Comparative effectiveness research in cancer genomics and precision medicine: current landscape and future prospects

Precision oncology in the age of integrative genomics

Precision oncology applies genomic and other molecular analyses of tumor biopsies to improve the diagnosis and treatment of cancers. In addition to identifying therapeutic options, precision oncology tracks the response of a tumor to an intervention at the molecular level and detects drug resistance and the mechanisms by which it occurs. Integrative genomics can include sequencing specific panels of genes, exomes, or the entire triad of the patient's germline, tumor exome, and tumor transcriptome. Although the capabilities of sequencing technologies continue to improve, widespread adoption of genomics-driven precision oncology in the clinic has been held back by logistical, regulatory, financial, and ethical considerations. Nevertheless, integrative clinical sequencing programs applied at the point of care have the potential to improve the clinical management of cancer patients.

Rural-urban and racial-ethnic differences in awareness of direct-to-consumer genetic testing

Background

Access to direct-to-consumer genetic testing services has increased in recent years. However, disparities in knowledge and awareness of these services are not well documented. We examined awareness of genetic testing services by rural/urban and racial/ethnic status.

Methods

Analyses were conducted using pooled cross-sectional data from 4 waves (2011–2014) of the Health Information National Trends Survey (HINTS). Descriptive statistics compared sample characteristics and information sources by rural/urban residence. Logistic regression was used to examine the relationship between geography, racial/ethnic status, and awareness of genetic testing, controlling for sociodemographic characteristics.

Results

Of 13,749 respondents, 16.7% resided in rural areas, 13.8% were Hispanic, and 10.1% were non-Hispanic black. Rural residents were less likely than urban residents to report awareness of genetic testing (OR = 0.74, 95% CI = 0.63–0.87). Compared with non-Hispanic whites, racial/ethnic minorities were less likely to be aware of genetic testing: Hispanic (OR = 0.68, 95% CI = 0.56–0.82); and non-Hispanic black (OR = 0.74, 95% CI = 0.61–0.90).

Conclusions

Rural-urban and racial-ethnic differences exist in awareness of direct-to-consumer genetic testing. These differences may translate into disparities in the uptake of genetic testing, health behavior change, and disease prevention through precision and personalized medicine.

Towards decision-making using individualized risk estimates for personalized medicine: A systematic review of genomic classifiers of solid tumors

Recent advances in the understanding of the genetic underpinnings of cancer offer the promise to customize cancer treatments to the individual through the use of genomic classifiers (GCs). At present, routine clinical utilization of GCs is uncommon and their current scope and status, in a broad sense, are unknown. As part of a registered review (PROSPERO 2014:CRD42014013371), we systematically reviewed the literature evaluating the utility of commercially available GCs by searching Ovid Medline (PubMed), EMBASE, the Cochrane Database of Systematic Reviews, and CINAHL on September 2, 2014. We excluded articles involving pediatric malignancies, non-solid or non-invasive cancers, hereditary risk of cancer, non-validated GCs, and GCs involving fewer than 3 biomarkers. A total of 3,625 studies were screened, but only 37 met the pre-specified inclusion criteria. Of these, 15 studies evaluated outcomes and clinical utility of GCs through clinical trials, and the remainder through the use of mathematical models. Most studies (29 of 37) were specific to hormone-receptor positive breast cancer, whereas only 4 studies evaluated GCs in non-breast cancer (prostate, colon, and lung cancers). GCs have spurred excitement across disciplines in recent decades. While there are several GCs that have been validated, the general quality of the data are weak. Further research, including prospective validation is needed, particularly in the non-breast cancer GCs.

The attitudes of Dutch fertility specialists towards the addition of genetic testing in screening of tubal factor infertility

BACKGROUND

This study aims to identify elements perceived by Dutch fertility specialists as barriers and facilitators for the introduction of genetic testing, and their attitudes towards the use of genetic information. The genetic test would be implemented in routine screening for tubal pathology and identifies SNPs relevant for the immune response causing tubal pathology.

METHODS

Experienced reproductive specialists working in Dutch Academic Hospitals were interviewed. Based on the results of four interviews a questionnaire was developed and used to survey medical doctors in six out of eight Dutch Academic hospitals.

RESULTS

60.4% (n=91) stated that the addition of genetic markers to the Chlamydia trachomatis antibody test (CAT) in screening for tubal pathology would increase screening accuracy. 68.2% (n=90) agreed they would require additional training on clinical genetics. Clinical utility (91.2%, n=91) and cost-effectiveness (95.6%, n=91) were recognized by the respondents as important factors in gaining support for the new screening strategy.

