Applications of Multinomial Dose-Response Models in Developmental Toxicity Risk Assessment

Reproductive and developmental anomalies induced by toxic chemicals may be identified using laboratory experiments with small mammalian species such as rats, mice, and rabbits. In this paper, dose-response models for correlated multinomial data arising in studies of developmental toxicity are discussed. These models provide a joint characterization of dose-response relationships for both embryolethality and teratogenicity. Generalized estimating equations are used for model fitting, incorporating overdispersion relative to the multinomial variation due to correlation among littermates. The fitted dose-response models are used to estimate benchmark doses in a series of experiments conducted by the U.S. National Toxicology Program. Joint analysis of prenatal death and fetal malformation using an extended Dirichlet-trinomial covariance function to characterize overdispersion appears to have statistical and computational advantages over separate analysis of these two end points. Benchmark doses based on overall toxicity are below the minimum of those for prenatal death and fetal malformation and may, thus, be preferred for risk assessment purposes.     

A Comparison of Methods for Estimating the Benchmark Dose Based on Overdispersed Data from Developmental Toxicity Studies

Developmental anomalies resulting from prenatal toxicity can be manifested in terms of both malformations among surviving offspring and prenatal death. Although these two endpoints have traditionally been analyzed separately in the assessment of risk, multivariate methods of risk characterization have recently been proposed. We examined this and other issues in developmental toxicity risk assessment by evaluating the accuracy and precision of estimates of the effective dose ( ED ₀₅) and the benchmark dose ( BMD ₀₅) using computer simulation. Our results indicated that different variance structures (Dirichlet-trinomial and generalized linear model) used to characterize overdispersion yielded comparable results when fitting joint dose response models based on generalized estimating equations. (The choice of variance structure in separate modeling was also not critical.) However, using the Rao-Scott transformation to eliminate overdispersion tended to produce estimates of the ED ₀₅ with reduced bias and mean squared error. Because joint modeling ensures that the ED ₀₅ for overall toxicity (based on both malformations and prenatal death) is always less than the ED ₀₅ for either malformations or prenatal death, joint modeling is preferred to separate modeling for risk assessment purposes.     

Modeling Fetal Death and Malformation in Developmental Toxicity Studies

We review approaches to dose-response modeling and risk assessment for binary data from developmental toxicity studies. In particular, we focus on jointly modeling fetal death and malformation and use a continuation ratio formulation of the multinomial distribution to provide a model for risk. Generalized estimating equations are used to account for clustering of animals within litters. The fitted model is then used to calculate doses corresponding to a specified level of excess risk. Two methods of arriving at a lower confidence limit or Benchmark dose are illustrated and compared. We also discuss models based on single binary end points and compare our approach to a binary analysis of whether or not the animal was 'affected' (either dead or malformed). The models are illustrated using data from four developmental toxicity studies in EG, DEHP, TGDM, and DYME conducted through the National Toxicology Program.     

Implications of Developmental Toxicity Study Design for Quantitative Risk Assessment

Standard experimental designs for conducting developmental toxicity studies typically include three- or four-dose levels in addition to a control group. Some researchers have suggested that designs with more exposure groups would improve dose-response characterization and risk estimation. Such proposals have not, however, been supported by the results of simulation studies, which instead back the use of fewer dose levels. This discrepancy is partly due to using a known dose–response pattern to generate data, making model choice obvious. While the carcinogenicity literature has explored implications of different study designs, little attention has been given to the role of design in developmental toxicity risk assessment (or noncancer toxicology in general). In this research, we explore the implications of various experimental designs for developmental toxicity by resampling data from a large study of 2,4,5-trichlorophenoxyacetic acid in mice. We compare the properties of benchmark dose (BMD) estimation for different design strategies by randomly selecting animals within particular dose groups from the entire 2,4,5-T database of over 77,000 birth outcomes to create smaller "pseudo-studies" that are representative of standard bioassay sample sizes. Our results show that experimental designs which include more dose levels have advantages in terms of risk characterization and estimation.     

