called the mutant allele fraction (Figure 1-27).
  • Mutations that contribute to the pathogenesis of a tumor, including driver mutations, usually have a higher mutant allele fraction. Because of their role in providing survival advantage and being present at the start of disease (initiation), they are likely present in more cells within a tumor.
• Conclusion – Genomic data from NGS provides a snapshot of the tumor’s genetic landscape. The tumor landscape is diverse and adaptable, which makes treatment of cancer with targeted therapies a clinical challenge. Mutant allele fraction is a measure of genetic heterogeneity but is dependent on the cells assessed.
• Moving Forward – Future strategies in the complex setting of genetic heterogeneity and clonal evolution may include development of therapies that target resistance mechanisms used in concert with serial screening (liquid biopsies). Cancer, therefore, would be approached as a chronic disease with the following series:

1. Targeted therapy
2. Detection of a resistance mechanism
3. Switch targeted therapy
4. Repeat

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Future of Genomic Medicine

The United States government has acknowledged the expanding role and importance of precision medicine with research and funding initiatives.

• Precision medicine initiative
  • The national cancer moonshot initiative is a coalition of resources (eg, pharmaceutical industry; biotechnology, academic and community oncologists; etc.) to advance access to improved cancer care.
• Big data/data sharing
  • CancerLinQ (learning intelligence network for quality) is a health information technology system developed by ASCO that uses real-time medical data (diagnoses, genomics, treatments and outcomes) from patients with cancer.
    • Physicians can query the database to make more informed care decisions based on data from other patients with similar diagnoses and treatment plans.

Precision Medicine Clinical Trials

Precision medicine clinical trials are currently underway, including genetically based clinical trials in which patients are matched to different treatment arms based on genomic alterations rather than cancer diagnosis (eg, histology), also known as basket trials.

• ASCO-TAPUR (Targeted Agent and Profiling Utilization Registry) — 15 treatment arms
• NCI-MATCH (Molecular Analysis for Therapy Choice) — 21 treatment arms

Additional trials are underway to determine the role of targeted therapies in earlier lines of therapy.

• ALCHEMIST (Adjuvant Lung Cancer Enrichment Marker Identification and Sequencing Trials) — EGFR- and ALK-directed therapies
• PEARLS study — PD-1/PD-L1–directed therapies (immunotherapy); study of pembrolizumab vs. placebo for participants with non–small cell lung cancer after resection with or without standard adjuvant therapy