neoantigens/: the tested screens at epitope resolution

Adds a neoantigens/ directory holding what the compendium was missing: the screened neoantigen
sets as short peptides rather than minigenes.

- neoantigens_tested_peptides.tsv.gz -- 423,085 screened 8-12mers with their wild-type counterpart
and restricting alleles, 178 CD8-immunogenic over 98 patients, across NCI (420,786), HiTIDE
(1,563) and TESLA (736), with the authors' own train/test split. Harmonized from
raw/immunogenicity/NCI_dataset_only_tested.txt, which had been sitting unharmonized.
- nci_gartner_mmp.tsv.gz -- 144 distinct confirmed CD8+ minimal epitopes with restricting HLA;
120 carry the wild-type mmp, so agretopicity is measurable rather than predicted.
- nci_gartner_nmers.tsv.gz -- the 9,541 screened mutations those came from.
- nci_gartner_samples.tsv.gz -- 98 patient class-I genotypes, which is what makes a per-patient
allele-aware scan possible at all.

Gartner et al., Nat Cancer 2021;2(5):563-574, doi:10.1038/s43018-021-00197-6, Suppl. Tables
1, 3, 11, 12, 18, 20.

Canonical columns stay as-reported; every predicted quantity carries a pred_ prefix, so affinity
and agretopicity are never populated from a prediction.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

DESCRIPTION.md

@@ -58,6 +58,10 @@ the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive, and the mTEC-
 | `immunogenicity/neoag_tested_mmu.tsv.gz` | 12 | Neoantigens — tested, **mouse MHC** | 1,977 murine tested neo-epitopes (IEDB), immunogenicity 0/1 (740 immunogenic); `mhc_species=MusMusculus` |
 | `immunogenicity/neoag_tested_hsa.tsv.gz` | 12 | Neoantigens — tested, **human MHC in mouse models** | 717 rows from the same IEDB export whose restriction is HLA — HLA-transgenic mice plus human-host epitopes (KRAS G12D, CDK4 R24C, PMEL); `mhc_species=HomoSapiens` |
 | `immunogenicity/nci_complete.tsv.gz` | 9 | Neoantigens — complete NCI screen (variant) | 1,326 mutant 25-mer minigenes across 46 GI-cancer patients with CD8/CD4 T-cell screen outcomes (28 CD8-immunogenic) — a predictor-agnostic *screened* set with real negatives. Standalone variant, **minigene-level** (`peptide` = minigene, `mhc_a` blank — not epitope-deconvolved). Source: Koşaloğlu-Yalçın et al., iScience 2022, Table S6 ([doi:10.1016/j.isci.2022.103850](https://doi.org/10.1016/j.isci.2022.103850), PMID 35128348) |
+| `neoantigens/neoantigens_tested_peptides.tsv.gz` | 16 | Neoantigens — tested, **epitope-level** | 423,085 screened 8–12mers with their wild-type counterpart and restricting alleles, 178 CD8-immunogenic, 98 patients, over three datasets (`NCI` 420,786 · `HiTIDE` 1,563 · `TESLA` 736) and the authors' own `split`. This is the screen at the resolution a pMHC model is scored at — the complement to the minigene-level `nci_complete`. Harmonized from `raw/immunogenicity/NCI_dataset_only_tested.txt` by `bench/neoag/ingest_tested.py` (2026-mhcmatch-benchmark). Predicted quantities keep a `pred_` prefix; `peptide`, `peptide_wt`, `mhc_a` and `immunogenicity` are as-reported |
+| `neoantigens/nci_gartner_mmp.tsv.gz` | 45 | NCI — confirmed CD8+ minimal epitopes | 147 rows / 144 distinct minimal mutant peptides (mmp) with restricting HLA; 120 carry the wild-type mmp, so agretopicity is **measurable rather than predicted**. `split` preserves the paper's train/test. Source: Gartner et al., Nat Cancer 2021, Suppl. Tables 3 & 20 ([doi:10.1038/s43018-021-00197-6](https://doi.org/10.1038/s43018-021-00197-6)) |
+| `neoantigens/nci_gartner_nmers.tsv.gz` | 21 | NCI — full screened nmer universe | 9,541 screened mutations as WT/mutant 25-mers (144 CD8+), with gene, mutation type, RNA-seq presence and exome VAF decile — the negative universe at the unit the assay used. Same source, Suppl. Tables 11 & 12 |
+| `neoantigens/nci_gartner_samples.tsv.gz` | 15 | NCI — patient class-I genotypes | 98 patients with full HLA-A/B/C genotype, histology and per-patient screening counts. The genotype is what makes a per-patient allele-aware scan possible. Same source, Suppl. Tables 1 & 18 |
 | `tcga/tcga_neoantigens.tsv.gz` | 10 | TCGA neoantigens | 2.24M expressed mutant-peptide–HLA binders across 8,505 TCGA donors (derived from open-access TCGA somatic + expression; per-barcode HLA/neoantigens as in TCIA / Thorsson 2018) |
 | `immunogenicity/hla_pop_freqs.tsv.gz` | — | HLA population freqs | EUR/ASN/AFR class-I (A/B/C) allele frequencies (AFND) |
 | `proteome/human.fasta.gz` | 4 | Human proteome (UP000005640) | self-reference proteome for similarity search |

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