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
Highlights
Food allergy is a growing food safety and public health concern
The web interface presents the database main fields in a searchable table view with the following fields for each allergen sequence entry: Species; Common Name, Description, Immunological Societies (IUIS) Name, Accession, Length, Year Adopted, and a “VIEW” clickable box leading to a window with the individual data for each sequence
Candidate entries for the 2017 COMprehensive Protein Allergen REsource (COMPARE) database were obtained from the National Center for Biotechnology Information (NCBI) Protein database as accessed through the main query window on May 14, 2016 using the following Boolean search: “allerg∗ AND [time period: from May 30, 2015 to May 14, 2016] AND [species: animals, plants, fungi and protists].”
Summary
Food allergy is a growing food safety and public health concern. Well-curated, publicly accessible allergen databases serve a range of public health roles, including informing experimental research programs, clinicians, and allergists and/or providing critical data to patients or the public. In the food safety space, an allergen database serves the purpose of evaluating concerns over the transfer of known allergens or potentially cross-reactive proteins to genetically-modified (GM) food crops or animals. Regulatory agencies evaluating the safety of biotechnology products for genetically-modified food and feeds require an assessment for potential allergenicity, including comparing novel or newly discovered proteins at the level of their primary amino acid sequence to known allergens, which further emphasizes the need for a comprehensive allergen database. Allergen databases support allergy science and safety by two distinct but related processes: [1] comparative processes to identify potential similarity between query sequences and allergens using bioinformatics tools, and [2] identification of the source organism for any listed allergen, allowing researchers to assess taxonomic relatedness among the organisms producing the allergens/proteins
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