PMID- 16810734
OWN - NLM
STAT- MEDLINE
DCOM- 20060915
LR  - 20070322
IS  - 1613-4125 (Print)
IS  - 1613-4125 (Linking)
VI  - 50
IP  - 7
DP  - 2006 Jul
TI  - Practical and predictive bioinformatics methods for the identification of 
      potentially cross-reactive protein matches.
PG  - 655-60
AB  - A bioinformatics comparison of proteins introduced into food crops through 
      genetic engineering provides a mechanism to identify those proteins that may 
      present an increased risk of allergic reactions for individuals with existing 
      allergies. The goal is to identify proteins that are known to be allergens or are 
      so similar to an allergen that they may induce allergic cross-reactions. Three 
      comparative approaches have traditionally been used, or considered for safety 
      evaluations. One identifies any short (6-8) amino acid segment of the protein 
      that exactly matches a known allergen sequence. The second is an overall primary 
      sequence comparison using Basic Local Alignment Search Tool (BLAST) or FASTA to 
      find matches of greater than 35% identity over 80 amino acids. The third is based 
      on 3-D prediction programs to identify 3-D similarities that might predict 
      potential cross-reactivity. The utility of each of these approaches was debated 
      in the bioinformatics workshop. The consensus agreement from the expert workshop 
      participants was that the short-segment match (e. g., 6-8 amino acids) provides 
      an unacceptably high rate of false positive matches and an uncertain rate of true 
      positive matches, and was not particularly useful for an allergenicity evaluation 
      performed in the context of comprehensive safety evaluation. There was no 
      consensus regarding the most appropriate bioinformatics method, an acceptable 
      scoring criteria for triggering closer examination subsequent to a positive 
      match, or an acceptable scoring mechanism for ranking the utility of the various 
      3-D approaches that were discussed during the workshop. However, the general 
      consensus was that the most practical approach at this time is to evaluate 
      primary sequence identities to known allergens using either FASTA or BLAST. While 
      there was good agreement that identities of greater than 35% over 80 or more 
      amino acids (recommended by Codex in 2003) is quite conservative, the conclusion 
      was that additional data or studies would be needed to justify changing this 
      criterion as there is some evidence that some individuals sensitized to proteins 
      in evolutionarily conserved protein families may experience cross-reactions to 
      proteins sharing approximately 40% identity.
FAU - Goodman, Richard E
AU  - Goodman RE
AD  - Food Allergy Research and Resource Program, Department of Food Science & 
      Technology, University of Nebraska, Lincoln, Nebraska, USA. 
      rgoodman2@unlnotes.unl.edu
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PT  - Review
PL  - Germany
TA  - Mol Nutr Food Res
JT  - Molecular nutrition & food research
JID - 101231818
RN  - 0 (Allergens)
RN  - 0 (Proteins)
SB  - IM
MH  - Algorithms
MH  - Allergens/*chemistry/*immunology
MH  - Amino Acid Sequence
MH  - *Antibody Specificity
MH  - Computational Biology/*methods
MH  - Databases, Protein
MH  - Food Hypersensitivity/diagnosis/immunology
MH  - Humans
MH  - Proteins/*chemistry/*immunology
MH  - Sequence Alignment
RF  - 23
EDAT- 2006/07/01 09:00
MHDA- 2006/09/16 09:00
CRDT- 2006/07/01 09:00
PHST- 2006/07/01 09:00 [pubmed]
PHST- 2006/09/16 09:00 [medline]
PHST- 2006/07/01 09:00 [entrez]
AID - 10.1002/mnfr.200500277 [doi]
PST - ppublish
SO  - Mol Nutr Food Res. 2006 Jul;50(7):655-60. doi: 10.1002/mnfr.200500277.