Stratified modestly weighted log-rank tests in settings with an anticipated delayed separation of survival curves

Delayed separation of survival curves is a common occurrence in confirmatory studies in immuno-oncology. Many novel statistical methods that aim to efficiently capture potential long-term survival improvements have been proposed in recent years. However, the vast majority do not consider stratification, which is a major limitation considering that most large confirmatory studies currently employ a stratified primary analysis. In this article, we combine recently proposed weighted log-rank tests that have been designed to work well under a delayed separation of survival curves, with stratification by a baseline variable. The aim is to increase the efficiency of the test when the stratifying variable is highly prognostic for survival. As there are many potential ways to combine the two techniques, we compare several possibilities in an extensive simulation study. We also apply the techniques retrospectively to two recent randomized clinical trials.     

Exact,Distribution Free Confidence Intervals for Late Effects in Censored Matched Pairs

When comparing censored survival times for matched treated and control subjects, a late effect on survival is one that does not begin to appear until some time has passed. In a study of provider specialty in the treatment of ovarian cancer, a late divergence in the Kaplan–Meier survival curves hinted at superior survival among patients of gynecological oncologists, who employ chemotherapy less intensively, when compared to patients of medical oncologists, who employ chemotherapy more intensively; we ask whether this late divergence should be taken seriously. Specifically, we develop exact, permutation tests, and exact confidence intervals formed by inverting the tests, for late effects in matched pairs subject to random but heterogeneous censoring. Unlike other exact confidence intervals with censored data, the proposed intervals do not require knowledge of censoring times for patients who die. Exact distributions are consequences of two results about signs, signed ranks, and their conditional independence properties. One test, the late effects sign test, has the binomial distribution; the other, the late effects signed rank test, uses nonstandard ranks but nonetheless has the same exact distribution as Wilcoxon's signed rank test. A simulation shows that the late effects signed rank test has substantially more power to detect late effects than do conventional tests. The confidence statement provides information about both the timing and magnitude of late effects (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Sample size and power for the weighted log-rank test and Kaplan-Meier based tests with allowance for nonproportional hazards

Asymptotic distributions under alternative hypotheses and their corresponding sample size and power equations are derived for nonparametric test statistics commonly used to compare two survival curves. Test statistics include the weighted log-rank test and the Wald test for difference in (or ratio of) Kaplan-Meier survival probability, percentile survival, and restricted mean survival time. Accrual, survival, and loss to follow-up are allowed to follow any arbitrary continuous distribution. We show that Schoenfeld's equation—often used by practitioners to calculate the required number of events for the unweighted log-rank test—can be inaccurate even when the proportional hazards (PH) assumption holds. In fact, it can mislead one to believe that 1:1 is the optimal randomization ratio (RR), when actually power can be gained by assigning more patients to the active arm. Meaningful improvements to Schoenfeld's equation are made. The present theory should be useful in designing clinical trials, particularly in immuno-oncology where nonproportional hazards are frequently encountered. We illustrate the application of our theory with an example exploring optimal RR under PH and a second example examining the impact of delayed treatment effect. A companion R package npsurvSS is available for download on CRAN.     

Present status of BCG immunotherapy of malignant melanoma

Summary BCG systemic adjuvant immunotherapy may be effective for improving both the recurrence and survival rates in patients with regional metastases from malignant melanoma. Clinical trials show that many of the principles derived from the study of animal tumor systems are applicable to human cancer in that immunotherapy is most effective for a small residual number of tumor cells. BCG treatment fulfills many of the ideal criteria for adjuvant treatment following surgery when disease burden is lowest. It is relatively nontoxic; it is effective for disseminated melanoma; it has systemic activity in the adjuvant treatment of subclinical metastases. However, until clinical trials are complete, BCG adjuvant therapy must be considered investigational.Supported by USPHS grants CA05252, CA12582, and NIH 0732001 CB43852.     

Endpoints,patient selection,and biomarkers in the design of clinical trials for cancer vaccines

Therapeutic cancer vaccines are an emerging and potentially effective treatment modality. Cancer vaccines are usually very well tolerated, with minimal toxicity compared with chemotherapy. Unlike conventional cytotoxic therapies, immunotherapy does not result in immediate tumor shrinkage but may alter growth rate and thus prolong survival. Multiple randomized controlled trials of various immunotherapeutic agents have shown a delayed separation in Kaplan–Meier survival curves, with no evidence of clinical benefit within the first 6–12 months of vaccine treatment. Overall survival benefit is seen in patients with lower disease burden who are not expected to die within those initial 6–12 months. The concept of improved overall survival without marked initial tumor reduction represents a significant shift from the current paradigms established by standard cytotoxic therapies. Future clinical studies of therapeutic vaccines should enroll patients with either lower tumor burden, more indolent disease or both, and must seek to identify early markers of clinical benefit that may correlate with survival. Until then, improved overall survival is the only clear, discriminatory endpoint for therapeutic vaccines as monotherapies.     

