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Marchetti F, Cardoso R, Chen CL, Douglas GR, Elloway J, Escobar PA, Harper T, Heflich RH, Kidd D, Lynch AM, Myers MB, Parsons BL, Salk JJ, Settivari RS, Smith-Roe SL, Witt KL, Yauk CL, Young R, Zhang S, Minocherhomji S. Error-corrected next generation sequencing - Promises and challenges for genotoxicity and cancer risk assessment. Mutat Res Rev Mutat Res 2023; 792:108466. [PMID: 37643677 DOI: 10.1016/j.mrrev.2023.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Error-corrected Next Generation Sequencing (ecNGS) is rapidly emerging as a valuable, highly sensitive and accurate method for detecting and characterizing mutations in any cell type, tissue or organism from which DNA can be isolated. Recent mutagenicity and carcinogenicity studies have used ecNGS to quantify drug-/chemical-induced mutations and mutational spectra associated with cancer risk. ecNGS has potential applications in genotoxicity assessment as a new readout for traditional models, for mutagenesis studies in 3D organotypic cultures, and for detecting off-target effects of gene editing tools. Additionally, early data suggest that ecNGS can measure clonal expansion of mutations as a mechanism-agnostic early marker of carcinogenic potential and can evaluate mutational load directly in human biomonitoring studies. In this review, we discuss promising applications, challenges, limitations, and key data initiatives needed to enable regulatory testing and adoption of ecNGS - including for advancing safety assessment, augmenting weight-of-evidence for mutagenicity and carcinogenicity mechanisms, identifying early biomarkers of cancer risk, and managing human health risk from chemical exposures.
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Affiliation(s)
| | | | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, DC, USA.
| | | | - Joanne Elloway
- Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Tod Harper
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Robert H Heflich
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Darren Kidd
- Labcorp Early Development Laboratories Limited, Harrogate, North Yorkshire, UK
| | | | - Meagan B Myers
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Barbara L Parsons
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | | | | | | | - Kristine L Witt
- NIEHS, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | | | - Robert Young
- MilliporeSigma, Rockville, MD, USA; Current: Consultant, Bethesda, MD, USA
| | | | - Sheroy Minocherhomji
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA; Current: Eli Lilly and Company, Indianapolis, IN, USA
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