Bioinformatics and the allergy assessment of agricultural biotechnology products: Industry practices and recommendations

Food safety assessment of an antifungal protein from Moringa oleifera seeds in an agricultural biotechnology perspective

“…Mo-CBP 3 protein showed no identity with any allergenic, toxic and/or antinutritional protein sequences deposited in seven large databases. The allergenic potential of a protein can be assessed by comparing its primary amino acid sequence with those of known allergens (FAO/WHO, 2001;Ladics, 2008;Codex Alimentarius, 2009;Cressman and Ladics, 2009;Ladics et al, 2011). Comparison of the full-length sequences of the four Mo-CBP 3 isoforms in ADFS, Allermatch™, AllergenOnline and SDAP allergen databases showed no similarity with any known allergenic proteins.…”

Comparative assessment of multiple criteria for the in silico prediction of cross-reactivity of proteins to known allergens

“…) Traditionally, such analysis consists of two components: A search for short linear epitopes as well as comparison of primary amino acid sequences using FASTA (Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) to locate possible shared conformations (Cressman and Ladics, 2009). Recent publications (EFSA, 2011;Goodman, 2008;Goodman and Tetteh, 2011;Harper et al, 2012;Herman et al, 2009;Ladics et al, 2011;Young et al, 2012) have argued that the standard search for a sequence of eight or more amino acids found in both the query and a known allergen provides little value; however it has been demonstrated that insertion of a short stretch of amino acids derived from a known allergen into the correct conformational context can result in an increase in specific IgE binding (Klinglmayr et al, 2009). Additionally, the default local alignment search criteria have been constrained by the imposition of a defined threshold (P35% sequence identity over an alignment length P80) (Ladics et al, 2007).…”

The Story Behind the Approval of the First Bt Maize Product

“…These databases grow daily so avoiding known bad actors is easy to accomplish. Furthermore, there are specific allergen databases such as allergenonline.com that allow more focused searches (Ladics et al 2011;Goodman et al 2008). Criteria laid out by regulatory agencies and by the Codex Alimentarius are highly conservative such that even though only a minute fraction of the proteins are actually allergenic about 15% of all proteins would be tagged as potential allergens when doing these kinds of searches.…”