vaccines: IVAC MUTANOME, the one table with a label on every manufactured unit

Sahin et al., Nature 547:222-226 (2017), Supplementary Table 2, retrieved through PubMed
(doi:10.1038/nature23003, PMID 28678784). 125 vaccine units across 13 patients, every one
assayed after vaccination: 75 responded, 60 CD4+, 31 CD8+, 50 measured negative.

Why this one is different from everything else in `vaccines/`. The NEO-PV-01 tables say what
was manufactured and what was monitored; only 19 units anywhere carry a per-unit outcome.
Here the trial assayed all ten units of each cassette, so the negatives are measured
negatives rather than units nobody looked at.

Two facts a reader needs and cannot get from the columns. The mutation sits at position 14 of
a full-length 27-mer -- verified against `aa_change` on every row by the ingest -- so anything
scoring by window has to span that residue; most 8-11mers of a 27-mer contain no mutation and
describe the germline protein. And this table is **held out of the EPIC fit**: no patient in
`neoantigens_tested_peptides.tsv.gz`, and 2 of the 125 units share even an 8-11mer with it.
That is the opposite of `nci_parkhurst_gi.parquet`, which is why that one needs `in_epic_fit`
and this one does not.

`resp_cd4`/`resp_cd8` are null on the single responding unit whose class the trial reports as
`n.k.`, never a silent zero.

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

vaccines/SOURCES.md

@@ -25,11 +25,13 @@ no such field — verified byte-identical across two runs.
 | `cassettes.parquet` | 1,506 | 1,496 | 81 | 2 | 14–30 |
 | `assayed_units.parquet` | 5,427 | 5,410 | 47 | 2 | 8–17 |
 | `unit_responses.parquet` | 19 | 19 | 4 | 1 | 14–17 |
+| `ivac_mutanome_units.parquet` | 125 | 125 | 13 | 1 | 14–27 |
 
 | trial | cassettes | units | cassette size | assayed pools | `EPT` | `ASP` |
 |---|--:|--:|:--:|--:|--:|--:|
 | `NEO-PV-01-NT001` | 60 | 1,005 | 9–20 | 34 | 2,195 | 1,961 |
 | `NEO-PV-01-NT002` | 21 | 501 | 11–30 | 13 | 400 | 871 |
+| `IVAC-MUTANOME` | 13 | 125 | 5–10 | 13 | — | — |
 
 Cassettes outnumber assayed pools because both trials published every patient's vaccine composition
 but monitored a subset. NT-002's 21 published cassettes are of 38 patients treated; NT-001's 60 are
@@ -77,6 +79,35 @@ responded to both. `peptide_wt` is the matched wild-type sequence. Every `peptid
 epitopes generating any T-cell response across its 13 assessed patients (39 % CD4⁺, 31 % CD8⁺), but
 as Figure 4B values rather than a table, so 501 units cannot be labelled and 19 can.
 
+### `ivac_mutanome_units.parquet` — what was manufactured **and** what responded
+
+The only deposited table carrying a **measured response label on every manufactured unit**. IVAC
+MUTANOME assayed all ten units of each patient's cassette after vaccination, so its 50 non-responding
+units are measured negatives rather than units nobody looked at.
+
+| column | provenance | notes |
+|---|---|---|
+| `trial` | **derived** | `IVAC-MUTANOME` |
+| `patient` | **experimental** | `P01`…`P19`, the trial's own alias |
+| `unit_id` | **experimental** | position on the pentatope, `A1`–`B5` |
+| `mutation_id` | **experimental** | `P04-C7-E258K` — patient, gene, substitution |
+| `gene`, `aa_change` | **experimental** | |
+| `peptide`, `peptide_len` | **experimental** / **derived** | the 27-mer as manufactured; 11 shorter, at a protein terminus |
+| `construct` | **derived** | `RNA-pentatope` — five units per RNA, two RNAs per patient |
+| `exon_expression` | **experimental** | the trial's own exon expression level |
+| `hla_i_score`, `hla_ii_score` | **experimental** | the trial's own binding scores, computed with each patient's real genotype; smaller is better |
+| `pre_existing` | **experimental** | a response detectable before vaccination |
+| `responded` | **experimental** | any post-vaccination T-cell response — **75 of 125** |
+| `resp_cd4`, `resp_cd8` | **experimental** | 60 and 31; a unit can raise both (19 did). Null on the one responding unit whose class the trial reports as `n.k.`, never a silent zero |
+
+**The mutation sits at position 14 of a full-length 27-mer**, verified against `aa_change` on every
+row by the ingest. Anything scoring this table by window should span that residue: most 8–11mers of a
+27-mer contain no mutation at all and describe the germline protein.
+
+**No IVAC patient is in `neoantigens/neoantigens_tested_peptides.tsv.gz`**, and only 2 of the 125
+units share even an 8–11mer with it, so this table is held out of the EPIC fit by patient and very
+nearly by sequence. That is the opposite of `nci_parkhurst_gi.parquet`, which needs `in_epic_fit`.
+
 ---
 
 ## Citations
@@ -95,6 +126,13 @@ and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cance
 doi:[10.1016/j.ccell.2022.08.003](https://doi.org/10.1016/j.ccell.2022.08.003) ·
 PMID [36027916](https://pubmed.ncbi.nlm.nih.gov/36027916/).
 
+**IVAC MUTANOME.** Sahin U, Derhovanessian E, Miller M, Kloke BP, Simon P, Löwer M, Bukur V,
+Tadmor AD, Luxemburger U, Schrörs B, …, Türeci Ö. "Personalized RNA mutanome vaccines mobilize
+poly-specific therapeutic immunity against cancer." *Nature* 2017;**547**(7662):222-226.
+doi:[10.1038/nature23003](https://doi.org/10.1038/nature23003) ·
+PMID [28678784](https://pubmed.ncbi.nlm.nih.gov/28678784/). Supplementary Table 2; record retrieved
+from PubMed.
+
 ---
 
 ## Companion tables deposited in the same pass

vaccines/ivac_mutanome_units.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:df7923bcf06f10a3b2aff13c81d4cb450a011cf97f59763339e0fa62836b54e0
+size 12458