pirl-unc / hitlist / 24204416728
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coverage: 33.983%. Remained the same
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Curate per-sample MHC alleles (93% coverage) (#21)

* Add per-sample MHC curation tracker

108 studies (224 samples) still need per-sample mhc field:
- Tier 1: 7 mono-allelic (link alleles to samples)
- Tier 2: 13 with hla_alleles dict (link to samples)
- Tier 3: 56 known cell lines (ATCC/literature lookup)
- Tier 4: 15 patient/tissue (paper supplementary)
- Tier 5: 17 non-human species

* Curate per-sample MHC for Tiers 1, 2, and 5 (37 studies)

Coverage: 108 → 203 / 332 samples (61%)

Tier 1 (mono-allelic): Link alleles to aggregated samples
- Sarkizova n=95 entry: all 95 alleles listed
- Abelin n=16: all 16 alleles, validation samples → unknown
- Schittenhelm: 8 HLA-B*27 subtypes
- Di Marco: 15 HLA-C + E*01:01 + G*01:01

Tier 2 (hla_alleles linking): Match PMID-level dict to samples
- Abelin 2019 MAPTAC: class I/II allele lists per sample type
- Bassani-Sternberg 2021 GBM: combined alleles across 3 lines
- van Balen 2020: DPB1 alleles
- Multi-donor studies → "unknown" (no per-donor resolution)

Tier 5 (non-human): Species-appropriate nomenclature
- 6 macaque Mamu alleles, 3 chicken BF2, 2 dog DLA-88
- 2 cattle BoLA, 2 pig SLA, mouse H-2, chimpanzee Patr-AL
- Tasmanian devil + fish → "unknown"

* Curate per-sample MHC for Tiers 3+4: cell lines + patient tissue

Coverage: 203 → 311 / 332 samples (93%)
- 207 samples with known alleles
- 104 samples marked "unknown" (multi-donor tissue, aggregated lines)
- 21 samples uncurated (need paper supplementary data)

Cell line HLA lookup built from cross-referencing existing YAML entries:
JY, THP-1, HEK293, HCT116, HeLa, A549, A375, BV173, MSTO-211H,
GRANTA-519, SaOS-2, GR-LCL, and mono-allelic transfectant lines.

Multi-donor tissue/primary cell samples → "unknown" where per-donor
HLA typing not available in YAML.

* Bump to 0.9.6 — 93% per-sample MHC coverage

311/332 samples have mhc field (207 known, 104 unknown).
21 samples remain uncurated (patient tissue needing paper lookup):
- Heyder 2016, Chong 2018,... (continued)

488 of 1436 relevant lines covered (33.98%)

0.34 hits per line

Jobs
ID Job ID Ran Files Coverage
1 24204416728.1 15
33.98
 GitHub Action Run
Source Files on build 24204416728