Further evaluation of the utility of "sliding window" FASTA in predicting cross-reactivity with allergenic proteins

Regulatory Toxicology and Pharmacology : RTP
Robert F Cressman, Gregory Ladics

Abstract

FAO/WHO has recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is greater than 35% identity over a sliding "window" of 80 amino acids. In a previous work, we evaluated the false positive and negative rates observed using the FAO/WHO criteria versus conventional, whole protein FASTA analyses [Ladics, G.S., Bannon, G.A., Silvanovich, A., Cressman, R.F., 2007. Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergens. Mol. Nutr. Food Res. 51 (8), 985-998]. A number of protein sequence datasets were used as queries against the FARRP 7 allergen database. Results indicated that conventional FASTA analysis produced fewer false positives then the "sliding window" search proposed by FAO/WHO. Further, both methods were able to identify the potential for cross-reactivity between the Bet v 1 family of proteins, indicating that the conventional FASTA search possessed sufficient sensitivity. Recently, collections of protein sequences from multiple crop species (corn, soy, barley, lettuce, sugar beets, and spinach) were subjected to the same screen against the FARRP7 allergen dataset....Continue Reading

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Citations

Oct 31, 2009·Clinical and Molecular Allergy : CMA·Rod A HermanArvind Thirumalaiswamysekhar
Dec 9, 2015·Computational Biology and Chemistry·Cristiano GarinoMarco Arlorio
Feb 16, 2011·Regulatory Toxicology and Pharmacology : RTP·Gregory S LadicsScott McClain
Jun 3, 2015·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Clidia E M PintoIlka M Vasconcelos
May 2, 2015·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Rod Aaron HermanSiva Kumpatla
Aug 8, 2012·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Gregory J YoungCathy X Zhong
Jul 21, 2012·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Krishna M MadduriRod A Herman
Aug 13, 2013·Regulatory Toxicology and Pharmacology : RTP·Henry P MirskyGregory S Ladics
Jun 24, 2014·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Ping SongSiva Kumpatla
Jul 7, 2012·PloS One·Sara Pereira MenezesAbelmon da Silva Gesteira
Feb 19, 2016·Molecular Nutrition & Food Research·Richard E GoodmanSteve L Taylor
Nov 10, 2018·Journal of Immunotoxicology·Gregory S Ladics
Jan 8, 2020·GM Crops & Food·Rod A Herman, Ping Song
Dec 18, 2020·Regulatory Toxicology and Pharmacology : RTP·Rod A HermanJason M Roper
Aug 24, 2017·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Yuan JinLeena Tripathi
Dec 5, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Mohamed AbdelmotelebRichard E Goodman
Jun 2, 2021·Critical Reviews in Food Science and Nutrition·Sara BenedéElena Molina

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