Joel Bercu1, Melisa J Masuda Herrera1, Alejandra Trejo-Martin1, Catrin Hasselgren2, Jean Lord3, Jessica Graham4, Matthew Schmitz5, Lawrence Milchak6, Colin Owens6, Surya Hari Lal7, Richard Marchese Robinson7, Sarah Whalley7, Phillip Bellion8, Anna Vuorinen8, Kamila Gromek9, William A Hawkins10, Iris Van de Gevel11, Kathleen Vriens11, Raymond Kemper12, Russell Naven12, Pierre Ferrer13, Glenn J Myatt14. 1. Gilead Sciences, 333 Lakeside Drive, Foster City, CA, USA. 2. Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA. 3. Ultragenyx, 60 Leveroni Court, Novato, CA, 94949, USA. 4. Bristol Myers Squibb, Drug Safety Evaluation, 1 Squibb Dr, New Brunswick, NJ, 08903, USA. 5. AbbVie Inc., North Chicago, IL, USA. 6. 3M Company, 3M Center, St. Paul, MN, 55144-1000, USA. 7. Syngenta Crop Protection, Product Safety Department, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK. 8. DSM Nutritional Products, Kaiseraugst, Switzerland. 9. Galapagos SASU, 102 Avenue Gaston Roussel, 93230, Romainville, France. 10. GlaxoSmithKline, Park Road, Ware, Hertfordshire, SG12 0DP, United Kingdom. 11. Janssen Pharmaceutical Companies of Johnson & Johnson, 2340, Beerse, Belgium. 12. Vertex Pharmaceuticals Inc., Discovery and Investigative Toxicology, 50 Northern Ave, Boston, MA, USA. 13. Department of Veterinary Physiology and Pharmacology, Interdisciplinary Faculty of Toxicology Program, Texas A&M University, 4466 TAMU, College Station, TX, 77843-4466, USA. 14. Leadscope (an Instem Company), 1393 Dublin Rd, Columbus, OH, 43215, USA. Electronic address: glenn.myatt@instem.com.
The study presented in Bercu et al. (2021)
was designed to understand whether (Quantitative) Structure-Activity Relationship
((Q)SAR) models are fit-for-purpose to use as part of classification and labelling. To
test this hypothesis, proprietary and marketed data on rat oral acute toxicity from 10
organizations representing chemicals typically assessed was compiled and run through
(Q)SAR models developed by Leadscope (an Instem company). The experimental and
prediction data from all collaborators was then combined and an assessment of whether
these models are fit-for-purpose was made based on their performance. In addition, an
expert review was performed and documented on a subset of the chemicals. Based on this
information, a decision tree was presented that showed how these models could be used to
support classification and labelling decisions. A reassessment of the results from one
of the collaborators was recently performed because: (a) some compounds were identified
as belonging to the (Q)SAR training sets; (b) some compounds were found to be duplicates
following computation of InChIs; (c) integration with a more highly curated set of
experimental data led to the experimental labels being updated for some compounds. The
revised results were then combined with other collaborators’ results. The revised
results do not change the conclusions or recommendations of the paper based on both the
overall and subset specific balanced statistics for the consensus predictions. For
example, the original abstract stated that approximately 95% of chemicals were either
correctly predicted or predicted in a more conservative GHS category, after removing a
small fraction of inconclusive - meaning indeterminate or out of domain - predictions.
In the original analysis this value was 94.82% whereas in the revised analysis the
figure is 94.84%. Similarly, in the original analysis, the average percentage of these
compounds, across all well-defined experimental categories, which were assigned to a
correct or more conservative category was around 80%. Excluding the two GHS category 1
compounds, since two compounds are too few to obtain robust statistics, the average
percentage of these compounds which are assigned to a correct or more conservative
category is 78%. The following figures and tables have been updated to reflect these
changes: Fig. 4, Tables 2–6, supplemental materials Tables
s1–s22. These
figures and tables are included in the supplemental material.
Authors: Joel Bercu; Melisa J Masuda-Herrera; Alejandra Trejo-Martin; Catrin Hasselgren; Jean Lord; Jessica Graham; Matthew Schmitz; Lawrence Milchak; Colin Owens; Surya Hari Lal; Richard Marchese Robinson; Sarah Whalley; Phillip Bellion; Anna Vuorinen; Kamila Gromek; William A Hawkins; Iris van de Gevel; Kathleen Vriens; Raymond Kemper; Russell Naven; Pierre Ferrer; Glenn J Myatt Journal: Regul Toxicol Pharmacol Date: 2020-12-17 Impact factor: 3.271