Cure Models
eBook - ePub

Cure Models

Methods, Applications, and Implementation

  1. 252 pages
  2. English
  3. ePUB (mobile friendly)
  4. Available on iOS & Android
eBook - ePub

Cure Models

Methods, Applications, and Implementation

About this book

Cure Models: Methods, Applications and Implementation is the first book in the last 25 years that provides a comprehensive and systematic introduction to the basics of modern cure models, including estimation, inference, and software. This book is useful for statistical researchers and graduate students, and practitioners in other disciplines to have a thorough review of modern cure model methodology and to seek appropriate cure models in applications. The prerequisites of this book include some basic knowledge of statistical modeling, survival models, and R and SAS for data analysis.

The book features real-world examples from clinical trials and population-based studies and a detailed introduction to R packages, SAS macros, and WinBUGS programs to fit some cure models. The main topics covered include

  • the foundation of statistical estimation and inference of cure models for independent and right-censored survival data,
  • cure modeling for multivariate, recurrent-event, and competing-risks survival data, and joint modeling with longitudinal data,
  • statistical testing for the existence and difference of cure rates and sufficient follow-up,
  • new developments in Bayesian cure models,
  • applications of cure models in public health research and clinical trials.

Information

Year
2021
Print ISBN
9780367690748
9780367145576
eBook ISBN
9780429628047

1

Introduction

1.1    A Brief Review of Cure Models

1.1.1    Time-to-Event Data and Cured Subjects

In many scientific studies, researchers are interested in time to the occurrence of a specific event of interest. When analyzing time-to-event data, it often happens that a certain proportion of subjects may never experience the event of interest and are considered to be cured. Cured subjects are immune or non-susceptible to the event. Time-to-event data with cured subjects are abundant in population health and medical studies. In some diseases, there is strong biological evidence that, when considering endpoints other than a natural death, the event would never occur for some fraction of the subjects. The assumption that some individuals will never experience the event may also be based solely on empirical considerations, such as the presence of a large number of long-term survivors. Recent progress in the diagnosis and treatment of cancer has led to substantial improvement in cancer survival. If patients are diagnosed early and receive effective treatment, e.g., the targeted therapy or immunotherapy, a subpopulation of the cancer patients eventually become cured from the disease, which leads to some long-term survivors if the follow-up time is long enough. The presence of cured subjects is often suggested by a Kaplan-Meier estimate of the marginal survival function, which shows a long and stable plateau with heavy censoring at the right extreme.
In sociology studies, the rates of life-long marriage and permanent employment are important concepts of social stability. An employee who has been with the same company for a sufficiently long time may be considered as unlikely to join other companies (Yamaguchi, 1992) and can be considered as cured or immune to the event of joining other companies. In criminal justice, the recidivism rate is an important feature to determining the effect of rehabilitation to stop offenders from committing crimes again and those subjects who will not commit crimes again after a long time may be considered as cured (Schmidt and Witte, 1989). The concept of cured subjects has applications in economics. For example, when considering the probability of default and the timing of default on loans, a company or subject who is not in default for a long time may be considered as cured (Tong et al., 2012). In reliability studies, one complex system is often considered as being composed of some subsystems in series. Usually, the failure of any subsystem would lead to the failure of the entire system. However, some subsystems’ lifetimes are long enough and even never fail during the life cycle of the entire system and they can be considered as cured. In political studies, the time to intervention over the course of a conflict and the conflicts that are never intervened for a long time may be considered as cured (Findley and Teo, 2006).

