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.

TOOL FOR SANGER SEQUENCING (GLASS)

Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in clinical setting.  However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise.

We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in ‘curated’ or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society.
GLASS is freely available at http://bat.infspire.org/genomepd/glass/ with source code at https://github.com/infspiredBAT/GLASS

Contact: karolpal.jr@gmail.com / nikos.darzentas@gmail.com or malcikova.jitka@fnbrno.cz.  Supplementary data are available at Bioinformatics online.

GLASS was updated on 18.05.2018 to correct an issue affecting the analysis of specific samples – please contact us directly (bat@infspire.org) if you need more information or help.

 

ONLINE SUPPORT FOR IMMUNOGLOBULIN GENE SEQUENCE INTERPRETATION  

A review board of experts is shown below to discuss general queries on IGHV gene interpretation or analyze actual IGHV sequences that can be difficult to interpret in everyone’s daily activity; to submit queries and/or sequences please go to the submission form here 

REVIEW BOARD

  • Andreas Agathangeledis – aagathangelidis@gmail.com
  • Chrysoula Belessi – cbelessi@gmail.com
  • Frederic Davi – fred.davi@psl.aphp.fr
  • Zadie Davis – Zadie.Davis@rbch.nhs.uk
  • Paolo Ghia – ghia.paolo@hsr.it
  • Anastasia Hadzidimitiou – anastasiaxtz@gmail.com
  • Anton Langerak – a.langerak@erasmusmc.nl
  • Kathy Potter – kp1@soton.ac.uk
  • Richard Rosenquist – richard.rosenquist@ki.se
  • Kostas Stamatopoulos – kostas.stamatopoulos@gmail.com
  • Lesley Ann Sutton –  lesley-ann.sutton@ki.se

COLLECTION OF PROBLEMATIC CASES AND DATABASE CREATION

“Problematic cases” exist that defy a clear-cut classification and include those showing any of the following features

  • Double in-frame rearrangements
  • Double in-frame rearrangements with discordant mutation status
  • Unmutated in-frame rearrangement coexisting with a mutated out-of-frame rearrangement
  • Unmutated heavy chain rearrangement associated with a mutated light chain rearrangement
  • Single transcribed out-of-frame rearrangements
  • Single transcribed rearrangements carrying stop codons
  • Rearrangements carrying any kind of deletions or insertions/duplications
  • In-frame rearrangements carrying a mutation either at IMGT codon C-104 (end of HFR3) or at W-118 (start of HFR4)
  • Rearrangements without a clearly defined junction

Though these cases are probably known to anyone working in IGHV analysis in CLL, they are limited in frequency, hampering a meaningful analysis at a single-institution level. Therefore, we propose to collect in a dedicated database all problematic cases in order to reach a significant number of them. Everyone in the CLL community is welcome to participate to this joint effort; to submit problematic IGHV sequences and participate to the project please go to the » submission form

COORDINATION

  • Lesley Ann Sutton –  lesley-ann.sutton@ki.se
  • Anastasia Hadzidimitriou – anastasiaxtz@gmail.com

USEFUL LINKS FOR IMMUNOGLOBULIN GENES ANALYSIS

New IMGT/V-Quest search page – http://imgt.cines.fr/IMGT_vquest/share/textes/index.html 

The IgBLAST webpage at NCBI – http://www.ncbi.nlm.nih.gov/igblast 

VBase/DNAPlot website – http://www.vbase2.org

The JoinSolver® website –  http://joinsolver.niams.nih.gov/index.htm

SoDa Dulci website – https://dulci.org/soda/

 

TP53 HELP DESK: ONLINE SUPPORT FOR TP53 MUTATIONAL ANALYSIS

Should you require any further assistance with TP53 sequence analysis, variant description or interpretation then you can contact the TP53 Help Desk by clicking here