Next Generation Sequencing Data for Use in Risk Assessment

Overview

Journal Curr Opin Toxicol

Date 2019 May 7

PMID 31058248

Citations 6

Authors

B Alex Merrick

Affiliations

Soon will be listed here.

Abstract

Next generation sequencing (NGS) represents several powerful platforms that have revolutionized RNA and DNA analysis. The parallel sequencing of millions of DNA molecules can provide mechanistic insights into toxicology and provide new avenues for biomarker discovery with growing relevance for risk assessment. The evolution of NGS technologies has improved over the last decade with increased sensitivity and accuracy to foster new biomarker assays from tissue, blood and other biofluids. NGS sequencing technologies can identify transcriptional changes and genomic targets with base pair precision in response to chemical exposure. Further, there are several exciting movements within the toxicology community that incorporate NGS platforms into new strategies for more rapid toxicological characterizations. These include the Tox21 in vitro high throughput transcriptomic screening program, development of organotypic spheroids, alternative animal models, mining archival tissues, liquid biopsy and epigenomics. This review will describe NGS-based technologies, demonstrate how they can be used as tools for target discovery in tissue and blood, and suggest how they might be applied for risk assessment.

Citing Articles

A comparison of the TempO-Seq and Affymetrix microarray platform using RTqPCR validation.

Wehr M, Reamon-Buettner S, Ritter D, Knebel J, Niehof M, Escher S BMC Genomics. 2024; 25(1):669.

PMID: 38961363 PMC: 11223392. DOI: 10.1186/s12864-024-10586-7.

ICH S1 prospective evaluation study and weight of evidence assessments: commentary from industry representatives.

Vahle J, Dybowski J, Graziano M, Hisada S, Lebron J, Nolte T Front Toxicol. 2024; 6:1377990.

PMID: 38845817 PMC: 11153695. DOI: 10.3389/ftox.2024.1377990.

High-Throughput Screening to Advance In Vitro Toxicology: Accomplishments, Challenges, and Future Directions.

Lynch C, Sakamuru S, Ooka M, Huang R, Klumpp-Thomas C, Shinn P Annu Rev Pharmacol Toxicol. 2023; 64:191-209.

PMID: 37506331 PMC: 10822017. DOI: 10.1146/annurev-pharmtox-112122-104310.

Gene expression profiling after exposure to a chemical carcinogen, Pentabrominated Diphenyl Ether, at different life stages.

Shockley K, Dunnick J Front Toxicol. 2023; 4:1028309.

PMID: 36687508 PMC: 9847571. DOI: 10.3389/ftox.2022.1028309.

Genome-wide expression screening in the cardiac embryonic stem cell test shows additional differentiation routes that are regulated by morpholines and piperidines.

Mennen R, Hallmark N, Pallardy M, Bars R, Tinwell H, Piersma A Curr Res Toxicol. 2022; 3:100086.

PMID: 36157598 PMC: 9489494. DOI: 10.1016/j.crtox.2022.100086.

References

Mav D, Shah R, Howard B, Auerbach S, Bushel P, Collins J . A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS One. 2018; 13(2):e0191105. PMC: 5819766. DOI: 10.1371/journal.pone.0191105. View

Yin Y, Lan J, Zhang Q . Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA. Methods Mol Biol. 2018; 1802:101-113. DOI: 10.1007/978-1-4939-8546-3_7. View

Wehmas L, Wood C, Gagne R, Williams A, Yauk C, Gosink M . Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples. Toxicol Sci. 2017; 162(2):535-547. PMC: 6800129. DOI: 10.1093/toxsci/kfx278. View

Wilson V, Keshava N, Hester S, Segal D, Chiu W, Thompson C . Utilizing toxicogenomic data to understand chemical mechanism of action in risk assessment. Toxicol Appl Pharmacol. 2011; 271(3):299-308. DOI: 10.1016/j.taap.2011.01.017. View