1.1.2    Survival Models and Cure Models

Standard statistical methods for time-to-event analysis, often called survival models, typically assume that every subject in the study population is susceptible to the event of interest and will eventually experience the event if the follow-up is sufficiently long. They do not account for cured subjects and can lead to biased estimates of the survival of susceptible subjects.
Survival models that take into account the possibility of cure are commonly referred to as cure models or cure rate models. A cure model allows a direct modeling of the cure proportion and the effect of covariates on the cure proportion. Additionally, the cure model also provides estimation and inference of the distribution of the survival time for uncured subjects or subjects who are not cured. Most of the existing cure models are modified survival models that include the probability of being cured. Based on how the cure proportion is introduced, the cure models can be roughly divided into two types: mixture cure models and non-mixture cure models.
Although the cure models have a shorter history compared to the standard survival models, they have been an area of active research in statistics since the early 1950s. The most widely used cure rate model is the mixture cure model which is also known as the standard cure rate model. This model was first introduced by Boag (1949). He introduced the traditional definition of a cured fraction for patients who have a specific illness, by a five-years survival rate. Although the definition of the cured fraction has changed and improved over the years, many authors developed and improved the original mixture model further. Berkson and Gage (1952) divided the population into two groups: susceptible individuals to the event of interest and insusceptible individuals. They suggested that a group of treated patients are considered to be cured if they have approximately the same survival distribution as the general population who have never had the disease of interest. Farewell (1982) used a mixture model as a combination of logistic model and Weibull distribution to model the toxicant and stress level for laboratory animals. Kuk and Chen (1992) proposed a semiparametric mixture cure model consisting of the logistic model for the probability of occurrence of the event of interest, and the proportional hazard model for the time to event of interest for uncured subjects. Maller and Zhou (1996) have collected a comprehensive account of mixture cure rate models with various survival functions. Goldman (1984), Taylor (1995), and Peng and Dear (2000), among others, have also investigated parametric, semiparametric, and nonparametric mixture cure rate models. Yu and Peng (2008) and Peng et al. (2007a) extended the mixture cure model to multivariate survival data. Both marginal survival models (Chen and Lu, 2012; Niu and Peng, 2014; Niu et al., 2018a) and random-effects frailty models (Peng and Taylor, 2011; Peng and Zhang, 2008a) have been proposed. More recently, Wu and Yin (2013) suggested quantile regression methods and martingale estimating equations for a better assessment of covariate effects on quantiles of a time-to-event of interest.
The non-mixture cure model is another type of cure models for modeling time-to-event data with a cure fraction. Non-mixture cure models were first introduced by Yakovlev et al. (1994a) and then discussed by Yakovlev et al. (1994b), Ibrahim et al. (2001), Chen et al. (1999), and Wang et al. (2012a). These models were motivated by an underlying biological mechanism for cancer cells, which assumes that the number of cancer cells after cancer treatment follows a Poisson distribution. Most of the current investigations on the non-mixture cure models are in the Bayesian context due to its special form. The non-mixture cure models can be expressed into the mixture cure models. However, the model interpretation, particularly the covariate effects on the distribution of the survival time of uncured subjects can have important differences between the two types of cure models.
Because of abundant time-to-event data with a cure fraction in many different disciplines, cure models have potentially wide applications in the disciplines. The novel applications of the cure models have help investigators understand the pattern and behavior of survival times after treatment or intervention. Particularly, in recent years there has been significant progress in the research and development of immune-oncology (I-O) therapy. Because the mechanisms of actions of immunotherapy are profoundly different from traditional chemotherapy and radiation therapy, the patient survival in the clinical trials of immunotherapy have demonstrated delayed clinical effects as well as long-term survival, and cure models can play an important role in revealing the complicated short-term and long-term effects of the therapy to cancer patients.
However, although there have been tremendous efforts and development in modeling of survival data with a cure fraction, there are very few books that provide a comprehensive coverage of the statistical concepts, methods, and applications of cure models. The applications of cure models, particularly those developed in recent years, in the disciplines are still limited, such as in the clinical literature (Othus et al., 2012; Yilmaz et al., 2013). The only published book that is devoted to cure models is Maller and Zhou (1996). However, it focused on large sample properties of estimation and tests for nonparametric and exponential-family based mixture cure models only and is not application-oriented. Moreover, the book was published more than 20 years ago and there has been no book since then that covers the rapid growth in research and applications of cure models in the last two decades. Ibrahim et al. (2001) devotes a chapter on specific Bayesian cure models. More recently there are a few review papers that cover more recent advances in cure models, such as Peng and Taylor (2014) and Amico and Van Keilegom (2018). Due to space limitations, the review papers do not include many details. Thus, a book that covers the rapid growth in research and applications of cure models in the last two decades and provides a comprehensive introduction of various cure models, their estimation methods and their applications using software programs that have been developed will provide a valuable resource for practitioners to apply cure models in various disciplines and for statistical researchers and students to further advance the investigation of analysis time-to-event data with a cure fraction.