CONCLUSION

In summary, respondents showed a positive attitude towards the implementation of a genetic test combined with CAT for tubal factor infertility (TFI) screening. To gain their support the majority of respondents agreed that clinical utility, specifically cost-effectiveness, is an important factor. Comprehensive research about economic implications and utility regarding the introduction of genomic markers should be the next step in the implementation strategy. Furthermore, education and training would need to be developed and offered to fertility care professionals about genetic markers, their interpretation, and implications for clinical decision-making.

Biomarker Tests for Molecularly Targeted Therapies: Laying the Foundation and Fulfilling the Dream

Precision medicine focuses on the management of individual patients on the basis of biomarkers and other distinguishing characteristics, with the overarching objective of improving clinical outcomes. The rapid proliferation of biomarker tests and targeted therapies has revolutionized patient care in a variety of serious disorders. Targeted cancer therapies interrupt oncogenic molecular pathways driven by mutations, overexpression, or translocation of specific genes. However, there is concern that the emergence of large-scale genomic data is exceeding our capacity to appropriately analyze and interpret the results.In 2014, the Institute of Medicine convened the Committee on Policy Issues in the Clinical Development and Use of Biomarkers for Molecularly Targeted Therapies. This committee conducted a study to develop recommendations to address diverse and interconnected development, regulatory, clinical practice, and reimbursement issues. The committee conducted an extensive search of the relevant literature and invited testimony from a wide range of experts in the field. The final report of the committee's study and deliberations was released on March 4, 2016, focusing on ways to achieve 10 goals to further advance the development and appropriate clinical use of biomarker tests for molecularly targeted therapies.This article presents an overview of the committee's study and resulting recommendations, which cover establishment of clinical utility, regulatory oversight, coverage and reimbursement, health system data integration, as well as education and access. The committee's recommendations presented and discussed here are fundamentally grounded in the understanding that, when properly validated and appropriately implemented, these assays and corresponding therapies hold considerable promise to enhance the quality of patient care and improve meaningful clinical outcomes.

Precision medicine: opportunities, possibilities, and challenges for patients and providers

Precision medicine approaches disease treatment and prevention by taking patients' individual variability in genes, environment, and lifestyle into account. Although the ideas underlying precision medicine are not new, opportunities for its more widespread use in practice have been enhanced by the development of large-scale databases, new methods for categorizing and representing patients, and computational tools for analyzing large datasets. New research methods may create uncertainty for both healthcare professionals and patients. In such situations, frameworks that address ethical, legal, and social challenges can be instrumental for facilitating trust between patients and providers, but must protect patients while not stifling progress or overburdening healthcare professionals. In this perspective, we outline several ethical, legal, and social issues related to the Precision Medicine Initiative's proposed changes to current institutions, values, and frameworks. This piece is not an exhaustive overview, but is intended to highlight areas meriting further study and action, so that precision medicine's goal of facilitating systematic learning and research at the point of care does not overshadow healthcare's goal of providing care to patients.

Methods: for studying pharmacogenetic profiles of combination chemotherapeutic drugs

INTRODUCTION

Molecular and genetic analysis of tumors and individuals has led to patient-centered therapies, through the discovery and identification of genetic markers predictive of drug efficacy and tolerability. Present therapies often include a combination of synergic drugs, each of them directed against different targets. Therefore, the pharmacogenetic profiling of tumor masses and patients is becoming a challenge, and several questions may arise when planning a translational study.

AREAS COVERED

The review presents the different techniques used to stratify oncology patients and to tailor antineoplastic treatments according to individual pharmacogenetic profiling. The advantages of these methodologies are discussed as well as current limits.

EXPERT OPINION

Facing the rapid technological evolution for genetic analyses, the most pressing issues are the choice of appropriate strategies (i.e., from gene candidate up to next-generation sequencing) and the possibility to replicate study results for their final validation. It is likely that the latter will be the major obstacle in the future. However, the present landscape is opening up new possibilities, overcoming those hurdles that have limited result translation into clinical settings for years.

Evaluating the clinical impact of a genomic classifier in prostate cancer using individualized decision analysis

BACKGROUND

Currently there is controversy surrounding the optimal way to treat patients with prostate cancer in the post-prostatectomy setting. Adjuvant therapies carry possible benefits of improved curative results, but there is uncertainty in which patients should receive adjuvant therapy. There are concerns about giving toxicity to a whole population for the benefit of only a subset. We hypothesized that making post-prostatectomy treatment decisions using genomics-based risk prediction estimates would improve cancer and quality of life outcomes.

METHODS

We developed a state-transition model to simulate outcomes over a 10 year horizon for a cohort of post-prostatectomy patients. Outcomes included cancer progression rates at 5 and 10 years, overall survival, and quality-adjusted survival with reductions for treatment, side effects, and cancer stage. We compared outcomes using population-level versus individual-level risk of cancer progression, and for genomics-based care versus usual care treatment recommendations.

