NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Auerbach S, Casey W, Chang D, et al. Standard Methods for Development of EPA Transcriptomic Assessment Products (ETAPs). Washington (DC): U.S. Environmental Protection Agency; 2024 Mar.

5REFERENCES

  1. Bhat VS, Hester SD, Nesnow S, Eastmond DA. 2013. Concordance of transcriptional and apical benchmark dose levels for conazole-induced liver effects in mice. Toxicol Sci 136:205–215. [PubMed: 23970803]
  2. Bianchi E, Costa E, Yan ZJ, Murphy L, Howell J, Anderson D, et al. 2021. A rat subchronic study transcriptional point of departure estimates a carcinogenicity study apical point of departure. Food Chem Toxicol 147:111869. [PubMed: 33217531]
  3. Cannizzo MD, Wood CE, Hester SD, Wehmas LC. 2022. Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicol Rep 9:883–894. [PMC free article: PMC9742836] [PubMed: 36518475]
  4. Chepelev NL, Gagné R, Maynor T, Kuo B, Hobbs CA, Recio L, et al. 2017. Transcriptional profiling of male F344 rats suggests the involvement of calcium signaling in the mode of action of acrylamide-induced thyroid cancer. Food Chem Toxicol 107:186–200. [PubMed: 28606764]
  5. Chepelev NL, Gagné R, Maynor T, Kuo B, Hobbs CA, Recio L, et al. 2018. Transcriptional profiling of male CD-1 mouse lungs and Harderian glands supports the involvement of calcium signaling in acrylamide-induced tumors. Regul Toxicol Pharmacol 95:75–90. [PubMed: 29475067]
  6. Clewell HJ, Efremenko A, Campbell JL, Dodd DE, Thomas RS. 2014. Transcriptional responses in the rat nasal epithelium following subchronic inhalation of naphthalene vapor. Toxicol Appl Pharmacol 280:78–85. [PubMed: 24976557]
  7. Dong H, Gill S, Curran IH, Williams A, Kuo B, Wade MG, et al. 2016. Toxicogenomic assessment of liver responses following subchronic exposure to furan in Fischer F344 rats. Arch Toxicol 90:1351–1367. [PMC free article: PMC4873526] [PubMed: 26194646]
  8. Dunnick JK, Shockley KR, Morgan DL, Brix A, Travlos GS, Gerrish K, et al. 2017. Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats. Arch Toxicol 91:1685–1696. [PMC free article: PMC5364093] [PubMed: 27638505]
  9. EPA. 1988. Recommendations for and Documentation of Biological Values for Use in Risk Assessment. EPA/600/6-87/008. CinCinnati, OH:U.S. Environmental Protection Agency.
  10. EPA. 1994. Methods for derivation of inhalation reference concentrations and application of inhalation dosimetry. EPA/600/8-90/066F. Research Triangle Park, NC:U.S. Environmental Protection Agency.
  11. EPA. 2000. Risk Characterization Handbook. EPA/100/B-00/002. Research Triangle Park, NC:U.S. Environmental Protection Agency.
  12. EPA. 2002. A Review of the Reference Dose and Reference Concentration Processes. EPA/630/P-02/002F. Washington, DC:US Environmental Protection Agency.
  13. EPA. 2011a. Recommended use of body weight 3/4 as the default method in derivation of the oral reference dose. EPA/100/R-11/0001. Washington, DC:U.S. Environmental Protection Agency.
  14. EPA. 2011b. Exposure Factors Handbook. EPA/600/R-09/052F. Washington, DC:U.S. Environmental Protection Agency.
  15. EPA. 2012. Benchmark Dose Technical Guidance. EPA/100/R-12/001. Washington, DC:U.S. Environmental Protection Agency.
  16. EPA. 2014. Guidance for Applying Quantitative Data to Develop Data-Derived Extrapolation Factors for Interspecies and Intraspecies Extrapolation. EPA/100/R-14/002F. Washington, DC:U.S. Environmental Protection Agency.
