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

Autor: van Dijk JP; RIKILT, Wageningen UR, Wageningen, The Netherlands. Electronic address: jeroen.vandijk@wur.nl., de Mello CS; RIKILT, Wageningen UR, Wageningen, The Netherlands; Federal University of Santa Catarina, Brazil., Voorhuijzen MM; RIKILT, Wageningen UR, Wageningen, The Netherlands., Hutten RC; Plant Breeding, Wageningen UR, Wageningen, The Netherlands., Arisi AC; Federal University of Santa Catarina, Brazil., Jansen JJ; Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands., Buydens LM; Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands., van der Voet H; Biometris, Wageningen UR, Wageningen, The Netherlands., Kok EJ; Federal University of Santa Catarina, Brazil.
Jazyk: angličtina
Zdroj: Regulatory toxicology and pharmacology : RTP [Regul Toxicol Pharmacol] 2014 Oct; Vol. 70 (1), pp. 297-303. Date of Electronic Publication: 2014 Jul 18.
DOI: 10.1016/j.yrtph.2014.07.013
Abstrakt: 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.
(Copyright © 2014 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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