RESULTS

Cancer progression outcomes, expected life-years (LYs), and expected quality-adjusted life-years (QALYs) were significantly different when individual genomics-based cancer progression risk estimates were used in place of population-level risk estimates. Use of the genomic classifier to guide treatment decisions provided small, but statistically significant, improvements in model outcomes. We observed an additional 0.03 LYs and 0.07 QALYs, a 12% relative increase in the 5-year recurrence-free survival probability, and a 4% relative reduction in the 5-year probability of metastatic disease or death.

CONCLUSIONS

The use of genomics-based risk prediction to guide treatment decisions may improve outcomes for prostate cancer patients. This study offers a framework for individualized decision analysis, and can be extended to incorporate a wide range of personal attributes to enable delivery of patient-centered tools for informed decision-making.

Molecular diagnostic testing in breast cancer

OBJECTIVES

An overview of molecular tests used in the treatment of breast cancer, organized by stage and clinical condition.

DATA SOURCES

Systematic review of scientific literature, guideline recommendations, and data published by test manufacturers.

CONCLUSION

Several molecular tests that analyze expression of cancer-related genes have been validated in clinical trials and are recommended by clinical practice guidelines to inform diagnosis and treatment decisions for personalized interventions.

IMPLICATIONS FOR NURSING PRACTICE

Molecular testing has become an important part of patient care for those with breast cancer. Oncology nurses must understand this methodology to prescribe tests, interpret the results, and provide guidance to patients.

Economic evaluation of first-line and maintenance treatments for advanced non-small cell lung cancer: a systematic review

During these last years, there have been an increased number of new drugs for non-small cell lung cancer (NSCLC), with a growing financial effect on patients and society. The purpose of this article was to review the economics of first-line and maintenance NSCLC treatments. We reviewed economic analyses of NSCLC therapies published between 2004 and 2014. In first-line settings, in unselected patients with advanced NSCLC, the cisplatin gemcitabine doublet appears to be cost-saving compared with other platinum doublets. In patients with nonsquamous NSCLC, the incremental cost-effectiveness ratios (ICERs) per life-year gained (LYG) were $83,537, $178,613, and more than $300,000 for cisplatin-pemetrexed compared with, respectively, cisplatin-gemcitabine, cisplatin-carboplatin-paclitaxel, and carboplatin-paclitaxel-bevacizumab. For all primary chemotherapy agents, use of carboplatin is associated with slightly higher costs than cisplatin. In all the analysis, bevacizumab had an ICER greater than $150,000 per quality-adjusted life-year (QALY). In epidermal growth factor receptor mutated advanced NSCLC, compared with carboplatin-paclitaxel doublet, targeted therapy based on testing available tissue yielded an ICER of $110,644 per QALY, and the rebiopsy strategy yielded an ICER of $122,219 per QALY. Compared with the triplet carboplatin-paclitaxel-bevacizumab, testing and rebiopsy strategies had ICERs of $25,547 and $44,036 per QALY, respectively. In an indirect comparison, ICERs per LYG and QALY of erlotinib versus gefitinib were $39,431 and $62,419, respectively. In anaplastic lymphoma kinase-positive nonsquamous advanced NSCLC, the ICER of first-line crizotinib compared with that of chemotherapy was $255,970 per QALY. For maintenance therapy, gefitinib had an ICER of $19,214 per QALY, erlotinib had an ICER of $127,343 per LYG, and pemetrexed had an ICER varying between $183,589 and $205,597 per LYG. Most recent NSCLC strategies are based on apparently no cost-effective strategies if we consider an ICER below $50,000 per QALY an acceptable threshold. We need, probably on a countrywide level, to have a debate involving public health organizations and pharmaceutical companies, as well as clinicians and patients, to challenge the rising costs of managing lung cancer.

Implementation of quantitative and systems pharmacology in large pharma

Quantitative and systems pharmacology concepts and tools are the foundation of the model-informed drug development paradigm at Merck for integrating knowledge, enabling decisions, and enhancing submissions. Rigorous prioritization of modeling and simulation activities has enabled key drug development decisions and led to a high return on investment through significant cost avoidance. Critical factors for the successful implementation, examples on impact on decision making with associated return of investment, and drivers for continued success are discussed.

Comparative effectiveness research in follicular lymphoma: current and future perspectives and challenges

Follicular lymphoma (FL) is the most common indolent non-Hodgkin's lymphoma in northern America. FL is an incurable disease with relapsing-remitting courses requiring serial intermittent treatments. Duration of remission will often become progressively shorter and most patients will die from refractory disease or transformation to aggressive lymphoma. Given the incurable nature of FL, current goals of treatment are focused on improving symptoms and survival by a variety of available treatment options, while considering potential adverse events. Although randomized controlled trials are universally perceived as the gold standard of clinical research, randomized controlled trials are not always practical and have several limitations. Therapeutic and diagnostic options of FLs are expanding faster than randomized controlled trials can test them, so employing comparative effectiveness research on other research designs are needed to efficiently improve global FL care. Implementing comparative effectiveness research with judicious use of appropriate research designs will hopefully fill current knowledge gaps and provide insights for FL managements.

