Literature DB >> 28987912

Framework for the quality assurance of 'omics technologies considering GLP requirements.

Hans-Martin Kauffmann1, Hennicke Kamp1, Regine Fuchs2, Brian N Chorley3, Lize Deferme4, Timothy Ebbels5, Jörg Hackermüller6, Stefania Perdichizzi7, Alan Poole8, Ursula G Sauer9, Knut E Tollefsen10, Tewes Tralau11, Carole Yauk12, Ben van Ravenzwaay13.   

Abstract

'Omics technologies are gaining importance to support regulatory toxicity studies. Prerequisites for performing 'omics studies considering GLP principles were discussed at the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) Workshop Applying 'omics technologies in Chemical Risk Assessment. A GLP environment comprises a standard operating procedure system, proper pre-planning and documentation, and inspections of independent quality assurance staff. To prevent uncontrolled data changes, the raw data obtained in the respective 'omics data recording systems have to be specifically defined. Further requirements include transparent and reproducible data processing steps, and safe data storage and archiving procedures. The software for data recording and processing should be validated, and data changes should be traceable or disabled. GLP-compliant quality assurance of 'omics technologies appears feasible for many GLP requirements. However, challenges include (i) defining, storing, and archiving the raw data; (ii) transparent descriptions of data processing steps; (iii) software validation; and (iv) ensuring complete reproducibility of final results with respect to raw data. Nevertheless, 'omics studies can be supported by quality measures (e.g., GLP principles) to ensure quality control, reproducibility and traceability of experiments. This enables regulators to use 'omics data in a fit-for-purpose context, which enhances their applicability for risk assessment.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Data storage; Documentation; Good laboratory practice (GLP); Independent quality assurance; Quality assurance inspection; Raw data definition; Reproducibility; Software validation; Standard operating procedure

Mesh:

Year:  2017        PMID: 28987912      PMCID: PMC6816020          DOI: 10.1016/j.yrtph.2017.10.007

Source DB:  PubMed          Journal:  Regul Toxicol Pharmacol        ISSN: 0273-2300            Impact factor:   3.271


  6 in total

1.  Metabolomics: a tool for early detection of toxicological effects and an opportunity for biology based grouping of chemicals-from QSAR to QBAR.

Authors:  B van Ravenzwaay; M Herold; H Kamp; M D Kapp; E Fabian; R Looser; G Krennrich; W Mellert; A Prokoudine; V Strauss; T Walk; J Wiemer
Journal:  Mutat Res       Date:  2012-01-26       Impact factor: 2.433

2.  Metabolomics as read-across tool: A case study with phenoxy herbicides.

Authors:  B van Ravenzwaay; S Sperber; O Lemke; E Fabian; F Faulhammer; H Kamp; W Mellert; V Strauss; A Strigun; E Peter; M Spitzer; T Walk
Journal:  Regul Toxicol Pharmacol       Date:  2016-09-13       Impact factor: 3.271

Review 3.  Framework for the quantitative weight-of-evidence analysis of 'omics data for regulatory purposes.

Authors:  Jim Bridges; Ursula G Sauer; Roland Buesen; Lize Deferme; Knut E Tollefsen; Tewes Tralau; Ben van Ravenzwaay; Alan Poole; Mark Pemberton
Journal:  Regul Toxicol Pharmacol       Date:  2017-10-14       Impact factor: 3.271

Review 4.  The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook.

Authors:  Ursula G Sauer; Lize Deferme; Laura Gribaldo; Jörg Hackermüller; Tewes Tralau; Ben van Ravenzwaay; Carole Yauk; Alan Poole; Weida Tong; Timothy W Gant
Journal:  Regul Toxicol Pharmacol       Date:  2017-09-18       Impact factor: 3.271

Review 5.  Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop.

Authors:  Roland Buesen; Brian N Chorley; Beatriz da Silva Lima; George Daston; Lize Deferme; Timothy Ebbels; Timothy W Gant; Amber Goetz; John Greally; Laura Gribaldo; Jörg Hackermüller; Bruno Hubesch; Danyel Jennen; Kamin Johnson; Jun Kanno; Hans-Martin Kauffmann; Madeleine Laffont; Patrick McMullen; Richard Meehan; Mark Pemberton; Stefania Perdichizzi; Aldert H Piersma; Ursula G Sauer; Kerstin Schmidt; Hervé Seitz; Kayo Sumida; Knut E Tollefsen; Weida Tong; Tewes Tralau; Ben van Ravenzwaay; Ralf J M Weber; Andrew Worth; Carole Yauk; Alan Poole
Journal:  Regul Toxicol Pharmacol       Date:  2017-09-25       Impact factor: 3.271

Review 6.  A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.

