Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map.

Background: Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method.

Results: The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca.

The genome of woodland strawberry (Fragaria vesca).

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F.

Optimism bias leads to inconclusive results-an empirical study.

Objective: Optimism bias refers to unwarranted belief in the efficacy of new therapies. We assessed the impact of optimism bias on a proportion of trials that did not answer their research question successfully and explored whether poor accrual or optimism bias is responsible for inconclusive results.

Study Design: Systematic review.

Incorporation of biomarker assessment in novel clinical trial designs: personalizing brain tumor treatments.

Advances in molecular genetics have aided the identification of potential biomarkers with significant clinical promise in neurooncology. These advances and the evolution of targeted therapeutics necessitate the development and incorporation of innovative clinical trial designs that can effectively validate and assess the clinical utility of biomarkers. In this article, we review the use and potential of several such designs in neurooncology trials in order to support the development of personalized treatment approaches for brain tumor patients.

Designing a randomized clinical trial to evaluate personalized medicine: a new approach based on risk prediction.

We define personalized medicine as the administration of treatment to only persons thought most likely to benefit, typically those at high risk for mortality or another detrimental outcome. To evaluate personalized medicine, we propose a new design for a randomized trial that makes efficient use of high-throughput data (such as gene expression microarrays) and clinical data (such as tumor stage) collected at baseline from all participants. Under this design for a randomized trial involving experimental and control arms with a survival outcome, investigators first estimate the risk of mortality in the control arm based on the high-throughput and clinical data.

Leveraging learning from a phase III colorectal cancer clinical trial: outcomes, methodology, meta-analysis and pharmacogenetics.

This paper summarizes the results of a National Cancer Institute (NCI) sponsored Phase III clinical trial led by the North Central Cancer Treatment Group (NCCTG) that enrolled patients with metastatic colorectal cancer (MCRC) on combination chemotherapy regimens in the late 1990s through 2003. The study changed clinical practice in the US and led to a new Food and Drug Agency (FDA) indication for the drug oxaliplatin. The time was opportune in the management of MCRC, when, after 50 years of using the single active agent 5-Fluorouracil (5-FU), two new cytotoxic agents, irinotecan and oxaliplatin, were found to be active in MCRC.

Preliminary evaluation of factors associated with premature trial closure and feasibility of accrual benchmarks in phase III oncology trials.

Background: A major challenge for randomized phase III oncology trials is the frequent low rates of patient enrollment, resulting in high rates of premature closure due to insufficient accrual.

Purpose: We conducted a pilot study to determine the extent of trial closure due to poor accrual, feasibility of identifying trial factors associated with sufficient accrual, impact of redesign strategies on trial accrual, and accrual benchmarks designating high failure risk in the clinical trials cooperative group (CTCG) setting.

Methods: A subset of phase III trials opened by five CTCGs between August 1991 and March 2004 was evaluated.

Randomized phase II trials: time for a new era in clinical trial design.

The classic single-arm oncology phase II trial designs for evaluating an experimental regimen/agent are limited by multiple sources of bias arising from the inability to separate trial effects (such as patient selection, trial eligibility, imaging techniques and assessment schedule, and treatment locations) from treatment effect on clinical outcomes. Changes in patient population based on biologic subsetting, newer imaging technologies, the use of alternative end points, constrained resources, and the multitude of promising therapies for a given disease make randomized phase II designs, with a concurrent control arm where necessary, attractive. In this brief report, we discuss the salient features of the randomized designs for phase II trials, which when properly applied under the constraints of their underlying inference framework can assure optimal use of limited phase III financial and patient resources.

Pharmacogenetic predictors of adverse events and response to chemotherapy in metastatic colorectal cancer: results from North American Gastrointestinal Intergroup Trial N9741.

Purpose: With three available chemotherapy drugs for advanced colorectal cancer (CRC), response rate (RR) and survival outcomes have improved with associated morbidity, accentuating the need for tools to select optimal individualized treatment. Pharmacogenetics identifies the likelihood of adverse events or response based on variants in genes involved in drug transport, metabolism, and cellular targets.

Patients And Methods: Germline DNA was extracted from 520 patients on the North American Gastrointestinal Intergroup N9741 study.

Defective mismatch repair as a predictive marker for lack of efficacy of fluorouracil-based adjuvant therapy in colon cancer.

Purpose: Prior reports have indicated that patients with colon cancer who demonstrate high-level microsatellite instability (MSI-H) or defective DNA mismatch repair (dMMR) have improved survival and receive no benefit from fluorouracil (FU) -based adjuvant therapy compared with patients who have microsatellite-stable or proficient mismatch repair (pMMR) tumors. We examined MMR status as a predictor of adjuvant therapy benefit in patients with stages II and III colon cancer.

Methods: MSI assay or immunohistochemistry for MMR proteins were performed on 457 patients who were previously randomly assigned to FU-based therapy (either FU + levamisole or FU + leucovorin; n = 229) versus no postsurgical treatment (n = 228).

Blinded independent central review of the progression-free survival endpoint.