Distance-based differential analysis of gene curves

MOTIVATION: Time course gene expression experiments are performed to study time-varying changes in mRNA levels of thousands of genes. Statistical methods from functional data analysis (FDA) have recently gained popularity for modelling and exploring such time courses. Each temporal profile is treated as the realization of a smooth function of time, or curve, and the inferred curve becomes the basic unit of statistical analysis. The task of identifying genes with differential temporal profiles then consists of detecting statistically significant differences between curves, where such differences are commonly quantified by computing the area between the curves or the l? distance. RESULTS: We propose a general test statistic for detecting differences between gene curves, which only depends on a suitably chosen distance measure between them. The test makes use of a distance-based variance decomposition and generalizes traditional MANOVA tests commonly used for vectorial observations. We also introduce the visual l? distance, which is shown to capture shape-related differences in gene curves and is robust against time shifts, which would otherwise inflate the traditional l? distance. Other shape-related distances, such as the curvature, may carry biological significance. We have assessed the comparative performance of the test on realistically simulated datasets and applied it to human immune cell responses to bacterial infection over time.     

A New Testing Approach for Comparing the Overall Homogeneity of Survival Curves

The assessment of overall homogeneity of time‐to‐event curves is a key element in survival analysis. The currently commonly used methods, e.g., log‐rank and Wilcoxon tests, may have a significant loss of statistical testing power under certain circumstances. In this paper a new statistical testing approach is developed to compare the overall homogeneity of survival curves. The proposed new method has greater power than the commonly used tests to detect overall differences between crossing survival curves. The small‐sample performance of the new test is investigated under a variety of situations by means of Monte Carlo simulations. Furthermore, the applicability of the proposed testing approach is illustrated by a real data example from a kidney dialysis trial. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A 15-year follow-up of AJCC stage III malignant melanoma patients treated postsurgically with Newcastle disease virus (NDV) oncolysate and determination of alterations in the CD8 T cell repertoire.

BACKGROUND: The development of effective adjuvant therapies for the treatment of high-risk melanoma patients is critical for the prevention of metastatic disease and improvement of patient survival. Active specific immunotherapy has been tested as an adjuvant treatment in numerous clinical trials with overall limited, but occasionally promising, success rates. Newcastle disease virus (NDV) oncolysate has been utilized as an adjunctive immunotherapeutic agent in the postsurgical management of these patients. A phase II study initiated in 1975 using adjuvant vaccine therapy composed of allogeneic and autologous human melanoma cells infected with live NDV (NDV oncolysate) in patients with AJCC stage III melanoma following therapeutic lymph node dissection has shown >60% survival rate at 10 years with no adverse effects. Continued long-term analysis of trials with promising early results as well as assessment of immunologic responses generated in these patients may result in improved therapeutic decisions for clinical trials in the future. MATERIALS AND METHODS: We analyzed the 15-year survival of patients treated postsurgically with NDV oncolysate in the phase II study described above. In an attempt to understand the immunological effects of this treatment, we have also carried out a comprehensive analysis of the peripheral blood T cell repertoire in these patients. RESULTS: The overall 15-year survival of this group of patients is 55%. Previous studies have suggested that improved outcome in patients undergoing immunotherapy is correlated with increased numbers of CD8(+)CD57(+) cells. In surviving patients, we observed a striking oligoclonality in the CD8(+) T cell population in peripheral blood, which reflects clonal expansions in the CD8(+)CD57(+) subset. CONCLUSIONS: The data suggest that adjuvant vaccination with NDV oncolysates is associated with prolonged survival of patients with lymph node-positive malignant melanoma and that CD8(+) T cells may be an important component of therapeutic efficacy.     

A statistical analysis for the mouse lymphoma cell forward mutation assay

This paper illustrates the usefulness of solvent control trials and presents a statistical analysis for mouse L5178Y lymphoma data. Examination of solvent control trials establishes that the natural logarithm of mutant frequency is approximately normally distributed and that both the mean and variance of mutant frequency vary by trial. There is little evidence of downturns at higher doses in the dose-response curves studied; therefore, a trend test is proposed for the detection of an increasing dose-response curve. A Monte Carlo investigation confirms that the proposed trend test is better able to detect an increasing dose-response than 4 alternate methods of analysis.     

