Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier

J.P. van Dijk, C.S. de Mello, M.M. Voorthuijzen, R.C.B. Hutten, A.C. Maisonnave Arisi, J.J. Jansen, L.M.C. Buydens, H. van der Voet, E.J. Kok

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

Abstract

An important part of the current hazard identification of novel plant varieties is comparative targeted analysis of the novel and reference varieties. Comparative analysis will become much more informative with unbiased analytical approaches, e.g. omics profiling. Data analysis estimating the similarity of new varieties to a reference baseline class of known safe varieties would subsequently greatly facilitate hazard identification. Further biological and eventually toxicological analysis would then only be necessary for varieties that fall outside this reference class. For this purpose, a one-class classifier tool was explored to assess and classify transcriptome profiles of potato (Solanum tuberosum) varieties in a model study. Profiles of six different varieties, two locations of growth, two year of harvest and including biological and technical replication were used to build the model. Two scenarios were applied representing evaluation of a ’different’ variety and a ‘similar’ variety. Within the model higher class distances resulted for the ‘different’ test set compared with the ‘similar’ test set. The present study may contribute to a more global hazard identification of novel plant varieties
Original languageEnglish
Pages (from-to)297-303
JournalRegulatory Toxicology and Pharmacology
Volume70
Issue number1
DOIs
Publication statusPublished - 2014

Fingerprint

Solanum tuberosum
Hazards
Classifiers
Safety
Transcriptome
Toxicology
Growth

Keywords

  • potato-tubers
  • microarray data
  • risk-assessment
  • food
  • identification
  • components
  • gene

Cite this

van Dijk, J.P. ; de Mello, C.S. ; Voorthuijzen, M.M. ; Hutten, R.C.B. ; Maisonnave Arisi, A.C. ; Jansen, J.J. ; Buydens, L.M.C. ; van der Voet, H. ; Kok, E.J. / Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier. In: Regulatory Toxicology and Pharmacology. 2014 ; Vol. 70, No. 1. pp. 297-303.
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Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier. / van Dijk, J.P.; de Mello, C.S.; Voorthuijzen, M.M.; Hutten, R.C.B.; Maisonnave Arisi, A.C.; Jansen, J.J.; Buydens, L.M.C.; van der Voet, H.; Kok, E.J.

In: Regulatory Toxicology and Pharmacology, Vol. 70, No. 1, 2014, p. 297-303.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - van Dijk, J.P.

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AU - Voorthuijzen, M.M.

AU - Hutten, R.C.B.

AU - Maisonnave Arisi, A.C.

AU - Jansen, J.J.

AU - Buydens, L.M.C.

AU - van der Voet, H.

AU - Kok, E.J.

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