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Encyclopedia of CLL Subsets - a Unique Bioinformatics Tool and Database for Analysis of Subsets of Stereotypical

T Reigl, K Stránská, V Bystrý

Klinicka Onkologie : Casopis Ceske a Slovenske Onkologicke Spolecnosti

|May 9, 2019

Insights

We developed the Encyclopedia of CLL Subsets, a web tool providing comprehensive data on stereotyped CLL subsets. This resource aids in understanding the clinical and biological variability of chronic lymphocytic leukemia (CLL).

Area of Science:

Bioinformatics
Oncology
Immunology

Background:

Chronic lymphocytic leukemia (CLL) exhibits significant clinical and biological heterogeneity.
Stereotyped B-cell receptor motifs define homogeneous CLL subsets with distinct characteristics.
A need exists for accessible information on these stereotyped CLL subsets.

Purpose of the Study:

To create a publicly available, web-based tool for accessing information on stereotyped CLL subsets.
To facilitate the analysis and understanding of the clinical and biological features of different CLL subsets.

Main Methods:

Utilized a dataset of 7,500 CLL patients (Agathangelidis et al., 2012).
Developed the Encyclopedia of CLL Subsets as part of the Antigen Receptor Research Tool (ARResT) platform.
Integrated machine text processing of PubMed literature for clinical and cytogenomic data, with expert curation.

Main Results:

Launched the Encyclopedia of CLL Subsets (http://arrest.tools/subsets), an interactive web application.
Provides curated information on major stereotyped CLL subsets, including clinical and cytogenomic data.
Includes the ARResT/AssignSubsets tool for assigning new immunoglobulin sequences to known subsets.

Conclusions:

The Encyclopedia of CLL Subsets is a valuable online resource for current knowledge on stereotyped CLL.
Enables users to analyze their own data and interpret results in the context of known subsets.
Has significant potential for integration into clinical routine for improved CLL management.

Read full analysis

Abstract

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 Encyclopedias 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 chronic lymphocytic leukemia immunogenetics immunoglobulins stereotyped BCR

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