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IMGT rules for quality assessment of IG and TR loci in genome assemblies

Introduction

IMGT defines criteria for available genome assemblies on the National Center of Biotechnology Information NCBI before undertaking the IMGT annotation of immunoglobulins (IG) and T cell receptors (TR) loci [1].

IMGT preselection criteria of a genome assembly

Genome assembly of interest is selected based on:

1. the completeness of the genome via NCBI (chromosome level, scaffolds level, contig level);
2. the classification of the genome: Representative genome;
3. the assembly type : haploid;
4. the most recent version of the assembly.

IMGT assessment of the locus quality

1. evaluation of the number of genes V, D, J and C on the locus;
2. evaluation of the number and length of gaps on the locus;
3. confirmation of the vector sequences absence on the locus;
4. organization of the genes into Cluster and/or Cassette ;
5. detection of IMGT Borne once available, on 5' and 3' of the locus;
6. final validation with existing scientific articles.

References

[1] Nguefack Ngoune, V. et al., IMGT® Biocuration and Analysis of the Rhesus Monkey IG Loci. Vaccines (Basel). 2022 Mar 3;10(3):394 PMID: 35335026, LIGM:504.