Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity
| Autor: | Eric W. Ganko, Scott McClain, B. Harper |
|---|---|
| Jazyk: | angličtina |
| Předmět: |
Crops
Agricultural DNA Bacterial Proteome Sequence analysis Bioinformatics Molecular Sequence Data Reading frame Crops Genetically modified crops Biology Toxicology Genome DNA sequencing Transgenic chemistry.chemical_compound Sequence Amino Acid Sequence Databases Protein Gene Plant Proteins Genetics Sequence Homology Amino Acid Protein Computational Biology food and beverages General Medicine Antigens Plant Plants Genetically Modified chemistry Allergenicity T-DNA Sequence Alignment DNA Biotechnology |
| Zdroj: | Regulatory Toxicology and Pharmacology. (3):426-432 |
| ISSN: | 0273-2300 |
| DOI: | 10.1016/j.yrtph.2012.05.014 |
| Popis: | Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence. |
| Databáze: | OpenAIRE |
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