Advances in clinical trial designs for predictive biomarker discovery and validation

Adaptive Signature Design- review of the biomarker guided adaptive phase -III controlled design

Genomics having a profound impact on oncology drug development necessitates the use of genomic signatures for therapeutic strategy and emerging medicine proposals. Since its advent in the arena of clinical trials biomarker-related predictive methods for the identification and selection of patient subgroups, with optimal treatment response, are widely used. Genetic signatures which are accountable for the differential response to treatments are experimentally recognizable and analytically validated in phase II stage of clinical trials. The availability of robust and validated biomarkers in phase III is limited. Hence, the development of a clinical trial design without the availability of biomarker identity for treatment-sensitive patients becomes indispensable. Adaptive Signature Design (ASD) is a design procedure of developing and validating a predictive classifier (diagnostic testing strategy) when the signature of subjects responding differentially to treatment is remote in the context of the study. This review provides a detailed methodology and statistical background of this pioneering design developed by Freidlin and Simon (2005). In addition, it concentrates on the advances in ASD regarding statistical issues such as predictive assay identification, classification techniques, statistical methods, subgroup search, choice of differentially expressed genes, and multiplicity correction. The statistical methodology behind the design is explained with the intent of building the ground steps for future research approachable, especially for beginning researchers. Most of the existing research articles give a microcosmic view of the design and lack in describing the details behind the methodology. This study covers those details and marks the novelty of our research.

Bayesian basket trial design with exchangeability monitoring

Precision medicine endeavors to conform therapeutic interventions to the individuals being treated. Implicit to the concept of precision medicine is heterogeneity of treatment benefit among patients and patient subpopulations. Thus, precision medicine challenges conventional paradigms of clinical translational which have relied on estimates of population-averaged effects to guide clinical practice. Basket trials comprise a class of experimental designs used to study solid malignancies that are devised to evaluate the effectiveness of a therapeutic strategy among patients defined by the presence of a particular drug target (often a genetic mutation) rather than a particular tumor histology. Acknowledging the potential for differential effectiveness on the basis of traditional criteria for cancer subtyping, evaluations of treatment effectiveness are conducted with respect to the "baskets" which collectively represent a partition of the targeted patient population consisting of discrete subtypes. Yet, designs of early basket trials have been criticized for their reliance on basketwise analysis strategies that suffered from limited power in the presence of imbalanced enrollment as well as failed to convey to the clinical community evidentiary measures for consistent effectiveness among the studied clinical subtypes. This article presents novel methodology for sequential basket trial design formulated with Bayesian monitoring rules. Interim analyses are based a novel hierarchical modeling strategy for sharing information among a collection of discrete potentially nonexchangeable subtypes. The methodology is demonstrated by analysis as well as permutation and simulation studies based on a recent basket trial designed to estimate the effectiveness of vemurafenib in BRAF^V600 mutant non-melanoma among six primary disease sites and histologies.

Biomarkers and Imaging of Breast Cancer

OBJECTIVE

The goals of this review are to provide background information on the definitions and applications of the general term "biomarker" and to highlight the specific roles of breast imaging biomarkers in research and clinical breast cancer care. A search was conducted of the main electronic biomedical databases (PubMed, Cochrane, Embase, MEDLINE [Ovid], Scopus, and Web of Science). The search was focused on review literature in general radiology and biomedical sciences and on reviews and primary research articles on biomarkers in breast imaging over the 15 years ending in June 2017. The keywords included "biomarker," "trial endpoints," "breast imaging," "breast cancer," "radiomics," and "precision medicine" in the titles and abstracts of the papers.

CONCLUSION

Clinical breast care and breast cancer-related research rely on imaging biomarkers for decision support. In the era of precision medicine and big data, the practice of radiology is likely to change. A closer integration of breast imaging with related biomedical fields and the creation of large integrated and shareable databases of clinical, molecular, and imaging biomarkers should allow the field to continue guiding breast cancer care and research.

The Identification of a Threshold of Long Work Hours for Predicting Elevated Risks of Adverse Health Outcomes

Working long hours has been associated with adverse health outcomes. However, a definition of long work hours relative to adverse health risk has not been established. Repeated measures of work hours among approximately 2,000 participants from the Panel Study of Income Dynamics (1986-2011), conducted in the United States, were retrospectively analyzed to derive statistically optimized cutpoints of long work hours that best predicted three health outcomes. Work-hours cutpoints were assessed for model fit, calibration, and discrimination separately for the outcomes of poor self-reported general health, incident cardiovascular disease, and incident cancer. For each outcome, the work-hours threshold that best predicted increased risk was 52 hours per week or more for a minimum of 10 years. Workers exposed at this level had a higher risk of poor self-reported general health (relative risk (RR) = 1.28; 95% confidence interval (CI): 1.06, 1.53), cardiovascular disease (RR = 1.42; 95% CI: 1.24, 1.63), and cancer (RR = 1.62; 95% CI: 1.22, 2.17) compared with those working 35-51 hours per week for the same duration. This study provides the first health risk-based definition of long work hours. Further examination of the predictive power of this cutpoint on other health outcomes and in other study populations is needed.