Results of randomized trials of immunotherapy for acute leukemia

Summary For more than a decade clinical trials have attempted to define the role of immunotherapy in the treatment of patients with acute leukemia. Based on animal studies which indicated that non-specific immune stimulation had an antitumor effect if the tumor burden was small, the use of immunotherapy during remission in patients with acute leukemia seemed appropriate following the initial report of the success of bacillus Calmette-Guerin (BCG) in prolonging remission duration and survival in acute lymphoblastic leukemia. Therefore a series of randomized clinical trials was initiated to confirm these original observations. In four studies comparing BCG inoculations, with or without allogeneic leukemia cells, and chemotherapy or no therapy, no advantage of immunotherapy was noted. Immunotherapy appeared to be equally as good as chemotherapy. A combination of BCG and chemotherapy showed some advantage in one study, but no advantage was noted in two other studies.In acute myeloblastic leukemia several randomized trials suggested that BCG or one of its derivatives when given alone, in combination with allogeneic cells, or with chemotherapy had a marginal effect in prolonging remission duration and survival when compared to chemotherapy or rno therapy.In conclusion, immunotherapy during remission has marginal activity in acute leukemia.     

Estimation of the ROC Curve under Verification Bias

The ROC (receiver operating characteristic) curve is the most commonly used statistical tool for describing the discriminatory accuracy of a diagnostic test. Classical estimation of the ROC curve relies on data from a simple random sample from the target population. In practice, estimation is often complicated due to not all subjects undergoing a definitive assessment of disease status (verification). Estimation of the ROC curve based on data only from subjects with verified disease status may be badly biased. In this work we investigate the properties of the doubly robust (DR) method for estimating the ROC curve under verification bias originally developed by Rotnitzky, Faraggi and Schisterman (2006) for estimating the area under the ROC curve. The DR method can be applied for continuous scaled tests and allows for a non‐ignorable process of selection to verification. We develop the estimator's asymptotic distribution and examine its finite sample properties via a simulation study. We exemplify the DR procedure for estimation of ROC curves with data collected on patients undergoing electron beam computer tomography, a diagnostic test for calcification of the arteries.     

Results in children of acute lymphoid leukaemia protocol ICIG-ALL 9 consisting of chemotherapy for only nine months followed by active immunotherapy

Summary Protocol ICIG-ALL 9 with only nine months' remission chemotherapy followed by active immunotherapy has given a proportion of about 50% of the patients on the plateau of the first remission curve, while 60% of the children are on the plateau of survival curve.These results do not differ from those of another protocol (ICIG-ALL 10) conducted on an identical population of patients and comprising a 25 month remission chemotherapy before immunotherapy.This observation, confirmed by a randomized trial of the EORTC Haemopathy Working Party, suggests that between the 9th and the 25th month, active immunotherapy is as efficient as maintenance chemotherapy.The overall results of this protocol with short chemotherapy followed by active immunotherapy have been compared with those of another prolonged maintenance chemotherapy before immunotherapy protocol (ICIG-ALL 11), and with published protocols comprising only long maintenance chemotherapy: protocol 9 is, as far as the first remission plateau and the survival plateau are concerned, superior to most of these protocols (if not all their branches).Lethal toxicity of active immunotherapy is nil, in contrast to the proportion of deaths (4–28%) occurring during remission in the patients submitted to maintenance chemotherapy.However, not all patients with so-called acute lymphoid leukaemias should be treated identically: our early prognosis parameters (WHO cytological types and volume of the tumour, in this study) allow us to distinguish a good prognosis group in which protocol 9 gave an 80% cure expectancy.The patients with a poor prognosis should be the object of further research for a more efficient therapy. Even if this should be more intensive, the risk is justified in this group, while it is not so for the good prognosis group.     

Predictive influence in the accelerated failure time model

We develop case deletion diagnostics for prediction of future observations in the accelerated failure time model. We view prediction to be an important inferential goal in a survival analysis and thus it is important to identify whether particular observations may be influencing the quality of predictions. We use the Kullback-Leibler divergence as a measure of the discrepancy between the estimated probability distributions for the full and the case-deleted samples. In particular, we focus on the effect of case deletion on estimated survival curves but where we regard the survival curve estimate as a vehicle for prediction. We also develop a diagnostic for assessing the effect of case deletion on inferences for the median time to failure. The estimated median can be used with both predictive and estimative purposes in mind. We also discuss the relationship between our suggested measures and the corresponding Cook distance measure, which was designed with the goal of assessing estimative influence. Several applications of the proposed diagnostics are presented.     