A Parametric Model for Detecting Hormetic Effects in Developmental Toxicity Studies

Hormetic effects have been observed at low exposure levels based on the dose-response pattern of data from developmental toxicity studies. This indicates that there might actually be a reduced risk of exhibiting toxic effects at low exposure levels. Hormesis implies the existence of a threshold dose level and there are dose-response models that include parameters that account for the threshold. We propose a function that introduces a parameter to account for hormesis. This function is a subset of the set of all functions that could represent a hormetic dose-response relationship at low exposure levels to toxic agents. We characterize the overall dose-response relationship with a piecewise function that consists of a hormetic u-shape curve at low dose levels and a logistic curve at high dose levels. We apply our model to a data set from an experiment conducted at the National Toxicology Program (NTP). We also use the beta-binomial distribution to model the litter response data. It can be seen by observing the structure of these data that current experimental designs for developmental studies employ a limited number of dose groups. These designs may not be satisfactory when the goal is to illustrate the existence of hormesis. In particular, increasing the number of low-level doses improves the power for detecting hormetic effects. Therefore, we also provide the results of simulations that were done to characterize the power of current designs in detecting hormesis and to demonstrate how this power can be improved upon by altering these designs with the addition of only a few low exposure levels.     

Regression Models and Risk Estimation for Mixed Discrete and Continuous Outcomes in Developmental Toxicology

Multivariate dose-response models have recently been proposed for developmental toxicity data to simultaneously model malformation incidence (a binary outcome), and reductions in fetal weight (a continuous outcome). In this and other applications, the binary outcome often represents a dichotomization of another outcome or a composite of outcomes, which facilitates analysis. For example, in Segment II developmental toxicology studies, multiple malformation types (i.e., external, visceral, skeletal) are evaluated on each fetus; malformation status may also be ordinally measured (e.g., normal, signs of variation, full malformation). A model is proposed is for fetal weight and multiple malformation variables measured on an ordinal scale, where the correlations between the outcomes and between the offspring within a litter are taken into account. Fully specifying the joint distribution of outcomes within a litter is avoided by specifying only the distribution of the multivariate outcome for each fetus and using generalized estimating equation methodology to account for correlations due to litter clustering. The correlations between the outcomes are required to characterize joint risk to the fetus, and are therefore a focus of inference. Dose-response models and their application to quantitative risk assessment are illustrated using data from a recent developmental toxicology experiment of ethylene oxide in mice.     

Design of Developmental Toxicity Studies for Assessing Joint Effects of Dose and Duration

In the assessment of developmental and reproductive effects, the timing and duration of exposures to chemical compounds or other environmental contaminants are of particular interest, as the gestational cycle is known to have periods of increased sensitivity. The goal of this research is to identify optimal experimental designs for conducting developmental toxicity studies when the effects of both exposure level and duration of exposure are of interest. The elements of the study design considered in this evaluation are the allocation of animals to dose-duration exposure groups and the determination of the most efficient intermediate exposure levels. The optimality of various designs is assessed via the accuracy of the estimated excess risk as well as testing criteria. Simulation studies are conducted to compare these criteria and determine optimal design strategies under various underlying dose-response patterns. Asymptotic results are also derived to lend support to the simulation studies.     

A Malformation Incidence Dose-Response Model Incorporating Fetal Weight and/or Litter Size as Covariates

A dose-response model is often fit to bioassay data to provide a mathematical relationship between the incidence of a developmental malformation and dose of a toxicant. To utilize the interrelations among the fetal weight, incidence of malformation and number of the live fetuses, a conditional Gaussian regression chain model is proposed to model the dose-response function for developmental malformation incidence using the litter size and/or the fetal weight as covariates. The litter size is modeled as a function of dose, the fetal weight is modeled as a function of dose conditional on the litter size, and the malformation incidence is modeled as a function of dose conditional on both the litter size and the fetal weight, which itself is also conditional on the litter size. Data from a developmental experiment conducted at the National Center for Toxicological Research to investigate the growth stunting and increased incidence of cleft palate induced by Dexamethasone (DEX) exposure in rats was used as an illustration.     

A Comparison of Three Methods for Calculating Confidence Intervals for the Benchmark Dose

Various methods exist to calculate confidence intervals for the benchmark dose in risk analysis. This study compares the performance of three such methods in fitting nonlinear dose-response models: the delta method, the likelihood-ratio method, and the bootstrap method. A data set from a developmental toxicity test with continuous, ordinal, and quantal dose-response data is used for the comparison of these methods. Nonlinear dose-response models, with various shapes, were fitted to these data. The results indicate that a few thousand runs are generally needed to get stable confidence limits when using the bootstrap method. Further, the bootstrap and the likelihood-ratio method were found to give fairly similar results. The delta method, however, resulted in some cases in different (usually narrower) intervals, and appears unreliable for nonlinear dose-response models. Since the bootstrap method is more time consuming than the likelihood-ratio method, the latter is more attractive for routine dose-response analysis. In the context of a probabilistic risk assessment the bootstrap method has the advantage that it directly links to Monte Carlo analysis.     

