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Preserve study-specific THP-1 HLA typing - #422

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iskandr merged 1 commit into
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fix-thp1-typing-416
Sep 4, 2026
Merged

Preserve study-specific THP-1 HLA typing#422
iskandr merged 1 commit into
mainfrom
fix-thp1-typing-416

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@iskandr

@iskandr iskandr commented Sep 4, 2026

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Summary

  • curate the three PMID 35051231 THP-1 arms with that study's homozygous class-I typing
    (HLA-A*02:01, HLA-B*15:11, HLA-C*03:03)
  • preserve PMID 33392160's independently reported heterozygous DSMZ ACC-16 typing
  • document that THP-1 HLA typing is study/sub-line-specific and add curation plus observation-join
    regressions
  • bump Hitlist to 1.57.2

Source resolution

Nicholas 2022 S1 repeats A02:01, B15:11, and C03:03 in both class-I haplotypes and the Results
describe its THP-1 culture as homozygous. Ghosh 2020 reports A
02:01/A24:02 and
B
15:11/B*35:01 for a culture obtained as DSMZ ACC-16. Cellosaurus preserves both typing records
and the documented THP-1 discrepancy, so the truthful representation is per-study typing rather
than a registry-wide superset.

No upstream issue is warranted: the source records expose the divergent typings; Hitlist was
substituting the heterozygous superset into the Nicholas study.

Verification

  • ./format.sh
  • ./lint.sh
  • ./test.sh — 1,192 passed, one expected warning
  • pytest -q tests/test_build_smoke.py — 2 passed
  • real PMID 35051231 B15:11 observation join contains neither A24:02 nor B*35:01 in exact or
    class-pool sample metadata
  • corpus-wide sample_ploidy_audit() is empty

Closes #416

@coveralls

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Coverage Report for CI Build 33881810600

Coverage remained the same at 83.005%

Details

  • Coverage remained the same as the base build.
  • Patch coverage: No coverable lines changed in this PR.
  • No coverage regressions found.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

No coverage regressions found.


Coverage Stats

Coverage Status
Relevant Lines: 8132
Covered Lines: 6750
Line Coverage: 83.01%
Coverage Strength: 0.83 hits per line

💛 - Coveralls

@iskandr
iskandr merged commit bb11d78 into main Sep 4, 2026
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@iskandr
iskandr deleted the fix-thp1-typing-416 branch September 4, 2026 14:58
@iskandr

iskandr commented Sep 4, 2026

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Merged and deployed.

  • Merge commit: bb11d78a54e63b4f5ca681e67e368fcee6b42213
  • Release gate: 1,216 tests passed with one expected warning
  • PyPI: Hitlist 1.57.2
  • Published artifacts: wheel (2,118,868 bytes) and sdist (2,279,997 bytes)

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Successfully merging this pull request may close these issues.

THP-1 class I: homozygous (PMID 35051231) vs heterozygous (DSMZ ACC-16 / PMID 33392160)

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