Mirsky Henry P, Cressman Robert F, Ladics Gregory S
DuPont Pioneer, Route 141, Henry Clay Bldg, #400, Wilmington, DE 19880-0400, USA.
Regul Toxicol Pharmacol. 2013 Nov;67(2):232-9. doi: 10.1016/j.yrtph.2013.08.001. Epub 2013 Aug 9.
Genetically modified crops are becoming important components of a sustainable food supply and must be brought to market efficiently while also safeguarding the public from cross-reactivity of novel proteins to known allergens. Bioinformatic assessments can help to identify proteins warranting further experimental checks for cross-reactivity. This study is a large-scale in silico evaluation of assessment criteria, including searches for: alignments between a query and an allergen having ≥ 35% identity over a length ≥ 80; any sequence (of some minimum length) found in both a query and an allergen; any alignment between a query and an allergen with an E-value below some threshold. The criteria and an allergen database (AllergenOnline) are used to assess 27,243 Viridiplantae proteins for potential allergenicity. (A protein is classed as a "real allergen" if it exceeds a test-specific level of identity to an AllergenOnline entry; assessment of real allergens in the query set is against a reduced database from which the identifying allergen has been removed.) Each criterion's ability to minimize false positives without increasing false negative levels of current methods is determined. At best, the data show a reduction in false positives to ∼6% (from ∼10% under current methods) without any increase in false negatives.
转基因作物正成为可持续粮食供应的重要组成部分，必须在有效推向市场的同时，保护公众免受新蛋白与已知过敏原交叉反应的影响。生物信息学评估有助于识别那些需要进一步进行交叉反应实验检测的蛋白质。本研究是对评估标准进行大规模的计算机模拟评估，包括搜索：查询序列与过敏原之间长度≥80且一致性≥35%的比对；查询序列和过敏原中都存在的任何（最短长度的）序列；查询序列与过敏原之间E值低于某个阈值的任何比对。这些标准和一个过敏原数据库（AllergenOnline）被用于评估27243种绿色植物蛋白的潜在致敏性。（如果一种蛋白质与AllergenOnline条目的一致性超过特定测试水平，则该蛋白质被归类为“真正的过敏原”；查询集中真正过敏原的评估是针对已去除识别过敏原的简化数据库进行的。）确定了每个标准在不增加当前方法假阴性水平的情况下将假阳性最小化的能力。数据显示，在不增加假阴性的情况下，假阳性最多可降至约6%（当前方法下为约10%）。