Biomarker-Guided Non-Adaptive Trial Designs in Phase II and Phase III: A Methodological Review

Biomarker-guided treatment is a rapidly developing area of medicine, where treatment choice is personalised according to one or more of an individual’s biomarker measurements. A number of biomarker-guided trial designs have been proposed in the past decade, including both adaptive and non-adaptive trial designs which test the effectiveness of a biomarker-guided approach to treatment with the aim of improving patient health. A better understanding of them is needed as challenges occur both in terms of trial design and analysis. We have undertaken a comprehensive literature review based on an in-depth search strategy with a view to providing the research community with clarity in definition, methodology and terminology of the various biomarker-guided trial designs (both adaptive and non-adaptive designs) from a total of 211 included papers. In the present paper, we focus on non-adaptive biomarker-guided trial designs for which we have identified five distinct main types mentioned in 100 papers. We have graphically displayed each non-adaptive trial design and provided an in-depth overview of their key characteristics. Substantial variability has been observed in terms of how trial designs are described and particularly in the terminology used by different authors. Our comprehensive review provides guidance for those designing biomarker-guided trials.

Biomarker-Guided Adaptive Trial Designs in Phase II and Phase III: A Methodological Review

BACKGROUND

Personalized medicine is a growing area of research which aims to tailor the treatment given to a patient according to one or more personal characteristics. These characteristics can be demographic such as age or gender, or biological such as a genetic or other biomarker. Prior to utilizing a patient's biomarker information in clinical practice, robust testing in terms of analytical validity, clinical validity and clinical utility is necessary. A number of clinical trial designs have been proposed for testing a biomarker's clinical utility, including Phase II and Phase III clinical trials which aim to test the effectiveness of a biomarker-guided approach to treatment; these designs can be broadly classified into adaptive and non-adaptive. While adaptive designs allow planned modifications based on accumulating information during a trial, non-adaptive designs are typically simpler but less flexible.

METHODS AND FINDINGS

We have undertaken a comprehensive review of biomarker-guided adaptive trial designs proposed in the past decade. We have identified eight distinct biomarker-guided adaptive designs and nine variations from 107 studies. Substantial variability has been observed in terms of how trial designs are described and particularly in the terminology used by different authors. We have graphically displayed the current biomarker-guided adaptive trial designs and summarised the characteristics of each design.

CONCLUSIONS

Our in-depth overview provides future researchers with clarity in definition, methodology and terminology for biomarker-guided adaptive trial designs.

Aspirin and Colorectal Cancer Prevention and Treatment: Is It for Everyone?

There is now a considerable body of data supporting the hypothesis that aspirin could be effective in the prevention and treatment of colorectal cancer, and a number of phase III randomised controlled trials designed to evaluate the role of aspirin in the treatment of colorectal cancer are ongoing. Although generally well tolerated, aspirin can have adverse effects, including dyspepsia and, infrequently, bleeding. To ensure a favourable balance of benefits and risks from aspirin, a more personalised assessment of the advantages and disadvantages is required. Emerging data suggest that tumour PIK3CA mutation status, expression of cyclo-oxygenase-2 and human leukocyte antigen class I, along with certain germline polymorphisms, might all help to identify individuals who stand to gain most. We review both the underpinning evidence and current data, on clinical, molecular and genetic biomarkers for aspirin use in the prevention and treatment of colorectal cancer, and discuss the opportunities for further biomarker research provided by ongoing trials.

Pharmacogenomic biomarkers for personalized medicine

Pharmacogenomics examines how the benefits and adverse effects of a drug vary among patients in a target population by analyzing genomic profiles of individual patients. Personalized medicine prescribes specific therapeutics that best suit an individual patient. Much current research focuses on developing genomic biomarkers to identify patients, to identify which patients would benefit from a treatment, have an adverse response, or no response at all, prior to treatment according to relevant differences in risk factors, disease types and/or responses to therapy. This review describes the use of the two personalized medicine biomarkers, prognostic and predictive, to classify patients into subgroups for treatment recommendation.

Fool's gold, lost treasures, and the randomized clinical trial

Background

Randomized controlled trials with a survival endpoint are the gold standard for clinical research, but have failed to achieve cures for most advanced malignancies. The high costs of randomized clinical trials slow progress (thereby causing avoidable loss of life) and increase health care costs.

