title: The value of short amino acid sequence matches for prediction of protein allergenicity.
abstract: Typically, genetically engineered crops contain traits encoded by one or a few newly expressed proteins. The allergenicity assessment of newly expressed proteins is an important component in the safety evaluation of genetically engineered plants. One aspect of this assessment involves sequence searches that compare the amino acid sequence of the protein to all known allergens. Analyses are performed to determine the potential for immunologically based cross-reactivity where IgE directed against a known allergen could bind to the protein and elicit a clinical reaction in sensitized individuals. Bioinformatic searches are designed to detect global sequence similarity and short contiguous amino acid sequence identity. It has been suggested that potential allergen cross-reactivity may be predicted by identifying matches as short as six to eight contiguous amino acids between the protein of interest and a known allergen. A series of analyses were performed, and match probabilities were calculated for different size peptides to determine if there was a scientifically justified search window size that identified allergen sequence characteristics. Four probability modeling methods were tested: (1) a mock protein and a mock allergen database, (2) a mock protein and genuine allergen database, (3) a genuine allergen and genuine protein database, and (4) a genuine allergen and genuine protein database combined with a correction for repeating peptides. These analyses indicated that searches for short amino acid sequence matches of eight amino acids or fewer to identify proteins as potential cross-reactive allergens is a product of chance and adds little value to allergy assessments for newly expressed proteins.
authors.affiliation: Monsanto Company, Product Characterization Center, Global Regulatory Affairs, St. Louis, Missouri 63167, USA. andre.silvanovich@monsanto.com
authors.forename: Andre
authors.initials: A
authors.lastname: Silvanovich
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Nemeth
authors.forename: Ping
authors.initials: P
authors.lastname: Song
authors.forename: Rod
authors.initials: R
authors.lastname: Herman
authors.forename: Laura
authors.initials: L
authors.lastname: Tagliani
authors.forename: Gary A
authors.initials: GA
authors.lastname: Bannon
mesh_terms: D000485:Allergens / Q000737:chemistry / Q000145:classification / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005512:Food Hypersensitivity / Q000209:etiology* / Q000517:prevention & control; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000276:immunology*; D030821:Plants, Genetically Modified / Q000737:chemistry / Q000145:classification / Q000276:immunology*; D017386:Sequence Homology, Amino Acid
chemical_list: D000485:Allergens; D010940:Plant Proteins