Specific and nonspecific immunotherapy as an adjunct to curative surgery for cancer of the lung.

Attempts to improve survival following curative surgery for non-small-cell lung cancer are reviewed. Most of these approaches have been designed to stimulate the resistance of lung cancer patients in a non-specific fashion. Living bacteria or products of dead bacteria have been given as adjunctive treatment. Various routes have been used; oral, intradermal, subdermal, or intrapleural, with either BCG or Corynebacterium parvum. No reproducible benefit has been observed. Levamisole has not been proven to be useful. Trials have yet to be completed to confirm the use of thymosin fraction V for small cell carcinoma in improving the effectiveness of chemotherapy. A pilot trial using specific active immunotherapy is described. Prolongation of survival four years after closure of the trial in those patients immunized, compared with non-immunized patients, has prompted two further clinical trials. A small trial has confirmed the effectiveness of specific immunotherapy as adjunctive therapy for squamous cell carcinoma. A large multicenter trial in Canada and the United States should be completed and open to analysis in 1984 and may shed light on the role of tumor-associated antigens in stimulating specific resistance to lung cancer.     

Clinical effect and safety of dendritic cell–cytokine-induced killer cell immunotherapy for pancreatic cancer: a systematic review and meta-analysis

BackgroundAlthough promising results have recently been reported using dendritic cells (DCs) and cytokine-induced killer cells (CIKs) to treat pancreatic cancer (PC), its clinical effect and safety are associated with some controversy, and lack sufficient evidence. Here, we conducted a meta-analysis of 21 clinical trials to better evaluate the efficacy of DC-CIK immunotherapy in clinical practice to treat PC.MethodsPubMed, Cochrane Library, China National Knowledge Infrastructure (CNKI) and Wanfang Data Knowledge Service Platform (WANFANG Data) were searched to identify clinical trials that used DC-CIK immunotherapy for PC. Meta-analysis was performed using RevMan 5.3 and Stata 12.0.ResultsA total of 21 clinical trials involving 1549 patients were included. Compared with traditional treatment, DC-CIK immunotherapy improved and increased the clinical indices such as complete remission, partial remission, overall response rate, disease control rate, overall survival (0.5-y OS, 1-y OS, 1.5-y OS, 2-y OS and 3-y OS), interferon γ and CD3+, CD4+, CD4+/CD8+ and CD3+CD56+ lymphocyte. Additionally, DC-CIK immunotherapy reduced stable disease, progression disease, mortality, CD8+, CD4+CD25+CD127 low lymphocyte and interleukin-4. Furthermore, it showed a low incidence of adverse reactions (22%).ConclusionIn contrast to traditional therapy, DC-CIK immunotherapy not only shows improved short-term effect, long-term effect and immunologic function, but also reduces mortality and negative immunoregulatory index, and shows mild adverse reactions. This is the first study to evaluate the clinical effect and safety of DC-CIK immunotherapy for PC, and it indicated that DC-CIK immunotherapy may be suitable for patients with advanced PC or intolerance to radiotherapy and chemotherapy.     

MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION

In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F_ST statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F_ST-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.     

Anti–Programmed Cell Death (PD)-1 Immunotherapy for Malignant Tumor: A Systematic Review and Meta-Analysis

This systematic review and meta-analysis evaluated anti–programmed cell death (PD)-1 immunotherapy (nivolumab or pembrolizumab) for overall efficacy, safety, and effective dose relative to standard chemotherapy or other conventional drugs in the treatment of malignant tumors. We searched the following databases, PubMed, Medline, Embase, Cochrane, Wangfang Data, Weipu, and China National Knowledge Infrastructure, and the reference lists of the selected articles for randomized controlled trials (RCTs) of anti–PD-1 therapies in humans. The outcome measures were overall survival, treatment response, and adverse events. Only four randomized controlled trials met our inclusion criteria. Three of these evaluated responses to nivolumab, whereas one tested pembrolizumab. The result of our analysis suggested that nivolumab may improve the overall response rate in treating melanoma relative to chemotherapy and has few associated adverse events. Similarly, in metastatic melanoma patients, nivolumab had a significant advantage over dacarbazine in terms of 1-year survival, progression-free survival, and objective response rate. Regarding dose levels of nivolumab for patients with metastatic renal cell carcinoma, the outcomes in response to 2 and 10 mg/kg were similar, but both had significant advantages over 0.3 mg/kg. In addition, pembrolizumab showed similar outcomes in response to 2- and 10-mg/kg treatment. Anti–PD-1 immunotherapy appears to be safe and effective for patients with melanoma or metastatic renal cell carcinoma. Our meta-analysis is limited, but additional clinical trials are warranted to verify this preliminary evidence of positive outcomes and before anti–PD-1 therapy can be recommended for routine clinical use.     

