T cell receptors in minimal residual disease analysis
Detection of minimal residual disease (MRD) is a powerful prognostic tool in many haematological malignancies including acute lymphoblastic leukemia (ALL). The present study was aimed to demonstrate the influence of TCR generation probability on MRD follow-up

Details: for further details see the publication (will be available soon)

Download: set of 91 TCR beta repertoires used for calculation of TCR beta generation probabilities is available here

tcR: all what you need for T-cell repertoire analysis in single R package
tcR is a platform designed for TCR repertoire data analysis in R. With the power and flexibility of R language and procedures supported by tcR users can perform advanced statistical analysis of TCR repertoires. Features of the package:

  • Shared clones statistics
    (number of shared clones, clonotypes, using V-segments or not; Jaccard index for number of shared clones; sequential intersection among the most abundant clones ("top-cross"))
  • V- and J-segments usage and it's analysis
    (PCA, Shannon Entropy, Jensen-Shannon Divergence)
  • Diversity evaluation
    (ecological diversity index, Gini index, inverse Simpson index, rarefaction analysis)
  • Artificial repertoire generation (beta chain only, for now)
  • Spectratyping
  • Various visualisation procedures

Download: GitHub

Manual: tcR package vignette

Publication: PubMed

TCR-alpha/beta repertoires in MZ twins
This study is the part of a bigger project which aims to investigate the influence of the genetic context on the T-cell diversity in humans. Here we compared alpha-beta TCR repertoires of several pairs of monozygotic (MZ) twins using an approach based on the Illumina sequencing. The TCR cDNA libraries were prepared using our RNA-based technology (the details are described in ref#1 and ref#2). Alpha and beta TCR repertoire reconstruction with error correction and clonotype formation was performed using an algorithm described in ref#3

Raw data are available at NCBI (SRA: SRP028752, BioProject: PRJNA214848)

Clonesets (txt.tar.gz) generated by MiTCR software with incorrect out-of-frame CDR3 sequences filtered out (for details see the main paper) are available as .txt-files and are ready for analysis with any apropriate software

Sequences of HLA-A*0201/CMV(NV9)-specific clonotypes from individual A2 (see the main paper) are available here

*Naming conventions are the following: Twin[pair A/B/C][index of twin 1 or 2]_[A or B for alpha and beta chain]