For humans, the IMGT nomenclature is so widely known and used that I think it should be retained as the foundation for the future. Whether or not that should include the IMGT fix for dealing with Corey’s sequences is another matter. I suspect that CNVs and structural variation may be so great that the D designation for duplicated genes will not help. The IMGT positional nomenclature, if it worked perfectly, would allow heterozygosity at a gene locus to be instantly recognizable, but it already fails on that score. It should be seen as quasi-positional, with the understanding that the determination of heterozygosity may sometimes be problematic, or even impossible.
The mouse IMGT nomenclature is surely dead in the water. I would retain the nomenclature for B6 mice, but until we have much more knowledge of the genes in other strains, it will be impossible to know whether or not that nomenclature can be developed for other strains. I would certainly say that it will be quite unsuited to the BALB/c and NOD repertoires, and if a new repertoire is to be developed for these and other strains, it should be independent of reported gene positions.
We need input from people working with other species if we are to resolve issues with those species, but still, here are a couple of my thoughts…
As a human/mouse researcher, I have not looked closely at other species, but the situation is confusing. The rat and platypus seem to have positional nomenclatures, but most other species just have a relatively short list of unmapped sequences. The ‘mapping’ of the rat and platypus sequences comes from analysis of genome reference sequences, but since the assemblies of the genome sequences for these species did not address the special challenges of BCR/TCR genes, they cannot be accepted as accurate. Most if not all rat sequences were separately identified, before being mapped using the rat genome reference sequence, so the mapping might be queried, but the sequences could be real. In the case of the platypus, not only could the mapping be queried, but since there is no corroboration for the sequences themselves, they too could be queried.
IGHV genes for other species have been reported, but are not yet found in the IMGT database. I would prefer to see such sequences named using a new non-position based nomenclature. But where do the responsibilities of the AIRR community lie? Should we and can we be concerned about germline genes in the elephant? Are there other organizations who we might partner with to advance AIRR studies in these species?