title: Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier.
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.
authors.affiliation: RIKILT, Wageningen UR, Wageningen, The Netherlands. Electronic address: jeroen.vandijk@wur.nl.
authors.forename: Jeroen P
authors.initials: JP
authors.lastname: van Dijk
authors.affiliation: RIKILT, Wageningen UR, Wageningen, The Netherlands; Federal University of Santa Catarina, Brazil.
authors.forename: Carla Souza
authors.initials: CS
authors.lastname: de Mello
authors.affiliation: RIKILT, Wageningen UR, Wageningen, The Netherlands.
authors.forename: Marleen M
authors.initials: MM
authors.lastname: Voorhuijzen
authors.affiliation: Plant Breeding, Wageningen UR, Wageningen, The Netherlands.
authors.forename: Ronald C B
authors.initials: RC
authors.lastname: Hutten
authors.affiliation: Federal University of Santa Catarina, Brazil.
authors.forename: Ana Carolina Maisonnave
authors.initials: AC
authors.lastname: Arisi
authors.affiliation: Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands.
authors.forename: Jeroen J
authors.initials: JJ
authors.lastname: Jansen
authors.affiliation: Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands.
authors.forename: Lutgarde M C
authors.initials: LM
authors.lastname: Buydens
authors.affiliation: Biometris, Wageningen UR, Wageningen, The Netherlands.
authors.forename: Hilko
authors.initials: H
authors.lastname: van der Voet
authors.affiliation: Federal University of Santa Catarina, Brazil.
authors.forename: Esther J
authors.initials: EJ
authors.lastname: Kok
mesh_terms: D020869:Gene Expression Profiling; D008962:Models, Theoretical; D030821:Plants, Genetically Modified / Q000633:toxicity*; D011198:Solanum tuberosum / Q000235:genetics*; D059467:Transcriptome
keywords: Chemometrics; Food safety evaluation; GM plants; One-class classifiers; Profiling; Transcriptomics