Maslov A, Quispe-Tintaya W, Gorbacheva T, White R, Vijg J . High-throughput sequencing in mutation detection: A new generation of genotoxicity tests?. Mutat Res. 2015; 776:136-43. PMC: 4532622. DOI: 10.1016/j.mrfmmm.2015.03.014. View

Li C, Cui J . Regulation of protein-coding gene and long noncoding RNA pairs in liver of conventional and germ-free mice following oral PBDE exposure. PLoS One. 2018; 13(8):e0201387. PMC: 6070246. DOI: 10.1371/journal.pone.0201387. View

Ghosh R, Pandey T, Dey P . Liquid biopsy: A new avenue in pathology. Cytopathology. 2018; 30(2):138-143. DOI: 10.1111/cyt.12661. View

Cimino M . Comparative overview of current international strategies and guidelines for genetic toxicology testing for regulatory purposes. Environ Mol Mutagen. 2006; 47(5):362-90. DOI: 10.1002/em.20216. View

Nuwaysir E, Bittner M, Trent J, Barrett J, Afshari C . Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog. 1999; 24(3):153-9. DOI: 10.1002/(sici)1098-2744(199903)24:3<153::aid-mc1>3.0.co;2-p. View

10.

Israel J, Chappell G, Simon J, Pott S, Safi A, Lewis L . Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. Mamm Genome. 2018; 29(1-2):153-167. PMC: 6095468. DOI: 10.1007/s00335-018-9739-6. View

11.

Heather J, Chain B . The sequence of sequencers: The history of sequencing DNA. Genomics. 2015; 107(1):1-8. PMC: 4727787. DOI: 10.1016/j.ygeno.2015.11.003. View

12.

Wu M, Liu S, Hu L, Qu H, Pan C, Lei P . Global transcriptomic analysis of zebrafish in response to embryonic exposure to three antidepressants, amitriptyline, fluoxetine and mianserin. Aquat Toxicol. 2017; 192:274-283. DOI: 10.1016/j.aquatox.2017.09.027. View

13.

Gomy I, Diz M . Hereditary cancer risk assessment: insights and perspectives for the Next-Generation Sequencing era. Genet Mol Biol. 2016; 39(2):184-8. PMC: 4910549. DOI: 10.1590/1678-4685-GMB-2014-0346. View

14.

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D . Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biol. 2015; 16:133. PMC: 4506430. DOI: 10.1186/s13059-015-0694-1. View

15.

Hester S, Bhat V, Chorley B, Carswell G, Jones W, Wehmas L . Editor's Highlight: Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded Samples. Toxicol Sci. 2016; 154(2):202-213. DOI: 10.1093/toxsci/kfw161. View

16.

Feng Y, Zhang Y, Ying C, Wang D, Du C . Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics. 2015; 13(1):4-16. PMC: 4411503. DOI: 10.1016/j.gpb.2015.01.009. View

17.

Harrill A, McCullough S, Wood C, Kahle J, Chorley B . MicroRNA Biomarkers of Toxicity in Biological Matrices. Toxicol Sci. 2016; 152(2):264-72. DOI: 10.1093/toxsci/kfw090. View

18.

Fox E, Reid-Bayliss K, Emond M, Loeb L . Accuracy of Next Generation Sequencing Platforms. Next Gener Seq Appl. 2015; 1. PMC: 4331009. DOI: 10.4172/jngsa.1000106. View

19.

Phillips J, Svoboda D, Tandon A, Patel S, Sedykh A, Mav D . BMDExpress 2: enhanced transcriptomic dose-response analysis workflow. Bioinformatics. 2018; 35(10):1780-1782. PMC: 6513160. DOI: 10.1093/bioinformatics/bty878. View

20.

Gai W, Sun K . Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy. Genes (Basel). 2019; 10(1). PMC: 6356936. DOI: 10.3390/genes10010032. View