IMGT

Intro

• Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it?
• Just like for all other nucleotide sequences: We need
  • submitted sequences (like Genbank)
  • "reference" sequences (like RefSeq)
  • genes (like NCBI Genes), i.e. a collection of reference sequences
  • and people that sort out this whole mess, the IMGT curators
• IMGT is a 90's generation website, like the genome browser
• Lots of static webpages, e.g. the new year wishes page

IMGT Structure

• The main reference database for immune loci is IMGT.org
• It consists of databases, tools and additional files (e.g. ontology, some notes, etc)
  • LIGM-DB: Nucleotide sequences of all kinds. Can be C, V, J, D, or combinations thereof.
    • Seems to be pulling in from Genbank and change their annotations slightly with different keywords
    • Automatic transformation or manual annotation?
    • Looks like they could have a BLAST-based pipeline that annotates the different fragments
    • Annotates Genbank sequences with the CVDJ-numbers
    • Example: Genbank AF139844
      • in IMGT: http://imgt.org/cgi-bin/IMGTlect.jv?query=201+AF139844
      • on NCBI: http://www.ncbi.nlm.nih.gov/nuccore/4732152?report=graph
      • Both look very similar, almost identical information
      • But IMGT has added the numbers of the VDJ fragments
      • Annotations that they add: Ftable
  • MHC-DB
    • Also pulls in from Genbank, changes their identifiers
    • Maps Genbank sequences to MHC-"clusters" of sequences
    • E.g. GQ240381 is annotated as a sequence of HLA06329 [1]
  • GENE-DB: A list of categorized VDJC sequences and all their alleles
    • Naming is <locus><type><subtype>-<positionOnGenome></OrphonIdentifier>*allele
    • e.g. IGHV1-18
    • -18 means that is is the 18th sequence in this locus. 1 is the subtype of the J sequence, as determined by curators, by phylogenetic similarity (??)
    • <positionOnGenome> starts from one and numbers the genes along the chromosome, see genome browser (switch on encode genes)
    • Orphons (old paper) seem to be (nonfunctional?) copies of receptors on other chromosomes
  • Repertoire: descriptions of loci, genes and 3D-structures
    • Example human IGH [2]
    • Provides nice lists of a loci, with all alleles, types, etc, e.g. human IGV [3]
  • Web Resources: A mixed bag with explanations on how they curate
    • Actually the best starting point