  17. EPA. 2022. ORD Staff Handook for Developing IRIS Assessments. EPA 600/R-22/268. Research Triangle Park, NC:U.S. Environmental Protection Agency.
  18. EPA. 2024. Scientific Studies Supporting Development of Transcriptomic Points of Departure for EPA Transcriptomic Assessment Products (ETAPs). EPA/600/X-23/084. Research Triangle Park, NC:U.S. Environmental Protection Agency.
  19. Gwinn WM, Auerbach SS, Parham F, Stout MD, Waidyanatha S, Mutlu E, et al. 2020. Evaluation of 5-day In Vivo Rat Liver and Kidney With High-throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes. Toxicol Sci 176:343–354. [PMC free article: PMC7416315] [PubMed: 32492150]
  20. Harrill JA, Everett LJ, Haggard DE, Sheffield T, Bundy JL, Willis CM, et al. 2021a. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. Toxicol Sci 181:68–89. [PMC free article: PMC10194851] [PubMed: 33538836]
  21. Harrill JA, Viant MR, Yauk CL, Sachana M, Gant TW, Auerbach SS, et al. 2021b. Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. Regul Toxicol Pharmacol 125:105020. [PMC free article: PMC8808338] [PubMed: 34333066]
  22. Howard BE, Phillips J, Miller K, Tandon A, Mav D, Shah MR, et al. 2016. SWIFT-Review: a text-mining workbench for systematic review. Systematic Reviews 5:87. [PMC free article: PMC4877757] [PubMed: 27216467]
  23. Jackson AF, Williams A, Recio L, Waters MD, Lambert IB, Yauk CL. 2014. Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan. Toxicol Appl Pharmacol 274:63–77. [PubMed: 24183702]
  24. Johnson KJ, Auerbach SS, Costa E. 2020. A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-liver Apical Point of Departure. Toxicol Sci 176:86–102. [PMC free article: PMC7357187] [PubMed: 32384157]
  25. Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. [PMC free article: PMC4655817] [PubMed: 25751142]
  26. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907–915. [PMC free article: PMC7605509] [PubMed: 31375807]
  27. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. [PMC free article: PMC2723002] [PubMed: 19505943]
  28. Lowe CN, Isaacs KK, McEachran A, Grulke CM, Sobus JR, Ulrich EM, et al. 2021. Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis. Anal Bioanal Chem 413:7495–7508. [PMC free article: PMC9589520] [PubMed: 34648052]
  29. Mansouri K, Grulke CM, Judson RS, Williams AJ. 2018. OPERA models for predicting physicochemical properties and environmental fate endpoints. J Cheminform 10:10. [PMC free article: PMC5843579] [PubMed: 29520515]
  30. Mansouri K, Cariello NF, Korotcov A, Tkachenko V, Grulke CM, Sprankle CS, et al. 2019. Open-source QSAR models for pKa prediction using multiple machine learning approaches. J Cheminform 11:60. [PMC free article: PMC6749653] [PubMed: 33430972]
  31. Moffat I, Chepelev N, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, et al. 2015. Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol 45:1–43. [PMC free article: PMC4521608] [PubMed: 25605026]
  32. Morgan RL, Whaley P, Thayer KA, Schunemann HJ. 2018. Identifying the PECO: A framework for formulating good questions to explore the association of environmental and other exposures with health outcomes. Environ Int 121:1027–1031. [PMC free article: PMC6908441] [PubMed: 30166065]
  33. NASEM. 2007. Toxicity Testing in the 21st Century: A Vision and a Strategy. Washington, D.C.:National Academies of Sciences, Engineering, and Medicine.
  34. NASEM. 2011. Guide for the Care and Use of Laboratory Animals. Washington, DC:U.S. National Academies of Sciences, Engineering, and Medicine.