Authors:  Timothy W Gant; Ursula G Sauer; Shu-Dong Zhang; Brian N Chorley; Jörg Hackermüller; Stefania Perdichizzi; Knut E Tollefsen; Ben van Ravenzwaay; Carole Yauk; Weida Tong; Alan Poole
Journal:  Regul Toxicol Pharmacol       Date:  2017-11-04       Impact factor: 3.271

  6 in total
  7 in total

1.  Building a Quality Management System in a Core Facility: A Genomics Core Case Study.

Authors:  Christopher W Gregory
Journal:  J Biomol Tech       Date:  2020-07

Review 2.  Mode of action-based risk assessment of genotoxic carcinogens.

Authors:  Andrea Hartwig; Michael Arand; Bernd Epe; Sabine Guth; Gunnar Jahnke; Alfonso Lampen; Hans-Jörg Martus; Bernhard Monien; Ivonne M C M Rietjens; Simone Schmitz-Spanke; Gerlinde Schriever-Schwemmer; Pablo Steinberg; Gerhard Eisenbrand
Journal:  Arch Toxicol       Date:  2020-06-15       Impact factor: 5.153

3.  A cross-sector call to improve carcinogenicity risk assessment through use of genomic methodologies.

Authors:  Carole L Yauk; Alison H Harrill; Heidrun Ellinger-Ziegelbauer; Jan Willem van der Laan; Jonathan Moggs; Roland Froetschl; Frank Sistare; Syril Pettit
Journal:  Regul Toxicol Pharmacol       Date:  2019-11-11       Impact factor: 3.271

Review 4.  Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop.

Authors:  Roland Buesen; Brian N Chorley; Beatriz da Silva Lima; George Daston; Lize Deferme; Timothy Ebbels; Timothy W Gant; Amber Goetz; John Greally; Laura Gribaldo; Jörg Hackermüller; Bruno Hubesch; Danyel Jennen; Kamin Johnson; Jun Kanno; Hans-Martin Kauffmann; Madeleine Laffont; Patrick McMullen; Richard Meehan; Mark Pemberton; Stefania Perdichizzi; Aldert H Piersma; Ursula G Sauer; Kerstin Schmidt; Hervé Seitz; Kayo Sumida; Knut E Tollefsen; Weida Tong; Tewes Tralau; Ben van Ravenzwaay; Ralf J M Weber; Andrew Worth; Carole Yauk; Alan Poole
Journal:  Regul Toxicol Pharmacol       Date:  2017-09-25       Impact factor: 3.271

5.  Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC-MS based untargeted metabolomics practitioners.

Authors:  Anne M Evans; Claire O'Donovan; Mary Playdon; Chris Beecher; Richard D Beger; John A Bowden; David Broadhurst; Clary B Clish; Surendra Dasari; Warwick B Dunn; Julian L Griffin; Thomas Hartung; Ping- Ching Hsu; Tao Huan; Judith Jans; Christina M Jones; Maureen Kachman; Andre Kleensang; Matthew R Lewis; María Eugenia Monge; Jonathan D Mosley; Eric Taylor; Fariba Tayyari; Georgios Theodoridis; Federico Torta; Baljit K Ubhi; Dajana Vuckovic
Journal:  Metabolomics       Date:  2020-10-12       Impact factor: 4.290

Review 6.  Use cases, best practice and reporting standards for metabolomics in regulatory toxicology.

Authors:  Mark R Viant; Timothy M D Ebbels; Richard D Beger; Drew R Ekman; David J T Epps; Hennicke Kamp; Pim E G Leonards; George D Loizou; James I MacRae; Bennard van Ravenzwaay; Philippe Rocca-Serra; Reza M Salek; Tilmann Walk; Ralf J M Weber
Journal:  Nat Commun       Date:  2019-07-10       Impact factor: 17.694

Review 7.  Beyond genomics: understanding exposotypes through metabolomics.

Authors:  Nicholas J W Rattray; Nicole C Deziel; Joshua D Wallach; Sajid A Khan; Vasilis Vasiliou; John P A Ioannidis; Caroline H Johnson
Journal:  Hum Genomics       Date:  2018-01-26       Impact factor: 4.639

  7 in total

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