TOOL FOR STEREOTYPED SUBSET ASSIGNMENT
A close collaboration between the Bioinformatics Analysis Team, the IgCLL group, the IG network of ERIC, and IMGT®, the bioinformatics application ARResT/AssignSubsets was built to robustly assign user-submitted sequences as new members to existing subsets of stereotyped antigen receptor sequences, currently stored in IMGT/CLL-DB – that implies that ARResT/AssignSubsets does not discover new subsets. This is currently applicable to the 19 major subsets of stereotyped B-cell receptors in CLL. Critically, major subsets account for >10% of the cohort, >40% of stereotyped cases, and >25% of patients requiring treatment, and seem to share clinicobiological features and, even, outcome.
Immunogenetic annotations of sequences are obtained from IMGT/V-QUEST, the widely-accepted reference for antigen receptor sequence analysis. Initially, and importantly, these are used by ARResT/SeqCure to report on issues with the sequences which could potentially compromise the analysis.
ARResT/AssignSubsets is freely available on the web at http://bat.infspire.org/arrest/assignsubsets/, with the publication by Vojtech Bystry, Andreas Agathangelidis, Vasilis Bikos, Lesley Ann Sutton, Panagiotis Baliakas, Anastasia Hadzidimitriou, Kostas Stamatopoulos, and Nikos Darzentas, also on behalf of ERIC, permanently linked through http://doi.org/10.1093/bioinformatics/btv456.