Genetic tests: clinical validity and clinical utility

When evaluating the appropriate use of new genetic tests, clinicians and health care policymakers must consider the accuracy with which a test identifies a patient's clinical status (clinical validity) and the risks and benefits resulting from test use (clinical utility). Genetic tests in current use vary in accuracy and potential to improve health outcomes, and these test properties may be influenced by testing technology and the clinical setting in which the test is used. This unit defines clinical validity and clinical utility, provides examples, and considers the implications of these test properties for clinical practice.

High-risk human papillomavirus detection in oropharyngeal, nasopharyngeal, and oral cavity cancers: comparison of multiple methods

IMPORTANCE

Human papillomaviruses are now recognized as an etiologic factor in a growing subset of head and neck cancers and have critical prognostic importance that affects therapeutic decision making. There is no universally accepted gold standard for high-risk HPV (hrHPV) assessment in formalin-fixed, paraffin-embedded (FFPE) tissue specimens, nor is there a clear understanding of the frequency or role of hrHPV in sites other than oropharynx.

OBJECTIVE

To determine the optimal assessment of hrHPV in FFPE head and neck tumor tissue specimens.

DESIGN, SETTING, PARTICIPANTS

In the setting of a large Midwestern referral center, assessment of hrHPV by p16 immunohistochemical staining, in situ hybridization, and polymerase chain reaction (PCR)-MassArray (PCR-MA), with L1 PGMY-PCR and sequencing to resolve method discordance, was conducted for 338 FFPE oropharyngeal, nasopharyngeal, and oral cavity tumor tissue specimens. Relative sensitivity and specificity were compared to develop a standard optimal test protocol. Tissue specimens were collected from 338 patients with head and neck cancer treated during the period 2001 through 2011 in the departments of Otolaryngology, Radiation Oncology, and Medical Oncology.

INTERVENTION

Patients received standard therapy.

MAIN OUTCOMES AND MEASURES

Optimal hrHPV identification, detection, and activity in head and neck cancers.

RESULTS

Using combined PCR-MA with L1 PGMY-PCR and sequencing for conclusive results, we found PCR-MA to have 99.5% sensitivity and 100% specificity, p16 to have 94.2% sensitivity and 85.5% specificity, and in situ hybridization to have 82.9% sensitivity and 81.0% specificity. Among HPV-positive tumors, HPV16 was most frequently detected, but 10 non-HPV16 types accounted for 6% to 50% of tumors, depending on the site. Overall, 86% of oropharynx, 50% of nasopharynx, and 26% of oral cavity tumors were positive for hrHPV.

CONCLUSIONS AND RELEVANCE

PCR-MA has a low DNA (5 ng) requirement effective for testing small tissue samples; high throughput; and rapid identification of HPV types, with high sensitivity and specificity. PCR-MA together with p16INK4a provided accurate assessment of HPV presence, type, and activity and was determined to be the best approach for HPV testing in FFPE head and neck tumor tissue specimens.

Horizon scanning for translational genomic research beyond bench to bedside

The dizzying pace of genomic discoveries is leading to an increasing number of clinical applications. However, very little translational research is ongoing beyond Bench to Bedside to assess validity, utility, implementation and outcomes of such applications. Here we report cross sectional results of ongoing horizon scanning of translational genomic research conducted between May 16, 2012 and May 15, 2013. Based on a weekly, systematic query of PubMed, we created a curated set of 505 beyond bench-to-bedside research publications, including 312 original research articles, 123 systematic and other reviews, 38 clinical guidelines, policies and recommendations, and 32 papers describing tools, decision support and educational materials. Most papers (62%) addressed a specific genomic test or other health application; almost half of these (n=180) were related to cancer. We estimate that these publications account for 0.5% of reported human genomics and genetics research during the same time. These data provide baseline information to track the evolving knowledge base and gaps in genomic medicine. Continuous horizon scanning is crucial for an evidence-based translation of genomic discoveries into improved health care and disease prevention.

Clinical integration of next generation sequencing: coverage and reimbursement challenges

Public and private payers face complex decisions regarding whether, when, and how to cover and reimburse for next generation sequencing (NGS)-based tests. Yet a predictable reimbursement pathway is critical both for patient access and incentives to provide the market with better clinical evidence. While preliminary data suggests that payers will use similar evidentiary standards as those used to evaluate established molecular diagnostic tests, the volume and complexity of information generated by NGS raises a host of additional considerations for payers that are specific to this technology.