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
• One of the big problems with receptor sequences is the numbering of the amino acids. IMGT numbers their amino acids more in accordance with function and 3D structure and is often preferred to the older, "Kabat" numbering.

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