Nextcast: A software suite to analyse and model toxicogenomics data

Angela Serra; Laura Aliisa Saarimäki; Alisa Pavel; Giusy Del Giudice; Michele Fratello; Luca Cattelani; Antonio Federico; Omar Laurino; Veer Singh Marwah; Vittorio Fortino; Giovanni Scala; Pia Anneli Sofia Kinaret; Dario Greco

doi:10.1016/j.csbj.2022.03.014

Nextcast: A software suite to analyse and model toxicogenomics data

Comput Struct Biotechnol J. 2022 Mar 18:20:1413-1426. doi: 10.1016/j.csbj.2022.03.014. eCollection 2022.

Authors

Angela Serra^{1

2

3}, Laura Aliisa Saarimäki^{1

2

3}, Alisa Pavel^{1

2

3}, Giusy Del Giudice^{1

2

3}, Michele Fratello^{1

2

3}, Luca Cattelani^{1

2

3}, Antonio Federico^{1

2

3}, Omar Laurino⁴, Veer Singh Marwah^{1

2}, Vittorio Fortino⁵, Giovanni Scala^{1

2

6}, Pia Anneli Sofia Kinaret^{1

2

3

7}, Dario Greco^{1

2

3

7}

Affiliations

¹ Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
² BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland.
³ Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.
⁴ Freelance developer, Boston, USA.
⁵ Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
⁶ Department of Biology, University of Naples Federico II, Naples, Italy.
⁷ Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Abstract

The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).

Keywords: Computational toxicology; Nextcast; Pipeline; Predictive toxicology; Software suite; Toxicogenomics.