A Simulation Study of the Influence of Study Design on the Estimation of Benchmark Doses for Developmental Toxicity1

The benchmark dose (BMD)⁴ approach is emerging as replacement to determination of the No Observed Adverse Effect Level (NOAEL) in noncancer risk assessment. This possibility raises the issue as to whether current study designs for endpoints such as developmental toxicity, optimized for detecting pair wise comparisons, could be improved for the purpose of calculating BMDs. In this paper, we examine various aspects of study design (number of dose groups, dose spacing, dose placement, and sample size per dose group) on BMDs for two endpoints of developmental toxicity (the incidence of abnormalities and of reduced fetal weight). Design performance was judged by the mean-squared error (reflective of the variance and bias) of the maximum likelihood estimate (MLE) from the log-logistic model of the 5% added risk level (the likely target risk for a benchmark calculation), as well as by the length of its 95% confidence interval (the lower value of which is the BMD). We found that of the designs evaluated, the best results were obtained when two dose levels had response rates above the background level, one of which was near the ED₀₅, were present. This situation is more likely to occur with more, rather than fewer dose levels per experiment. In this instance, there was virtually no advantage in increasing the sample size from 10 to 20 litters per dose group. If neither of the two dose groups with response rates above the background level was near the ED₀₅, satisfactory results were also obtained, but the BMDs tended to be more conservative (i.e., lower). If only one dose level with a response rate above the background level was present, and it was near the ED₀₅, reasonable results for the MLE and BMD were obtained, but here we observed benefits of larger dose group sizes. The poorest results were obtained when only a single group with an elevated response rate was present, and the response rate was much greater than the ED₀₅. The results indicate that while the benchmark dose approach is readily applicable to the standard study designs and generally observed dose-responses in developmental assays, some minor design modifications would increase the accuracy and precision of the BMD.     

Comparing Experimental Designs for Benchmark Dose Calculations for Continuous Endpoints

The BMD (benchmark dose) method that is used in risk assessment of chemical compounds was introduced by Crump (1984) and is based on dose-response modeling. To take uncertainty in the data and model fitting into account, the lower confidence bound of the BMD estimate (BMDL) is suggested to be used as a point of departure in health risk assessments. In this article, we study how to design optimum experiments for applying the BMD method for continuous data. We exemplify our approach by considering the class of Hill models. The main aim is to study whether an increased number of dose groups and at the same time a decreased number of animals in each dose group improves conditions for estimating the benchmark dose. Since Hill models are nonlinear, the optimum design depends on the values of the unknown parameters. That is why we consider Bayesian designs and assume that the parameter vector has a prior distribution. A natural design criterion is to minimize the expected variance of the BMD estimator. We present an example where we calculate the value of the design criterion for several designs and try to find out how the number of dose groups, the number of animals in the dose groups, and the choice of doses affects this value for different Hill curves. It follows from our calculations that to avoid the risk of unfavorable dose placements, it is good to use designs with more than four dose groups. We can also conclude that any additional information about the expected dose-response curve, e.g., information obtained from studies made in the past, should be taken into account when planning a study because it can improve the design.     

Bootstrap Estimation of Benchmark Doses and Confidence Limits with Clustered Quantal Data

The benchmark dose (BMD) is an exposure level that would induce a small risk increase (BMR level) above the background. The BMD approach to deriving a reference dose for risk assessment of noncancer effects is advantageous in that the estimate of BMD is not restricted to experimental doses and utilizes most available dose-response information. To quantify statistical uncertainty of a BMD estimate, we often calculate and report its lower confidence limit (i.e., BMDL), and may even consider it as a more conservative alternative to BMD itself. Computation of BMDL may involve normal confidence limits to BMD in conjunction with the delta method. Therefore, factors, such as small sample size and nonlinearity in model parameters, can affect the performance of the delta method BMDL, and alternative methods are useful. In this article, we propose a bootstrap method to estimate BMDL utilizing a scheme that consists of a resampling of residuals after model fitting and a one-step formula for parameter estimation. We illustrate the method with clustered binary data from developmental toxicity experiments. Our analysis shows that with moderately elevated dose-response data, the distribution of BMD estimator tends to be left-skewed and bootstrap BMDL s are smaller than the delta method BMDL s on average, hence quantifying risk more conservatively. Statistically, the bootstrap BMDL quantifies the uncertainty of the true BMD more honestly than the delta method BMDL as its coverage probability is closer to the nominal level than that of delta method BMDL. We find that BMD and BMDL estimates are generally insensitive to model choices provided that the models fit the data comparably well near the region of BMD. Our analysis also suggests that, in the presence of a significant and moderately strong dose-response relationship, the developmental toxicity experiments under the standard protocol support dose-response assessment at 5% BMR for BMD and 95% confidence level for BMDL.     

