ARResT/AssignSubsets    assigning new members to existing subsets

one (1) sequence will be analysed - example (copy-paste below) ; if a subset is assigned, click on it to view it on the encyclopedia
   main coders
Tomas Reigl   @ CEITEC MU, Brno
Karol Pal   @ CEITEC MU, Brno
Nikos Darzentas   @ UKSH, Kiel & CEITEC MU, Brno

Karla Plevová   @ CEITEC MU, Brno
Kamila Stránská   @ CEITEC MU, Brno

   alumni coders and developers
Vojta Bystry   @ CEITEC MU, Brno
Adam Krejci   @ CEITEC MU, Brno
Andrea Grioni   @ CEITEC MU, Brno

   acknowledging feedback and support from
Panagiotis Baliakas   @ Uppsala University, Uppsala, Sweden
Richard Rosenquist   @ Uppsala University, Uppsala, Sweden
Paolo Ghia   @ IRCCS San Raffaele Scientific Institute, Milan, Italy
Frederic Davi   @ Hopital Pitie-Salpetriere and University Pierre et Marie Curie, Paris, France

acknowledging all underlying work, support, and advice from the IgCLL group
acknowledging all contributors and contributions to IMGT/CLL-DB

Supported by Ministry of Health of the Czech Republic, grant nr. 16-34272A. All rights reserved.
if you still have questions, please email us

Q: How can I contribute data?
A: Visit IMGT/CLL-DB and specifically its bylaws, and/or email us directly.
  Encyclopedia  of  CLL Subsets
                 a unique knowledgebase and novel bioinformatics tools
                 towards personalised biomedical and clinical applications
current set  
DISCLAIMER - please take great care to understand the data, study linked/relevant publications, appreciate implications, and ask for clarifications before making critical/clinical decisions
Chronic lymphocytic leukemia, or CLL, is the most common adult leukemia in the West. It is documented as a biologically and clinically heterogeneous malignancy with varying clinical outcome.
A remarkable phenomenon in CLL is the presence of numerous subsets of patients with highly similar, or stereotyped, B cell receptors (BcR) – or “CLL subsets”, which we reported as involving one in three cases in the studied cohort. These subsets are mainly defined by a high amino acid identity within the complementarity-determining region 3 (CDR3), the main determinant of antigen specificity. Currently, there are nineteen (19) CLL subsets with 20 cases or more, which we have termed ‘major’.
This conceptual approach places CLL subsets at the center of patient stratification and offers to identify reliable associations with any aspect of CLL, from genetics to clinical evolution, response to treatment, and mechanisms of resistance.

The Encyclopedia of CLL Subsets is a unique knowledgebase on these usefully homogeneous groups of CLL patients.
Around it, layers of novel bioinformatics solutions enable researchers and clinicians alike to tap into this reference resource to get insights, link their data robustly, collaborate productively.

treemap overview grouped by...

DESCRIPTION: major and minor subsets, and the heterogeneous cohort, organised as an interactive map
NOTE: by default, the placement of subsets is random, and therefore any conclusions apart from relative sizes is not relevant
- but, select e.g. 'mutational status' from the widget and subsets are organised per such category,
  in this case 'unmutated' and 'mutated'
- then double-clicking on subsets zooms in, and hovering-over will show you such categories, then you can zoom in again...

barplot overview of...

DESCRIPTION: distribution of features for all subsets per selected feature type (see drop-down widget on the left)
NOTE: click on a column to 'break it down' ('drill-down')

barplot overview

This panel is the gateway to PubMed-available publications we collect around subsets (we explain how below, see 'collection' tab for full list). Email us if you believe we can do more and better, e.g. if we're missing anything.

how we collect
1. We query PubMed with: ("2002"[Date - Publication] : "3000"[Date - Publication]) AND (cll OR "chronic lymphocytic leukemia" OR "chronic lymphocytic leukaemia"[Title/Abstract]) AND (subset* AND stereotyp*[Title/Abstract])
2. We have a list of our 'core' subset publications, with which we query PubMed to gather publications that cite them.
3. We add and remove publications based on expert manual curation.
= queried + core + citing +/- manually added/removed

how we analyse
1. Currently, we mine subset mentions in titles, abstracts, and full texts where available. We also include some context, although this might not be enough - we'll improve on that.
DESCRIPTION: subset mentions in titles, abstracts, and full text where available, with some context included    
DISCLAIMER: work-in-progress so there might be false positives/negatives and other (known) issues ; read the full publication if it catches your eye ; send feedback ('#' column is a unique row ID, helpful to communicate specific issues)
NOTE: only sentences with subsets shown, plus context     NOTE: subset colours are consistent across site     NOTE: in sentence #s: 't'=title, 'a'=abstract, 'f'=full text     TIP: find all analysed publications in 'collection'     TIP: click PMID to go to PubMed