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nmdp-bioinformatics / py-ard

HLA ARD Reduction in Python
https://py-ard.org/
GNU Lesser General Public License v3.0
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Redux mode for first-field DNA specificities #327

Open lgragert opened 3 weeks ago

lgragert commented 3 weeks ago

py-ARD doesn't seem to have a redux mode for first-field DNA nomenclature yet.

The current US organ allocation system supports all three of these HLA specificities: DRB3*02:02, DRB3*02, and DR52, but py-ARD doesn't have a way to map between all of these categories yet. DRB3/4/5 alleles like DRB3*02:02 would have a rollup of DRB3*02 that is more specific than the serologic antigen rollup of DR52.

DQA1 and DPA1 loci don't have WHO-recognized serologic specificities, so this would be the only way to do a more ambiguous rollup for alleles such as DPA1*02:07.

Some GL strings with full-field HLA alleles will encompass several first-field specificities, which all should be provided in the output.

lgragert commented 1 week ago

Also noting that users that attempt an antigen-level redux for C*12 through C*18 alleles will return a null result from py-ARD. For example, for the allele specificity C*12:03, py-ARD does not have a more ambiguous redux category.

If we decide to support first-field DNA nomenclature rollup, should we provide an option to have the antigen redux for HLA-C also perform a first-field rollup for C*12 through C*18 alleles?