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FIFRA Science Advisory Panel Meeting

Prioritization of EDSP

Universe of Chemicals 

Using Computational Toxicology Tools

Arlington, VA

January 29, 2013
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1.1 Please comment on appropriateness of the overall conceptual 

approach for prioritizing the EDSP chemical inventory (note: 

subsequent charge questions address issues associated with 

specific components of the prioritization approach). In your 

comments, please address:

The extent to which EPA’s description of the process 

transparently captures and describes the key technical 

steps of the prioritization scheme and whether there are 

other scientific considerations the agency should 

incorporate into its EDSP prioritization scheme;

The robustness of the scientific support for the overall 

approach and, in particular, the logical sequence of filters, 

and 

Whether changes to the approach could set priorities more 

efficiently and effectively

Question 1. Overall Prioritization Approach

Section 2.2; also see Section 9
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2.1 Please comment on the proposed exclusion criteria for each 

physicochemical property as appropriate for identifying 

chemicals that are untestable and/or unable to elicit systemic 

toxicity. Please include a discussion of the extent to which 

varying the range of exclusion criterion can influence confidence 

in identifying chemicals that are untestable and/or unable to 

elicit systemic effects (i.e., those substances that are unlikely to 

trigger the molecular initiating event). Please include in your 

comments: 

Whether there are additional chemical characteristics that 

should be considered (e.g., volatility),

Whether there are additional data sources for each 

parameter identified (e.g., ChemAxon for pKa values, 

EpiSuite for half life values, etc.), and how to consider 

multiple data sources in a weight of evidence approach.

Question 2. Physicochemical Properties

Section 2.2.2
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2.1 (Continued)

Whether the exclusion criteria cut offs and the confidence 

that application of the exclusion criteria will reasonably 

identify those substances that are untestable and/or unable 

to trigger the molecular initiating event of the ER pathway. 

Also please discuss options for evaluating cases where 

uncertainty in a chemical’s specific parameter range 

overlaps a p-chem filter cut off. Please consider in your 

comments the following exclusion criteria:

- pKa values <2 or >11.5;

- Hydrolysis half life of <40 days and

- Charged species of 99% or greater at pH 7

Question 2. Physicochemical Properties

Section 2.2.2
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3.1 Please comment on the approach used to build ESv2 through 

chemical testing and effect-based category and read across 

methods to provide a scientifically defensible approach to 

predict ER binding potential for a larger number of chemical 

groups, particularly with regard to defining new groups from 

within the Mixed Organics and Mixed Phenols. Please indicate 

any considerations unique to ESv2 that indicate the approach 

used to develop ESv1 (SAP, 2009a) needs to be modified.

3.2 Building from the ESv1 training set, please comment on the level 

of scientific confidence that a chemical is unlikely to initiate the 

ER AOP, if the in vitro assay TrSet data shows no activity. Please 

comment on the extent to which the level of confidence may 

vary by chemical category.

Question 3. ER Expert System Development 

Section 3
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The agency is proposing to use the HTP data to expand the ER expert system 

(i.e., ESv3). Therefore, it is important to understand how the HTP data are 

generated and interpreted for the intended use. 

4.1 Given the importance of a well-defined endpoint to determining if/how 

endpoint data are appropriately used, the panel is asked to comment on:

Whether the assays are sufficiently described so that others can 

reconstruct the assay conditions and data analysis and to what 

extent additional information would be useful?

Whether EPA has described sufficiently the important experimental 

conditions that affect the assay measurements, and whether EPA 

has sufficiently discussed their potential impact on assay results 

and interpretation of the results?

Question 4. Overall Prioritization Approach

Sections 4-6
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The agency is proposing to use the HTP data to expand the ER expert system 

(i.e., ESv3). Therefore, it is important to understand how the HTP data are 

generated and interpreted for the intended use. 

4.1 (Continued)

Whether the chemical library (e.g., purity and analysis), chemical 

exposure (e.g., solvents used, chemical dilutions), and plates and 

plate layouts provides information necessary for data 

interpretation?

The adequacy of test concentrations (maximum and minimum 

concentration tested) and cutoffs, and whether the concentration 

cutoffs affected some assays results more than others, especially in 

the context of false negatives. 

Question 4. Overall Prioritization Approach

Sections 4-6
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The agency is proposing to use the HTP data to expand the ER expert system 

(i.e., ESv3). Therefore, it is important to understand how the HTP data are 

generated and interpreted for the intended use. 

4.2 With respect to data interpretation, please comment on the approach 

for defining an active chemical (i.e., to initiate the ER AOP) and an 

inactive chemical (i.e., unlikely to initiate the ER AOP) compound and 

whether the method of data interpretation is adequately described and 

if the rationale for the approach is sufficiently presented. Please include 

in your comments:

The adequacy of the approach to generate the data plots; how and 

what parameters are calculated, etc.,

How the background data were used to establish the control level, 

Whether the process for identifying assay interference is 

adequately described, 

Adequacy of data normalization, outlier identification, curve fitting, 

background subtractions, and all other data processing and 

calculation techniques, and appropriateness of the statistical 

analyses. 