Summary of the Workshop on Issues in Risk Assessment: Quantitative Methods for Developmental Toxicology

This report summarizes the proceedings of a conference on quantitative methods for assessing the risks of developmental toxicants. The conference was planned by a subcommittee of the National Research Council's Committee on Risk Assessment Methodology ⁴ in conjunction with staff from several federal agencies, including the U.S. Environmental Protection Agency, U.S. Food and Drug Administration, U.S. Consumer Products Safety Commission, and Health and Welfare Canada. Issues discussed at the workshop included computerized techniques for hazard identification, use of human and animal data for defining risks in a clinical setting, relationships between end points in developmental toxicity testing, reference dose calculations for developmental toxicology, analysis of quantitative dose-response data, mechanisms of developmental toxicity, physiologically based pharmacokinetic models, and structure-activity relationships. Although a formal consensus was not sought, many participants favored the evolution of quantitative techniques for developmental toxicology risk assessment, including the replacement of lowest observed adverse effect levels (LOAELs) and no observed adverse effect levels (NOAELs) with the benchmark dose methodology.     

On Determining the BMD from Multiple Outcomes in Developmental Toxicity Studies when One Outcome is Intentionally Missing

Public health concerns over the occurrence of developmental abnormalities that can occur as a result of prenatal exposure to drugs, chemicals, and other environmental factors has led to a number of developmental toxicity studies and the use of the benchmark dose (BMD) for risk assessment. To characterize risk from multiple sources, more recent analytic methods involve a joint modeling approach, accounting for multiple dichotomous and continuous outcomes. For some continuous outcomes, evaluating all subjects may not be feasible, and only a subset may be evaluated due to limited resources. The subset can be selected according to a prespecified probability model and the unobserved data can be viewed as intentionally missing in the sense that subset selection results in missingness that is experimentally planned. We describe a subset selection model that allows for sampling pups with malformations and healthy pups at different rates, and includes the well‐known simple random sample (SRS) as a special case. We were interested in understanding how sampling rates that are selected beforehand influence the precision of the BMD. Using simulations we show how improvements over the SRS can be obtained by oversampling malformations, and how some sampling rates can yield precision that is substantially worse than the SRS. We also illustrate the potential for cost saving with oversampling. Simulations are based on a joint mixed effects model, and to account for subset selection, use of case weights to obtain valid dose‐response estimates.     

Issues in Qualitative and Quantitative Risk Analysis for Developmental Toxicology1

The qualitative and quantitative evaluation of risk in developmental toxicology has been discussed in several recent publications.(^1–3) A number of issues still are to be resolved in this area. The qualitative evaluation and interpretation of end points in developmental toxicology depends on an understanding of the biological events leading to the end points observed, the relationships among end points, and their relationship to dose and to maternal toxicity. The interpretation of these end points is also affected by the statistical power of the experiments used for detecting the various end points observed. The quantitative risk assessment attempts to estimate human risk for developmental toxicity as a function of dose. The current approach is to apply safety (uncertainty) factors to die no observed effect level (NOEL). An alternative presented and discussed here is to model the experimental data and apply a safety factor to an estimated risk level to achieve an “acceptable” level of risk. In cases where the dose-response curves upward, this approach provides a conservative estimate of risk. This procedure does not preclude the existence of a threshold dose. More research is needed to develop appropriate dose-response models that can provide better estimates for low-dose extrapolation of developmental effects.     

