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

Ronald van Ree; Dexter Sapiter Ballerda; M Cecilia Berin; Laurent Beuf; Alexander Chang; Gabriele Gadermaier; Paul A Guevera; Karin Hoffmann-Sommergruber; Emir Islamovic; Liisa Koski; John Kough; Gregory S Ladics; Scott McClain; Kyle A McKillop; Shermaine Mitchell-Ryan; Clare A Narrod; Lucilia Pereira Mouriès; Syril Pettit; Lars K Poulsen; Andre Silvanovich; Ping Song; Suzanne S Teuber; Christal Bowman

doi:10.3389/falgy.2021.700533

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

Front Allergy. 2021 Aug 6:2:700533. doi: 10.3389/falgy.2021.700533. eCollection 2021.

Authors

Ronald van Ree¹, Dexter Sapiter Ballerda², M Cecilia Berin³, Laurent Beuf⁴, Alexander Chang², Gabriele Gadermaier⁵, Paul A Guevera², Karin Hoffmann-Sommergruber⁶, Emir Islamovic⁷, Liisa Koski⁸, John Kough⁹, Gregory S Ladics¹⁰, Scott McClain¹¹, Kyle A McKillop², Shermaine Mitchell-Ryan⁸, Clare A Narrod², Lucilia Pereira Mouriès⁸, Syril Pettit⁸, Lars K Poulsen¹², Andre Silvanovich¹³, Ping Song¹⁴, Suzanne S Teuber^{15

16

17}, Christal Bowman¹⁸

Affiliations

¹ Departments of Experimental Immunology and of Otorhinolaryngology, Amsterdam University Medical Centers, Amsterdam, Netherlands.
² Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD, United States.
³ Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁴ Limagrain Field Seeds, Centre de Recherche, Route d'Ennezat, Chappes, France.
⁵ Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria.
⁶ Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria.
⁷ Regulatory Science Seeds and Traits, BASF Corporation, Morrisville, NC, United States.
⁸ Health and Environmental Sciences Institute (HESI), Washington, DC, United States.
⁹ Office of Pesticide Programs, Microbial Pesticides Branch, US Environmental Protection Agency, Washington, DC, United States.
¹⁰ IFF Inc., Wilmington, DE, United States.
¹¹ Syngenta Crop Protection LLC, Research Triangle Park, NC, United States.
¹² Allergy Clinic, Department of Dermatology and Allergy, Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
¹³ Bayer U.S., Crop Science Regulatory Science Building FF4, Chesterfield, MO, United States.
¹⁴ Seeds Regulatory Science, Corteva Agriscience LLC, Indianapolis, IN, United States.
¹⁵ Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.
¹⁶ Division of Rheumatology, Allergy, and Clinical Immunology, Davis, CA, United States.
¹⁷ Veterans Affairs Northern California Healthcare System, Mather, CA, United States.
¹⁸ Formerly: Human Safety Regulatory Toxicology, Bayer CropScience LP, Research Triangle Park, NC, United States.

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.

Keywords: GMO; allergen database; allergenicity assessment; bioinformatics; risk assessment; sequence comparison.

Copyright © 2021 van Ree, Sapiter Ballerda, Berin, Beuf, Chang, Gadermaier, Guevera, Hoffmann-Sommergruber, Islamovic, Koski, Kough, Ladics, McClain, McKillop, Mitchell-Ryan, Narrod, Pereira Mouriès, Pettit, Poulsen, Silvanovich, Song, Teuber and Bowman.