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Explain how serology is handled in matching and scoring #1076

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zabeen opened this issue Sep 25, 2023 · 2 comments
Closed

Explain how serology is handled in matching and scoring #1076

zabeen opened this issue Sep 25, 2023 · 2 comments
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algorithmic Involves a change to the algorithmic logic of Atlas, likely needing approval from HLA experts. documentation Improvements or additions to documentation hla-metadata-dictionary Work relates to the "HLA Metadata Dictionary", a data store used to assist with hla nomenclature matching-algorithm Work relates to the algorithm which matches and scores donors for given patient HLA wmda-uat Tickets raised as an outcome of UAT by WMDA users

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@zabeen
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zabeen commented Sep 25, 2023

  • serology in matching (including how serology is converted into list of P groups)
  • serology in scoring
  • Include examples
@zabeen zabeen added algorithmic Involves a change to the algorithmic logic of Atlas, likely needing approval from HLA experts. documentation Improvements or additions to documentation hla-metadata-dictionary Work relates to the "HLA Metadata Dictionary", a data store used to assist with hla nomenclature matching-algorithm Work relates to the algorithm which matches and scores donors for given patient HLA labels Sep 25, 2023
@zabeen zabeen self-assigned this Sep 25, 2023
@zabeen zabeen added the wmda-uat Tickets raised as an outcome of UAT by WMDA users label Sep 25, 2023
@zabeen
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zabeen commented Sep 27, 2023 •
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Super User Testing Investigation

See Discussions:

Case 20

  • B*15:01:01 vs B71
  • Scoring: serology mismatch as B*15:01:01 only matches B15/62
  • Matching: P group match on 15:01P due to following relationship:
    {
        "ser": "70",
        "pGrp": "15:01P",
        "alleles": [
            "15:140",
            "15:228",
            "15:247",
            "15:476",
            "15:482",
            "15:501",
            "15:514",
            "15:515",
            "15:533:01",
            "15:533:02",
            "15:535",
            "15:600",
            "15:601",
            "15:605",
            "15:621",
            "15:624",
            "15:631",
            "15:632",
            "15:635",
            "15:639",
            "15:640",
            "15:647",
            "15:104",
            "15:201",
            "15:227",
            "15:320",
            "15:321Q",
            "15:441",
            "15:443",
            "15:456",
            "15:457",
            "15:464",
            "15:465",
            "15:466",
            "15:471",
            "15:472",
            "15:474",
            "15:536",
            "15:538",
            "15:542",
            "15:547",
            "15:558",
            "15:568",
            "15:572",
            "15:591",
            "15:593",
            "15:666"
        ],
        "gGrps": [
            "15:01:01G"
        ]
    }

Case 29

  • B*15:21 vs B62
  • Scoring: serology mismatch as B*15:21 only matches B15/75
  • Matching: P group match on 15:21P due to following relationship:
    {
        "ser": "15",
        "pGrp": "15:21P",
        "alleles": [
            "15:615"
        ],
        "gGrps": [
            "15:21:01G"
        ]
    }

Case 32

  • B*15:25 vs B71
  • Scoring: serology mismatch as B*15:21 only matches B15/62
  • Matching: P group match on 15:25P due to following relationship:
    {
        "ser": "70",
        "pGrp": "15:25P",
        "alleles": [
            "15:271",
            "15:543",
            "15:564"
        ],
        "gGrps": [
            "15:25:01G"
        ]
    }

@zabeen zabeen changed the title Extend Atlas README with info on how serology is handled in matching and scoring Explain how serology is handled in matching and scoring Sep 27, 2023
zabeen added a commit that referenced this issue Oct 11, 2023
@zabeen
docs: #1076: Document how HMD interprets serology typings.
6ff347c
@zabeen zabeen assigned mmelchers and RimkePostel and unassigned zabeen Oct 17, 2023
zabeen added a commit that referenced this issue Oct 19, 2023
@zabeen
docs: #1076: Document how HMD interprets serology typings.
29e6326
zabeen added a commit that referenced this issue Oct 19, 2023
@zabeen
docs: #1076: Document how HMD interprets serology typings.
6b0c68f
@zabeen
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zabeen commented Nov 16, 2023

I am closing ticket based on positive reviews from users in meeting today - if amendments to docs need to be made, a new ticket can be raised.

@zabeen zabeen closed this as completed Nov 16, 2023
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algorithmic Involves a change to the algorithmic logic of Atlas, likely needing approval from HLA experts. documentation Improvements or additions to documentation hla-metadata-dictionary Work relates to the "HLA Metadata Dictionary", a data store used to assist with hla nomenclature matching-algorithm Work relates to the algorithm which matches and scores donors for given patient HLA wmda-uat Tickets raised as an outcome of UAT by WMDA users
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@zabeen @mmelchers @RimkePostel