Quantitative Risk Assessment for Developmental Neurotoxic Effects

Developmental neurotoxicity concerns the adverse health effects of exogenous agents acting on neurodevelopment. Because human brain development is a delicate process involving many cellular events, the developing fetus is rather susceptible to compounds that can alter the structure and function of the brain. Today, there is clear evidence that early exposure to many neurotoxicants can severely damage the developing nervous system. Although in recent years, there has been much attention given to model development and risk assessment procedures for developmental toxicants, the area of developmental neurotoxicity has been largely ignored. Here, we consider the problem of risk estimation for developmental neurotoxicants from animal bioassay data. Since most responses from developmental neurotoxicity experiments are nonquantal in nature, an adverse health effect will be defined as a response that occurs with very small probability in unexposed animals. Using a two-stage hierarchical normal dose-response model, upper confidence limits on the excess risk due to a given level of added exposure are derived. Equivalently, the model is used to obtain lower confidence limits on dose for a small negligible level of risk. Our method is based on the asymptotic distribution of the likelihood ratio statistic (cf. Crump, 1995). An example is used to provide further illustration.     

Model Averaging Using the Kullback Information Criterion in Estimating Effective Doses for Microbial Infection and Illness

Since the National Food Safety Initiative of 1997, risk assessment has been an important issue in food safety areas. Microbial risk assessment is a systematic process for describing and quantifying a potential to cause adverse health effects associated with exposure to microorganisms. Various dose-response models for estimating microbial risks have been investigated. We have considered four two-parameter models and four three-parameter models in order to evaluate variability among the models for microbial risk assessment using infectivity and illness data from studies with human volunteers exposed to a variety of microbial pathogens. Model variability is measured in terms of estimated ED01s and ED10s, with the view that these effective dose levels correspond to the lower and upper limits of the 1% to 10% risk range generally recommended for establishing benchmark doses in risk assessment. Parameters of the statistical models are estimated using the maximum likelihood method. In this article a weighted average of effective dose estimates from eight two- and three-parameter dose-response models, with weights determined by the Kullback information criterion, is proposed to address model uncertainties in microbial risk assessment. The proposed procedures for incorporating model uncertainties and making inferences are illustrated with human infection/illness dose-response data sets.     

Ebola Virus Dose Response Model for Aerosolized Exposures: Insights from Primate Data

This study develops dose–response models for Ebolavirus using previously published data sets from the open literature. Two such articles were identified in which three different species of nonhuman primates were challenged by aerosolized Ebolavirus in order to study pathology and clinical disease progression. Dose groups were combined and pooled across each study in order to facilitate modeling. The endpoint of each experiment was death. The exponential and exact beta-Poisson models were fit to the data using maximum likelihood estimation. The exact beta-Poisson was deemed the recommended model because it more closely approximated the probability of response at low doses though both models provided a good fit. Although transmission is generally considered to be dominated by person-to-person contact, aerosolization is a possible route of exposure. If possible, this route of exposure could be particularly concerning for persons in occupational roles managing contaminated liquid wastes from patients being treated for Ebola infection and the wastewater community responsible for disinfection. Therefore, this study produces a necessary mathematical relationship between exposure dose and risk of death for the inhalation route of exposure that can support quantitative microbial risk assessment aimed at informing risk mitigation strategies including personal protection policies against occupational exposures.     

Assessing Overall Risk in Reproductive Experiments

Toxicologists are often interested in assessing the joint effect of an exposure on multiple reproductive endpoints, including early loss, fetal death, and malformation. Exposures that occur prior to mating or extremely early in development can adversely affect the number of implantation sites or fetuses that form within each dam and may even prevent pregnancy. A simple approach for assessing overall adverse effects in such studies is to consider fetuses or implants that fail to develop due to exposure as missing data. The missing data can be imputed, and standard methods for the analysis of quantal response data can then be used for quantitative risk assessment or testing. In this article, a new bias-corrected imputation procedure is proposed and evaluated. The procedure is straightforward to implement in standard statistical packages and has excellent operating characteristics when used in combination with a marginal model fit with generalized estimating equations. The methods are applied to data from a reproductive toxicity study of Nitrofurazone conducted by the National Toxicology Program.     

Optimal Experimental Design Strategies for Detecting Hormesis

Hormesis is a widely observed phenomenon in many branches of life sciences, ranging from toxicology studies to agronomy, with obvious public health and risk assessment implications. We address optimal experimental design strategies for determining the presence of hormesis in a controlled environment using the recently proposed Hunt‐Bowman model. We propose alternative models that have an implicit hormetic threshold, discuss their advantages over current models, and construct and study properties of optimal designs for (i) estimating model parameters, (ii) estimating the threshold dose, and (iii) testing for the presence of hormesis. We also determine maximin optimal designs that maximize the minimum of the design efficiencies when we have multiple design criteria or there is model uncertainty where we have a few plausible models of interest. We apply these optimal design strategies to a teratology study and show that the proposed designs outperform the implemented design by a wide margin for many situations.