  35. NTP. 2018. NTP Research Report on National Toxicology Program Approach to Genomic Dose-Response Modeling. NTP-RR-5. Research Triangle Park, NC:National Toxicology Program, U.S. Department of Health and Human Services. [PubMed: 30321009]
  36. OECD. 2022. OECD Omics Reporting Framework Guidance Document - DRAFT. Paris:Organization for Economic Cooperation and Development.
  37. Phillips JR, Svoboda DL, Tandon A, Patel S, Sedykh A, Mav D, et al. 2019. BMDExpress 2: enhanced transcriptomic dose-response analysis workflow. Bioinformatics 35:1780–1782. [PMC free article: PMC6513160] [PubMed: 30329029]
  38. Recio L, Friedman M, Marroni D, Maynor T, Chepelev NL. 2017. Impact of Acrylamide on Calcium Signaling and Cytoskeletal Filaments in Testes From F344 Rat. Int J Toxicol 36:124–132. [PubMed: 28403741]
  39. Rowlands JC, Budinsky R, Gollapudi B, Black MB, Wolfinger RD, Cukovic D, et al. 2013. A genomics-based analysis of relative potencies of dioxin-like compounds in primary rat hepatocytes. Toxicol Sci 136:595–604. [PubMed: 24046277]
  40. Shockley KR, Cora MC, Malarkey DE, Jackson-Humbles D, Vallant M, Collins BJ, et al. 2020. Comparative toxicity and liver transcriptomics of legacy and emerging brominated flame retardants following 5-day exposure in the rat. Toxicol Lett 332:222–234. [PMC free article: PMC7903589] [PubMed: 32679240]
  41. Thayer KA, Angrish M, Arzuaga X, Carlson LM, Davis A, Dishaw L, et al. 2022a. Systematic evidence map (SEM) template: Report format and methods used for the US EPA Integrated Risk Information System (IRIS) program, Provisional Peer Reviewed Toxicity Value (PPRTV) program, and other “fit for purpose” literature-based human health analyses. Environ Int 169:107468. [PubMed: 36174483]
  42. Thayer KA, Shaffer RM, Angrish M, Arzuaga X, Carlson LM, Davis A, et al. 2022b. Use of systematic evidence maps within the US environmental protection agency (EPA) integrated risk information system (IRIS) program: Advancements to date and looking ahead. Environ Int 169:107363. [PubMed: 36057470]
  43. Thomas RS, Allen BC, Nong A, Yang L, Bermudez E, Clewell HJ, 3rd, et al. 2007. A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure. Toxicol Sci 98:240–248. [PubMed: 17449896]
  44. Thomas RS, Clewell HJ, 3rd, Allen BC, Wesselkamper SC, Wang NC, Lambert JC, et al. 2011. Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment. Toxicol Sci 120:194–205. [PubMed: 21097997]
  45. Thomas RS, Himmelstein MW, Clewell HJ, 3rd, Yang Y, Healy E, Black MB, et al. 2013a. Cross-species transcriptomic analysis of mouse and rat lung exposed to chloroprene. Toxicol Sci 131:629–640. [PubMed: 23125180]
  46. Thomas RS, Wesselkamper SC, Wang NC, Zhao QJ, Petersen DD, Lambert JC, et al. 2013b. Temporal concordance between apical and transcriptional points of departure for chemical risk assessment. Toxicol Sci 134:180–194. [PubMed: 23596260]
  47. Yang L, Allen BC, Thomas RS. 2007. BMDExpress: a software tool for the benchmark dose analyses of genomic data. BMC Genomics 8:387. [PMC free article: PMC2198920] [PubMed: 17961223]
  48. Zhou YH, Cichocki JA, Soldatow VY, Scholl EH, Gallins PJ, Jima D, et al. 2017. Editor’s Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse. Toxicol Sci 160:95–110. [PMC free article: PMC5837274] [PubMed: 28973375]