Q48 enumeration: every antigen, identifier and query this beat ran - including what was searched and rejected, and the three identifier traps found live
also called Q48 enumeration · surface antigen beat ledger
This is the bookkeeping entry for the surface-antigen beat: what was looked up, what was found, what was deliberately not written, and every search that came back empty with the proof that the search itself worked. It exists so that somebody repeating this work next year repeats the decisions and not just the searches.
The same thing, for a scientist
**Status: run, 2026-09-20.** This entry records the beat's enumeration, its **bounded counted absences** (every zero with a date, an exact query string, a tool and a passing positive control), its **bounded rejections** (papers and targets considered and dropped, which the brief notes leave no trace anywhere else in this graph), and the **three identifier traps found live** during the work. **Headline measurements, all 2026-09-20.** | antigen | node files naming it (before this beat) | had an entry? | class | |---|---:|---|---| | NG2/CSPG4 | 59 | yes | protein | | **CD15** | **24** | **no** | glycan - no gene | | **HLA-DR** | **15** | **no** | two-chain complex | | **TdT** (`DNTT`: 4) | **14** | **no** | protein, wrong name used | | **CD65** | **13** | **no** | glycolipid - no gene | | **CD65s** | **8** | **no** | glycolipid - no gene | | **CD371** | **7** | **no** | protein (CLEC12A) | | **CLEC12A** | **4** | **no** | protein | **The beat's central negative finding.** The repair that looks obvious - add HGNC previous symbols and aliases to the named-but-unwritten queue - **fixes TdT and breaks CD15**, because `CD15` is a previous official HGNC symbol of *FUT4*. Blindness becomes false confidence. See `concept-a-cd-number-is-not-a-gene`.
Bounded counted absences - every zero, with its control
Rule 67 compliance: each test below was run through the identical code path as its controls, on 2026-09-20, with PubMed querytranslation read back. No parenthesised der(n) token and no unquoted multi-word phrase was used.
| # | query | tool | result | control(s) through the same path |
|---|---|---|---|---|
| 1 | CLEC12A AND (KMT2A OR MLL) AND (knockout OR knockdown OR CRISPR OR dependency) | PubMed | 0 | CLEC12A = 156; KMT2A OR MLL = 9,229; CLEC12A AND leukemia = 54 |
| 2 | (CLEC12A OR CLL-1 OR CD371 OR MICL) AND (KMT2A OR MLL) AND (knockout OR knockdown OR CRISPR OR dependency OR essential) | PubMed | 1, title-checked to zero | same as above |
| 3 | CLEC12A AND (KMT2A OR MLL) AND (knockout OR CRISPR OR dependency) | Europe PMC full text | 74, of which 2 titles name CLEC12A or an alias, neither a KMT2A functional test | CLEC12A = 1,361; CLEC12A AND (KMT2A OR MLL) = 142 |
| 4 | (FUT4 OR FUT9) AND (KMT2A OR MLL) | PubMed | 1 (PMID 32347296, FUT4 only) | FUT4 OR FUT9 = 350; CD15 AND (KMT2A OR MLL) = 36 |
| 5 | (HLA-DRA OR HLA-DRB1) AND (KMT2A OR MLL) AND leukemia | PubMed | 2, title-checked: one transplant-matching, one chromatin | HLA-DRA OR HLA-DRB1 = 12,630; "HLA-DR" AND (KMT2A OR MLL) = 44 |
| 6 | DNTT AND (KMT2A OR MLL) | PubMed | 2 | (terminal deoxynucleotidyl transferase OR TdT) AND (KMT2A OR MLL) = 39 |
| 7 | HGNC /search/alias_symbol/CD65 and /search/CD65 | HGNC REST | empty | identical calls returned FUT4 for CD15 and CLEC12A for CD371 |
What each absence licenses, stated narrowly:
- #1-#3: no published functional test of CLEC12A dependence in KMT2A-rearranged leukaemia. Residual: 72 Europe PMC full-text co-mentions were title-checked, not read.
- #4: the enzymes that build CD15 are essentially absent from the KMT2A literature, which discusses the epitope 36 times.
- #5: no study reports whether HLA-DR expression on KMT2A-rearranged blasts differs from other B-precursor ALL.
- #6: a symbol-keyed literature sweep for TdT finds 2 of 39 papers, and the decisive one (PMID 34148065) is not among them.
- #7:
CD65is unresolvable in HGNC - the honest blank.
One instrument caveat that cuts against this beat's own framing. PubMed's counts are not like-for-like across these rows: CD15 expands to "lewis x antigen"[Supplementary Concept], CLEC12A and FUT4 and DNTT expand through ... protein human Supplementary Concepts, while FUT9, CD65 and CD65s are bare All-Fields string matches with no expansion at all. Ratios across differently-indexed terms overstate the gap. The in-graph regex counts, where no expansion happens on either side, are the cleaner measurement.
Bounded rejections - considered and not written, with what would change my mind
The brief notes that bounded rejection does not exist anywhere in this graph and is the larger half of a negative. These are this beat's.
- PMID 33097838, A trispecific killer engager molecule against CLEC12A effectively induces NK-cell mediated killing of AML cells (Leukemia, 2021). On-beat modality, not written as its own entry because the beat's CLEC12A therapeutic coverage is already carried by two clinical studies 12 and a preclinical gated design; a third preclinical modality adds little. Would change my mind: if a TriKE entered clinical trial in KMT2A-rearranged disease.
