Encyclopedia of CLL Subsets – a Unique Bioinformatics Tool and Database for Analysis of Subsets of Stereotypical B-Cell Receptors in CLL


Authors: T. Reigl 1;  K. Stránská 1,2;  V. Bystrý 1;  A. Krejčí 1;  A. Grioni 1;  Š. Pospíšilová 1,2;  N. Darzentas 1;  K. Plevová 1,2
Authors‘ workplace: CEITEC – Středoevropský technologický institut, Masarykova univerzita, Brno 2 Interní hematologická a onkologická klinika LF MU a FN Brno 1
Published in: Klin Onkol 2019; 32(Supplementum1): 167-170
Category: Article

Východiska: Chronická lymfocytární leukemie (CLL) se vyznačuje vysokou klinickou i biologickou variabilitou. Ta je úzce spjata s řadou buněčných a molekulárních znaků, mezi něž patří sekvenční motivy B buněčných receptorů. Tyto motivy se u třetiny pacientů s CLL vyskytují v téměř identické (stereotypní) podobě, což je umožňuje zařadit do homogenních skupin, tzv. stereotypních subsetů CLL.

Overview

Background: Chronic lymphocytic leukemia (CLL) is clinically and biologically highly variable disease which is closely related with multiple cellular and molecular markers, including sequence motifs of B-cell receptors. These motifs are highly similar (stereotyped) within one third of CLL patients and create homogeneous groups called stereotyped CLL subsets. The homogeneity is reflected also in clinical and biological characteristics of the disease. To facilitate access to the information about individual subsets, we have created a publicly available web-based tool Encyclopedia of CLL Subsets.

Materials and methods: The Encyclopedia of CLL subsets belongs to our bioinformatics platform Antigen Receptor Research Tool (ARResT) developed for analysis, clustering, and annotation of immunoglobulin sequences. To gather primary knowledge about the subsets, we have analyzed a dataset of 7,500 CLL patients published by Agathangelidis et al in 2012 [1]. We have created an overview of major stereotyped subsets and their characteristics. Additional clinical and cytogenomic information about individual subsets has been obtained by machine text processing of available literature from server PubMed and is regularly updated.

Results: We have created a unique web-based application Encyclopedia of CLL Subsets available from http: //arrest.tools/subsets for an interactive access to the information about stereotyped CLL subsets. A user can obtain and compare basic information about the major subsets including their clinical and cytogenomic characteristics. These have been manually curated from machine processed results from PubMed database by experts in CLL research. Through the Encyclopedia’s user interface, user can also directly use our published tool ARResT/AssignSubsets to assign new immunoglobulin sequences to the major subsets.

Conclusion: The Encyclopedia of CLL Subsets is a publicly available online tool facilitating access to the most recent research knowledge about stereotyped CLL subsets and enabling analysis of own data and interpretation of the results. This gives the Encyclopedia a great potential for its use in clinical routine.

This work was supported by Czech Ministry of Health grant No. 34272A. All rights reserved.

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.

Submitted: 1. 3. 2019

Accepted: 4. 3. 2019

Keywords:

bioinformatics – immunogenetics – immunoglobulins – stereotyped BCR


Sources

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