The COMPARE Database: A Public Resource for Allergen Identification, Adapted for Continuous Improvement

Abstract

Motivation: The availability of databases identifying allergenic proteins via a transparent and consensus-based scientific approach is of prime importance to support the safety review of genetically-modified foods and feeds, and public safety in general. Over recent years, screening for potential new allergens sequences has become more complex due to the exponential increase of genomic sequence information. To address these challenges, an international collaborative scientific group coordinated by the Health and Environmental Sciences Institute (HESI), was tasked to develop a contemporary, adaptable, high-throughput process to build the COMprehensive Protein Allergen REsource (COMPARE) database, a publicly accessible allergen sequence data resource along with bioinformatics analytical tools following guidelines of FAO/WHO and CODEX Alimentarius Commission.Results: The COMPARE process is novel in that it involves the identification of candidate sequences via automated keyword-based sorting algorithm and manual curation of the annotated sequence entries retrieved from public protein sequence databases on a yearly basis; its process is meant for continuous improvement, with updates being transparently documented with each version; as a complementary approach, a yearly key-word based search of literature databases is added to identify new allergen sequences that were not (yet) submitted to protein databases; in addition, comments from the independent peer-review panel are posted on the website to increase transparency of decision making; finally, sequence comparison capabilities associated with the COMPARE database was developed to evaluate the potential allergenicity of proteins, based on internationally recognized guidelines, FAO/WHO and CODEX Alimentarius Commission

How Do Pollen Allergens Sensitize?

“…At present, structures of several thousand allergens have been determined, and the mechanism of action has been investigated for many of them ( Bogdanov et al, 20212058 ; Finkina et al, 2021 ; Melnikova et al, 2021 ). In order to take into account the risk factors for an occurrence of allergic diseases, databases of allergens are created and improved ( Guryanova, 2018 ; van Ree et al, 2021 ). Main characteristics of allergens including molecular masses, epitope structures, cross-reactivity, presence in foods and geographical distribution are collected there.…”

Comprehensive COMPARE database reduces allergenic risk of novel food proteins

“…However, the practice of including sequences based solely on in vitro IgE binding and including partial sequences, while conservative for risk assessment, necessarily lead to an overestimate of the number of newly identified sequences that are clinically relevant to allergy. 7 …”

“…The COMPARE allergen database is currently the most widely used by developers of GE crops for the bioinformatic investigation of newly expressed proteins in GE crops. 7 This database was initiated in 2017 based largely on the existing version of the Allergen Online (AOL) database. 8 Curated updates have been subsequently made to the COMPARE database annually since that time, allowing the series of five additional groups of sequences added in each update (2018 to 2022) to be investigated for novelty compared with entries in the previous versions of the database ( https://comparedatabase.org/ ).…”

NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction

“…Therefore, we constructed a new validation dataset to further evaluate and benchmark against AlgPred2. Here, allergens were retrieved from Allergen Nomenclature 36 , Allerbase 37 , COMPARE 38 , Allergome 39 , and SDAP 10 databases (On December 2021). Allergenic protein sequences that were identical to positive sequences in the training dataset were excluded.…”