1.2    Aim and Scope of the Book

The goal of this book is to give a comprehensive introduction to cure models. It includes many recent advances in cure model research. It covers both statistical methodology and applications of cure models in many disciplines with software packages. Particularly, this book provides extensive discussions about the applications of cure models in cancer research and oncology clinical trials. We hope this book may serve as a useful desk reference for scientists and researchers engaged in biological research and related areas, and biostatisticians who provide statistical support for clinical trials and public health decision-making. More importantly, we would like to provide graduate students with an advanced textbook with both statistical methods and real applications.
The scope of this book includes basics of the cure models as well as many recent developments related to the methodological issues and software implementations of cure models for right-censored time-to-event data subject to non-informative censoring. Due to the limited time, we are unable to include cure models that are developed for interval-censored data and truncated data. The software implementations are only limited to those developed in R (R Core Team, 2013), SAS™ (SAS Institute, Cary NC), WinBUGS (Lunn et al., 2000), and OpenBUGS (Lunn et al., 2009). Programs developed in other software environments, such as STATA, are not included.
The rest of the book is organized as follows. Chapter 2 introduces the basics of parametric mixture and non-mixture cure models and the EM-based estimation methods that have been pivotal in the cure model methodology. Model assessment methods and some existing R packages and SAS macros for parametric cure models are also presented with real-world data sets as examples. Chapter 3 focuses on the basics of the semiparametric and nonparametric mixture and non-mixture cure models, the estimation methods, and implementations in existing R packages and SAS macros illustrated with real-world data sets. These two chapters lay the foundation of cure models and are essential for understanding statistical estimation and inference of cure models. Chapters 4, 5, 6 cover more advanced topics in cure modeling. Chapter 4 covers various modeling approaches to multivariate, recurrent-event, and competing-risks survival data. Both marginal and random-effects (frailty) cure models are described. Chapter 5 describes joint models of longitudinal and survival data with a cure fraction and illustrates the advantage of joint models using a real case study. The joint models provide efficient and unbiased estimates of the trajectories of longitudinal data. Chapter 6 focuses on the statistical testing for the existence and difference of cure rates and also the identifiability and sufficient follow-up issues in cure model estimation. Bayesian methods have been widely used for survival modeling including cure models. Chapter 7 presents some new developments and models that emerged recently after the review of Bayesian cure models in Ibrahim et al. (2001). General implementations of Bayesian analysis using BUGS program are also presented. The last two chapters cover practical applications of cure models in public health research and clinical trials. Particularly, Chapter 8 presents the application of cure models in the population-based cancer survival analysis. Chapter 9 discusses statistical issues in the design and analysis of cancer clinical trials with a possible cure fraction. Comparisons regarding the relative merits and disadvantages of the adaptive design methods in clinical research and development are discussed whenever deemed appropriate. R programs that implement a suite of tools for applied researchers in clinical trials are provided.
In each chapter, whenever possible, real examples from clinical trials or public health research are used to demonstrate the use of cure models. If applicable, topics for future research are provided too.

2

The Parametric Cure Model

2.1 Introduction

This chapter focuses on cure models that are fully parametrically specified. The parameters in such models can be readily estimated using the maximum likelihood method, and thus the properties of the estimates can be established using the maximum likelihood theory. Parametric cure models also allow extrapolation in prediction, which can be attractive in practice. The chapter is ...

Table of contents

  1. Cover
  2. Half Title
  3. Series Page
  4. Title Page
  5. Copyright Page
  6. Dedication
  7. Table of Contents
  8. Preface
  9. Glossary
  10. 1 Introduction
  11. 2 The Parametric Cure Model
  12. 3 The Semiparametric and Nonparametric Cure Models
  13. 4 Cure Models for Multivariate Survival Data and Competing Risks
  14. 5 Joint Modeling of Longitudinal and Survival Data with a Cure Fraction
  15. 6 Testing the Existence of Cured Subjects and Sufficient Follow-up
  16. 7 Bayesian Cure Model
  17. 8 Analysis of Population-Based Cancer Survival Data
  18. 9 Design and Analysis of Cancer Clinical Trials
  19. Bibliography
  20. Index

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