Presented are the efforts of the Pharmaceutical Research and Manufacturing Association PFS Working Group to address concerns related to blinded independent central review of locally evaluated progression times and the proposed audit methodology to minimize potential biases, along with the U.S. Food and Drug Administration's comments on this work.

Evaluation of the value of attribution in the interpretation of adverse event data: a North Central Cancer Treatment Group and American College of Surgeons Oncology Group investigation.

Purpose: In March 1998, Common Toxicity Criteria (CTC) version 2.0 introduced the collection of attribution of adverse events (AEs) to study drug. We investigate whether attribution adds value to the interpretation of AE data.

Benefit of adjuvant chemotherapy for resectable gastric cancer: a meta-analysis.

Context: Despite potentially curative resection of stomach cancer, 50% to 90% of patients die of disease relapse. Numerous randomized clinical trials (RCTs) have compared surgery alone with adjuvant chemotherapy, but definitive evidence is lacking.

Objectives: To perform an individual patient-level meta-analysis of all RCTs to quantify the potential benefit of chemotherapy after complete resection over surgery alone in terms of overall survival and disease-free survival, and to further study the role of regimens, including monochemotherapy; combined chemotherapy with fluorouracil derivatives, mitomycin C, and other therapies but no anthracyclines; combined chemotherapy with fluorouracil derivatives, mitomycin C, and anthracyclines; and other treatments.

Model-based phase I designs incorporating toxicity and efficacy for single and dual agent drug combinations: methods and challenges.

Novel therapies are challenging the standards of drug development. Agents with specific biologic targets, unknown dose-efficacy curves, and limited toxicity mandate novel designs to identify biologically optimal doses. We review two model-based designs that utilize either a proportional odds model or a continuation ratio model to identify an optimal dose of a single or two-agent combination in a Phase I setting utilizing both toxicity and efficacy data.

Predictive biomarker validation in practice: lessons from real trials.

Background: With the advent of targeted therapies, biomarkers provide a promising means of individualizing therapy through an integrated approach to prediction using the genetic makeup of the disease and the genotype of the patient. Biomarker validation has therefore become a central topic of discussion in the field of medicine, primarily due to the changing landscape of therapies for treatment of a disease and these therapies purported mechanism(s) of action.

Purpose: In this report, we discuss the merits and limitations of some of the clinical trial designs for predictive biomarker validation using examples from ongoing or completed clinical trials.

Biomarkers and surrogate end points--the challenge of statistical validation.

Biomarkers and surrogate end points have great potential for use in clinical oncology, but their statistical validation presents major challenges, and few biomarkers have been robustly confirmed. Provisional supportive data for prognostic biomarkers, which predict the likely outcome independently of treatment, is possible through small retrospective studies, but it has proved more difficult to achieve robust multi-site validation. Predictive biomarkers, which predict the likely response of patients to specific treatments, require more extensive data for validation, specifically large randomized clinical trials and meta-analysis.

SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.

As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA.

What constitutes reasonable evidence of efficacy and effectiveness to guide oncology treatment decisions?

The need to practice evidence-based medicine is the current prevailing paradigm within the medical community. Evidence to guide practice can and should come from a variety of sources, including clinical trials, observational studies, and meta-analyses of both or either. This paper discusses the relative strengths and weaknesses of data that arise from these various sources.

The design of phase II clinical trials testing cancer therapeutics: consensus recommendations from the clinical trial design task force of the national cancer institute investigational drug steering committee.

The optimal design of phase II studies continues to be the subject of vigorous debate, especially studies of newer molecularly targeted agents. The observations that many new therapeutics "fail" in definitive phase III studies, coupled with the numbers of new agents to be tested as well as the increasing costs and complexity of clinical trials, further emphasize the critical importance of robust and efficient phase II design. The Clinical Trial Design Task Force (CTD-TF) of the National Cancer Institute (NCI) Investigational Drug Steering Committee (IDSC) has published a series of discussion papers on phase II trial design in Clinical Cancer Research.

Obesity is an independent prognostic variable in colon cancer survivors.

Purpose: Obesity is associated with an increased risk of colon cancer. However, the influence of body mass index (BMI) on the prognosis of colon cancer survivors and its relationship to gender remains unknown.

Experimental Design: BMI (kg/m(2)) was categorized in patients with tumor-node-metastasis stage II and III colon carcinomas (n = 4,381) enrolled in seven randomized trials of 5-fluorouracil-based adjuvant chemotherapy.

Comparison of error rates in single-arm versus randomized phase II cancer clinical trials.

PURPOSE To improve the understanding of the appropriate design of phase II oncology clinical trials, we compared error rates in single-arm, historically controlled and randomized, concurrently controlled designs. PATIENTS AND METHODS We simulated error rates of both designs separately from individual patient data from a large colorectal cancer phase III trials and statistical models, which take into account random and systematic variation in historical control data. RESULTS In single-arm trials, false-positive error rates (type I error) were 2 to 4 times those projected when modest drift or patient selection effects (eg, 5% absolute shift in control response rate) were included in statistical models.