Discussion

A malignancy may be caused by several different mutations. Therapies effective vs one mutation may be discarded due to lack of statistical significance across the entire population. Conversely, expensive large randomized trials may have sufficient statistical power to demonstrate benefit despite the therapy only working in subgroups. Non-cost-effective therapy is then applied to all patients (including subgroups it cannot help). Randomized trials comparing therapies with different mechanisms of action are misleading since they may conclude the therapies are “equivalent” despite benefitting different subpopulations, or may erroneously conclude that one therapy is superior simply because it targets a larger subpopulation. Furthermore, minor variances in patient selection may determine study outcome, a therapy may be discarded as ineffective despite substantial benefit in one subpopulation if harmful in another, randomized trials may more effectively detect therapies with minor benefit in most patients vs marked benefit in subpopulations, and randomized trials in unselected patients may erroneously conclude that “shot-gun” combinations are superior to single agents when sequential administration of personalized single agents might work better and spare patients treatment with drugs that cannot help them. We must identify predictive biomarkers early by comparing responding to progressing patients in phase I-II trials. Enriching randomized trials for biomarker-positive patients can markedly reduce required patient numbers and costs despite expensive screening for biomarker-positive patients. Available data support approval of new drugs without randomized trials if they yield single-agent sustained responses in patients refractory to standard therapies. Conversely, new approaches are needed to guide development of drug combinations since both standard phase II approaches and phase II-III randomized trials have a high risk of misleading.

Summary

Traditional randomized clinical trials approaches are often inefficient, wasteful, and unreliable. New clinical research paradigms are needed. The primary outcome of clinical research should be “Who (if anyone) benefits?” rather than “Does the overall group benefit?”

Assessment of reproducibility of cancer survival risk predictions across medical centers

BACKGROUND

Two most important considerations in evaluation of survival prediction models are 1) predictability - ability to predict survival risks accurately and 2) reproducibility - ability to generalize to predict samples generated from different studies. We present approaches for assessment of reproducibility of survival risk score predictions across medical centers.

METHODS

Reproducibility was evaluated in terms of consistency and transferability. Consistency is the agreement of risk scores predicted between two centers. Transferability from one center to another center is the agreement of the risk scores of the second center predicted by each of the two centers. The transferability can be: 1) model transferability - whether a predictive model developed from one center can be applied to predict the samples generated from other centers and 2) signature transferability - whether signature markers of a predictive model developed from one center can be applied to predict the samples from other centers. We considered eight prediction models, including two clinical models, two gene expression models, and their combinations. Predictive performance of the eight models was evaluated by several common measures. Correlation coefficients between predicted risk scores of different centers were computed to assess reproducibility - consistency and transferability.

RESULTS

Two public datasets, the lung cancer data generated from four medical centers and colon cancer data generated from two medical centers, were analyzed. The risk score estimates for lung cancer patients predicted by three of four centers agree reasonably well. In general, a good prediction model showed better cross-center consistency and transferability. The risk scores for the colon cancer patients from one (Moffitt) medical center that were predicted by the clinical models developed from the another (Vanderbilt) medical center were shown to have excellent model transferability and signature transferability.

CONCLUSIONS

This study illustrates an analytical approach to assessing reproducibility of predictive models and signatures. Based on the analyses of the two cancer datasets, we conclude that the models with clinical variables appear to perform reasonable well with high degree of consistency and transferability. There should have more investigations on the reproducibility of prediction models including gene expression data across studies.

Analysis of protein biomarkers in human clinical tumor samples: critical aspects to success from tissue acquisition to analysis

There has been increased interest in the analysis of protein biomarkers in clinical tumor tissues in recent years. Tissue-based biomarker assays can add value and aid decision-making at all stages of drug development, as well as being developed for use as predictive biomarkers and for patient stratification and prognostication in the clinic. However, there must be an awareness of the legal and ethical issues related to the sourcing of human tissue samples. This article also discusses the limits of scope and critical aspects on the successful use of the following tissue-based methods: immunohistochemistry, tissue microarrays and automated image analysis. Future advances in standardization of tissue biobanking methods, immunohistochemistry and quantitative image analysis techniques are also discussed.

Use of standard markers and incorporation of molecular markers into breast cancer therapy: Consensus recommendations from an International Expert Panel

Breast cancer is a heterogeneous disease of different subtypes on the molecular, histopathological, and clinical level. Genomic profiling techniques have led to several prognostic and predictive gene signatures of breast cancer that may further refine outcome prediction, especially in clinically equivocal situations. In particular, the predictive value of today's most important therapeutic targets, ER and HER2, are strongly influenced by the proliferative status of the tumor. Genomic assays are generally performed in a centralized manner, whereas routine pathological evaluation is mostly done on a decentralized basis, making the comparison of these methods difficult. Thus, there remains considerable uncertainty about the use of the new molecular markers in routine clinical decision making and their role in patient selection or stratification for future clinical trials. To address this concern, a group of representatives from breast cancer research groups in the areas of breast pathology, genomic profiling, and clinical trials critically reviewed all available data. Consensus recommendations are made on the practical use of molecular markers in breast cancer management and their incorporation into future clinical trials.

Biomarkers for Basal-like Breast Cancer

Initially recognized through microarray-based gene expression profiling, basal-like breast cancer, for which we lack effective targeted therapies, is an aggressive form of carcinoma with a predilection for younger women. With some success, immunohistochemical studies have attempted to reproduce the expression profile classification of breast cancer through identification of subtype-specific biomarkers. This review aims to present an in depth summary and analysis of the current status of basal-like breast cancer biomarker research. While a number of biomarkers show promise for future clinical application, the next logical step is a comprehensive investigation of all biomarkers against a gene expression profile gold standard for breast cancer subtype assignment.