Deleted alleles when matching/scoring XX codes

[zabeen]

When running exercise 1 of the WMDA consensus dataset (#964), one major cause of discrepant mismatch counts was B*39:XX vs. *38:XX.

The explanation for this is that the more recent versions of the hla_nom contain the following deleted alleles:

B*;38:156;20190530;20210430;39:171;Name assigned in error
B*;38:157;20190530;20210430;39:172;Name assigned in error
B*;38:158;20190530;20210430;39:173;Name assigned in error
B*;38:159;20190530;20210430;39:174;Name assigned in error

At present, the HLA metadata of deleted alleles is still used when generating the HMD so that such alleles do not throw 404 HMD exceptions. Where the deleted allele has been renamed, the metadata of the new allele is saved against the deleted allele name. In the case of the above B*38 alleles, this means metadata for the corresponding B*39 alleles are saved against them in the HMD. E.g., B*38:156 has the matching P group of B*39:171.

Metadata for XX codes is generated by grouping together all alleles with the same locus and first field. In the case of B*38:XX, this includes the four deleted B*38 alleles that have been renamed to B*39 alleles. This is why B*39:XX vs. B*38:XX was called a potential P group match.

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If such a match is considered unexpected/undesirable, then the solution would be to exclude deleted allele metadata when generating lookup metadata for XX codes.