非小细胞肺癌的免疫治疗进展

肺癌是最致命的恶性肿瘤之一,也是男性肿瘤患者致死率最高的,5年生存率低于18%。尽管非小细胞肺癌(non-small cell lung cancer,NSCLC)在手术治疗、化疗、放疗以及靶向治疗方面均取得了一定的成果,但晚期NSCLC的预后依然很差。免疫治疗为NSCLC患者提供了一个新的治疗方向。免疫治疗目前主要研究方向在免疫检查点抑制剂(Ipilimumab、Nivolumab、MK-3475)和肿瘤疫苗(MAGE-A3,L-BLP25,TG4010,Belagenpumatucel-L)等。免疫治疗具有针对性强、副作用少、效率高的特点,并在Ⅱ、Ⅲ期临床试验中取得了较好的疗效,成为在手术、化疗、放疗以及靶向治疗后一种新的重要治疗手段。本文就当前非小细胞肺癌免疫治疗原理、临床试验及待解决问题作一综述。     

胶质瘤的免疫治疗策略及进展

胶质瘤是最常见的原发性颅内肿瘤之一,具有较高的发病率及死亡率。目前,传统的手术治疗辅助放化疗效果不佳。肿瘤的免疫治疗作为一种新兴的疗法在胶质瘤的治疗中已经取得了一定的疗效。本文将全面的总结归纳胶质瘤的三类免疫治疗方法:主动免疫疗法、被动免疫疗法和免疫调节疗法的内容以及现阶段的进展,并提出胶质瘤的免疫治疗潜在的问题:如接受免疫治疗的患者的免疫状态评估体系不健全、缺乏个性化治疗手段、经济效益以及伦理等问题。同时本文将提出免疫治疗在胶质瘤应用上的展望:1)采用手术治疗、放化疗与免疫治疗相结合的立体式鸡尾酒疗法,在增强各种治疗方法疗效的同时弥补传统治疗方法的不足;2)寻找合适的免疫治疗靶点;3)重点研究结合了过继性细胞免疫治疗与体液免疫治疗优势的治疗方法:嵌合抗原受体修饰的T细胞治疗胶质瘤。     

Strengths and weaknesses of immunotherapy for advanced non-small-cell lung cancer: a meta-analysis of 12 randomized controlled trials

Background

Lung cancer is one of the leading causes of cancer death worldwide. Non-small-cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancers. Immunotherapy has yielded no consistent benefit to date for those patients. Assessing the objective efficacy and safety of immunotherapy for advanced NSCLC patients will help to instruct the future development of immunotherapeutic drugs.

Methodology and Principal Findings

We performed a meta-analysis of 12 randomized controlled trials including 3134 patients (1570 patients in the immunotherapy group and 1564 patients in the control group) with histologically confirmed stage IIIA, IIIB, or IV NSCLC. The analysis was executed with efficacy end points regarding overall survival (OS), progression-free survival (PFS), complete response (CR), partial response (PR), and total effective rate. Overall unstratified OS, PFS, PR, and total effective rate were significantly improved in advanced NSCLC patients in the immunotherapy group (P = 0.0007, 0.0004, 0.002, 0.003, respectively), whereas CR was not improved (P = 0.97). Subgroup analysis showed that monoclonal antibody (mAb) immunotherapy significantly improved the PFS, PR, and total effective rate and showed a trend of improving OS of advanced NSCLC patients compared with the control group, with one kind of adverse event being significantly dominant. Compared with the control group, the vaccine subgroup showed no significant difference with regard to serious adverse events, whereas cytokine immunotherapy significantly induced three kinds of serious adverse events.

Conclusions

Immunotherapy works efficiently on advanced NSCLC patients. Of several immunotherapies, mAb therapy may be a potential immunotherapy for advanced NSCLC patients, and become a standard complementary therapeutic approach in the future if the issues concerning toxicity and allergenicity of mAbs have been overcome.