Benchmark Dose analysis
The Benchmark Dose (BMD) approach is a scientifically more advanced method compared to the No Observed Adverse Effect Level (NOAEL) approach for deriving a Reference Point (Point of Departure) for risk assessment (EFSA, 2017). The BMD method pre-defines a specific effect size, referred to as the Benchmark response(BMR) (BMR) and estimates the dose (BMD) associated with the specified effect. The BMD is estimated from the complete dose response dataset by fitting dose-response models. Statistical uncertainties in the data are taken into account in the confidence interval around the BMD, the lower limit of which (denoted as BMDL) is the Point of Departure (or Reference Point) for deriving exposure limits.
Key elements of PROAST
PROAST can be applied to:
- dose-response data from all sorts of in vivo studies (animal, human or eco-toxicological)
- concentration-response data from in vitro studies
- high throughput data (e.g. gene expression as a function of dose)
- dose-response data from mixture studies
- combined dose-response datasets for similar endpoints in a single analysis
- non-linear regression in any other field of science, including the option to compare the relationships among subgroups
- the complete data from a toxicological study, by performing a quick (automated) analysis of a whole series of endpoints in a single run.
An important feature of PROAST is that it allows for comparing dose-responses among various subgroups, e.g. among sexes, among study durations, or among replicate studies. Based on statistical analysis, PROAST indicates if the various dose-response relationships differ among the subgroups, and if so, in what sense (e.g. in background response, in sensitivity to the chemical, or in dose-response shape).
Main changes with previous version
The current EFSA guidance on applying the BMD approach (EFSA, 2017) differs in various ways from the previous EFSA guidance (2009). These changes have been implemented in PROAST versions from 62.0 onwards. Two major changes resulting from the new EFSA guidance are:
- selection of models is based on the AIC rather than the likelihood ratio test
- in continuous data, only models 3 and 5 from the exponential and Hill families of models are considered, and from these two models the one with lowest AIC is used for calculating the BMD confidence interval.
PROAST versus BMDS
US-EPA developed the Benchmark Dose Software (BMDS).This package is also suitable for dose-response analysis and deriving a BMDL from dose-response data. RIVM and EPA aim to achieve consistency between the BMDS and PROAST software, but there are still some differences, including a number of default settings for statistical assumptions. Further, the two software packages differ in functionalities (see EFSA, 2017, Appendix A, for a summary of differences between BMDS and PROAST). Examples of useful functionalities in PROAST are the possibility of statistically comparing dose-responses among subgroups (covariate analysis), and the larger flexibility in plotting. PROAST closely follows the EFSA guidance on the BMD approach, while BMDS does not allow for performing BMD analyses according to EFSA guidance in all respects.
PROAST as an R package or as a web application
PROAST has been originally developed as a package in R. The R software is freely and easily downloadable (see manuals in the PROAST folder in the link below). Of course, you need some minimal knowledge of how R works, which is discussed in the manuals as well.
There are also two web applications of PROAST available, which may be particularly useful if you want to quickly apply PROAST, avoiding R and the installation of software on your computer. These web applications do not include all functionalities of the R package of PROAST, but the usual dose-response analysis of toxicity data can be done in these web tools. The links are:
For the first link you need to create an account (which can be done easily), the second link can be used without an account. The PROAST folder (see link below) contains a brief manual for the second web application (called “PROAST MANUAL WebApp.docx”). A manual for the first application can be found on the website itself (see “about” in the upper right corner). Further, it may be helpful to have a look at the PROAST manuals in the PROAST folder, as they provide some example analyses, and more background information on the methods used in PROAST.
The web applications will probably satisfy infrequent users of PROAST. However, if you use PROAST on a more regular basis, the stand alone version of PROAST may be more convenient, making it worthwhile to put some effort in getting acquainted with working in R. Furthermore, not all options in PROAST have been implemented in the current web applications.
Installation of PROAST on your machine
To install the PROAST software (copyright RIVM) on your computer, download the zipped folder “PROAST65.5.folder.zip” to your computer. Unzip the folder and you will see a number of files (including the zipped PROAST software, called proast65.6.zip – do NOT unzip it).
First users may go to the document “PROAST quick start.doc”. The installation of the software is discussed in “PROAST MANUAL GUI version.docx”.
Note that Mac users should install proast65.5.tgz rather than proast65.5.zip.
As PROAST is an R package, it is relatively easy to make a new version available after fixing any bugs in the software code. After any change in the code, the PROAST package receives another version number, whether it relates to a small change (e.g., fixed bug) or a relatively large change (e.g., change in methodological approach due to updated guidance). In this way, outcomes from analyses in the past that differ from those in the present may be checked to be due to a different PROAST version being used, and if so, if this relates to a bug, a different default setting, or a change in methods used. In general, however, the outcomes from different PROAST versions will be similar.
It is recommended to save all PROAST versions that you used (i.e. the zip or tgz file), preferably in a special folder on your computer, so that you can always reproduce calculations in the past. Also, you will need the zip (or tgz) file when you install a new R version. If you find that outcomes differ when using a newer version for the same analysis, and cannot find the cause, you may contact email@example.com.
Updates or questions
If you are interested to be informed about updates of PROAST or other relevant information, send an e-mail to firstname.lastname@example.org. You can also use this email address to ask questions, or report bugs or weaknesses in the software. We will try to answer questions on the use of PROAST, as long as their number does not explode.
A concise discussion of the BMD approach can be found in EFSA (2017). See Slob and Setzer (2015; Crit Rev Toxicol 44, 270-297) as an example of the use of PROAST in a more advanced setting, including dose-response analysis with covariates.