ARResT/AssignSubsets: A novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy

Vojtech Bystry, Andreas Agathangelidis, Vasilis Bikos, Lesley Ann Sutton, Panagiotis Baliakas, Anastasia Hadzidimitriou, Kostas Stamatopoulos, Nikos Darzentas

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Motivation: An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for ∼30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement. Results: We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution.

Original languageEnglish
Pages (from-to)3844-3846
Number of pages3
JournalBioinformatics
Volume31
Issue number23
DOIs
Publication statusPublished - Jun 18 2015

Fingerprint

B Cells
Leukemia
B-Cell Chronic Lymphocytic Leukemia
Receptor
Immunoglobulins
B-Lymphocytes
Cells
Immunoglobulin
Immunogenetics
Subset
Assignment
Statistical Modeling
Learning
Annotation
Restriction
Requirements

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

ARResT/AssignSubsets : A novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. / Bystry, Vojtech; Agathangelidis, Andreas; Bikos, Vasilis; Sutton, Lesley Ann; Baliakas, Panagiotis; Hadzidimitriou, Anastasia; Stamatopoulos, Kostas; Darzentas, Nikos.

In: Bioinformatics, Vol. 31, No. 23, 18.06.2015, p. 3844-3846.

Research output: Contribution to journalArticle

Bystry, Vojtech ; Agathangelidis, Andreas ; Bikos, Vasilis ; Sutton, Lesley Ann ; Baliakas, Panagiotis ; Hadzidimitriou, Anastasia ; Stamatopoulos, Kostas ; Darzentas, Nikos. / ARResT/AssignSubsets : A novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. In: Bioinformatics. 2015 ; Vol. 31, No. 23. pp. 3844-3846.
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