Question 4. Overall Prioritization Approach

Sections 4-6
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The agency is proposing to use the HTP data to expand the ER expert system 

(i.e., ESv3). Therefore, it is important to understand how the HTP data are 

generated and interpreted for the intended use. 

4.3 Would you recommend other considerations or approaches to analyzing 

the HTP data? 

Question 4. Overall Prioritization Approach

Sections 4-6
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5.1 Please comment on the selection of reference chemicals and 

whether they are sufficient to assess the performance of each 

HTP assay for ER agonists. How well do the reference chemicals 

represent the range of potencies needed to establish the 

reliability and relevance of these assays for use in EDSP chemical 

prioritization for the inert ingredients, fragrances, and SDWA 

chemicals? 

5.2 Please comment on whether the Agency’s evaluation of the 

performance of the HTP ER binding and activation assays has 

considered and accurately assessed all relevant aspects of the 

assays. For example, have signal-to-noise ratios, background 

subtraction and interferences been adequately characterized 

when describing the strengths and limitations of the assay?

Question 5. Performance Evaluation of the HTP 

ER Binding and Transcriptional 

Activation Assays Against a Set of 

Reference Chemicals 

Section 6
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5.3 Based on analyses in sections 5 and 6, please comment on the 

comparative performance of the 8 HTP assays for detecting ER 

reference agonists (e.g., do some assays perform differently, and 

if so to what extent?) Was sufficiently detailed information 

provided explaining the likely reasons for assay differences, 

when they are observed (e.g., cutoffs, assay interferences, 

background differences)?

Question 5. Performance Evaluation of the HTP 

ER Binding and Transcriptional 

Activation Assays Against a Set of 

Reference Chemicals 

Section 6
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6.1 Please comment on the agency’s assessment of how HTP in vitro 

assays performed with respect to expectations of performance 

for chemicals within chemical categories when compared with 

the in vitro training set data used to build the ESv1/2. 

6.2 Please comment on EPA's approach to comparing the ES TrSet

data with the HTP data and the interpretations regarding 

discordant results between the two assay approaches. Please 

recommend other considerations or approaches to conducting 

this comparative analysis?

6.3 Given that there may be varying occurrences of false negatives 

and false positives based on different sources of training set 

data, please include in your comments options for addressing 

these uncertainties for different categories in the context of 

building ESv3? 

Question 6. Analysis of ER Expert Training Set 

and HTP in vitro Assay Data 

Section 7
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7.1 Please comment on the adequacy and efficiency of the category 

based approach to select chemicals for testing to expand the 

training sets in terms of covering the ~1700 chemicals not 

covered in the domain of ESv2.

7.2 Based on the HTP assay performance (analysis of reference 

chemicals and comparative analysis with the ES TrSet), please 

comment on the adequacy of the HTP data for advancing the ER 

expert system’s rules to cover the additional groups of chemicals 

in ESv3.

Question 7. Category-Based Approach and 

Strategic Testing to Expand the ES 

applicability domain with 

additional in vitro data 

Section 8
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7.3 To the extent there are differences between the ES TrSet and 

HTP data in detecting the ability of chemicals to initiate the ER 

AOP, especially in the context of minimizing ‘false negatives’ for 

low potency compounds, please comment on the strengths and 

limitations of combining data from the different assays to 

generate training set data for building the structure based rules 

within the ESv3. What are the strengths and limitations of using 

training set data from assays that have the same or similar 

degree of sensitivity. 

Question 7. Category-Based Approach and 

Strategic Testing to Expand the ES 

applicability domain with 

additional in vitro data 

Section 8
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8.1 Please provide any initial thoughts on how varying empirical 

and/or computational techniques could be employed to account 

for metabolites that may trigger the ER MIE. 

Question 8. In Vitro Testing and Computer 

Based Simulations:

Addressing Active Metabolites

Section 7.4.3
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9.1 Please comment on whether the principles and concepts used to 

develop the ER expert system are generally applicable for any 

category-based prioritization system for other molecular 

initiating events (e.g., other AOPs for perturbing estrogen, 

androgen receptor, and thyroid hormone systems)? 

9.2 What lessons have been learned from the development of the 

ER focused prioritization model that will facilitate more efficient 

and effective development of an effect-based prioritization 

model for the androgen pathway.

9.3 What will be the challenges in developing a prioritization using in 

vitro methods and computer based simulations for the thyroid 

hormone system? 

Question 9. Use of the AOP and CategoryBased Testing Strategies for Other 

Endocrine Pathways

Section 9