- PMID 37848261, Asymmetric anti-CLL-1xCD3 bispecific antibody, ABL602 2+1, with attenuated CD3 affinity (JITC, 2023). Same reason; noted because low-affinity-CD3 design is the bispecific analogue of the interferon-gamma attenuation strategy in the risk entry. Would change my mind: clinical data.
- PMID 34253594, Anti-CD19 CAR T Cells That Secrete a Biparatopic Anti-CLEC12A Bridging Protein (Mol Cancer Ther, 2021). Directly relevant to CD19-to-myeloid lineage switch in KMT2A-r disease and arguably belongs in this graph - but it belongs in the CD19/lineage-switch beat, not here, and per the brief I do not write into another beat's territory. Flagged to the coordinator as a gap.
- PMID 39133622 (tandem CD33-CLL1 CAR-T) and PMID 35261791 (PD-1 knockdown CLL-1 CAR-T case reports). Small series and case reports; the phase 1 data in 1 and 2 dominate them. Would change my mind: nothing short of a controlled comparison.
- PMID 33220589's CD123 conclusion. Read and deliberately left in
gene-clec12a's counter-evidence rather than written up, becausegene-il3raalready exists and owns CD123. - The sialyltransferase that makes CD65s. ST3GAL4 (Q11206, 333 aa) and ST3GAL6 (Q9Y274, 331 aa) were resolved in UniProt and deliberately not asserted, because no source read on this beat attributes the VIM-2 epitope to either. Recording this unresolved is the correct outcome. Would change my mind: a paper attributing the VIM-2 ganglioside to a named sialyltransferase in myeloid cells.
- CLEC12B (Q2HXU8, 276 aa). Looked up as an identifier control; no leukaemia relevance found, no entry written.
- PMID 26571505 was named in the dispatch brief as background and then withdrawn by the coordinator mid-beat as belonging to another agent's beat. Not searched, not read, not cited.
Three identifier traps found live on this beat
Trap A - CLL1 is a gene synonym of two reviewed human genes, and the wrong one sorts first. gene:CLL1 AND organism_id:9606 AND reviewed:true returns COLEC10 (Q9Y6Z7, Collectin-10 / CL-L1, 277 aa) before CLEC12A (Q5QGZ9, 265 aa). Twelve residues apart - tighter than the SMC1A/SMC3 pair (16) that rule 66 calls the limit of the length defence. Add CLEC12B (Q2HXU8, 276 aa) and three unrelated proteins lie within 12 residues. verify-accessions.py's length assertion provides no protection here; only gene_primary does. CL-L1 and CLL-1 differ by one hyphen and name different proteins. 3
Trap B - CD15 is a PREVIOUS OFFICIAL HGNC SYMBOL of FUT4. An antigen with no gene has, historically, been the official name of an enzyme gene, and HGNC free-text search still returns FUT4 for the string. The obvious repair to the named-but-unwritten queue introduces this error while fixing the TdT one. 4
Trap C - the length band on this beat is pathologically crowded. HLA-DRA 254, CLEC12A 265, HLA-DRB1 266, CLEC12B 276, COLEC10 277. Five proteins, four of them unrelated, within 23 residues. By contrast FUT4 (530) and FUT9 (359) are 171 apart and DNTT (509) is isolated. A length check is a real discriminator for some genes on this beat and worthless for others, and nothing in the check tells you which case you are in. 35
And one near-miss worth recording as a process failure. A DOI for PMID 9376686 was written into a draft evidence block as 10.1093/glycob/7.7.973 before the record was fetched. The true DOI is 10.1093/glycob/7.6.835. It was caught by fetching the record before the file was written, not by a checker. This is the brief's rule - when you have the fetched record open, copy every identifier out of it - failing in real time, and it is logged here rather than quietly fixed.
| script | no committed script; run interactively via NCBI E-utilities, Europe PMC REST, UniProt REST and HGNC REST on 2026-09-20 |
|---|---|
| status | run |
| result summary | 16 entries written to data/graph/nodes/surface-antigens/. Seven bounded counted absences recorded with passing positive controls. Three identifier traps found live: the CLL1/COLEC10/CLEC12B 12-residue collision, CD15 as a previous HGNC symbol of FUT4, and a five-protein 23-residue length band that defeats the length check. One DOI near-miss caught by re-fetching before writing. |
| bounded absences | 7 |
inputs
[ "PubMed E-utilities esearch/efetch", "Europe PMC REST search", "UniProt REST uniprotkb/search", "HGNC REST fetch and search", "regex sweep of data/graph/nodes/*/*.json" ]
graph mentions 2026 09 20 — the numbers behind the chart
{
"NG2": 59,
"CD15": 24,
"HLA-DR": 15,
"TdT": 14,
"CD65": 13,
"CD65s": 8,
"CD371": 7,
"DNTT": 4,
"CLEC12A": 4,
"FUT4": 2,
"FUT9": 1,
"total_node_files": 1465
}bounded rejections
[ "33097838 TriKE", "37848261 ABL602 bispecific", "34253594 CD19-CAR CLEC12A bridging protein (belongs to the CD19 beat)", "39133622 tandem CD33-CLL1 CAR", "35261791 PD-1 knockdown CLL-1 CAR case reports", "33220589 CD123 conclusion (gene-il3ra owns it)", "ST3GAL4/ST3GAL6 as the CD65s sialyltransferase (unresolved, deliberately not asserted)", "CLEC12B (identifier control only)" ]
entries written
[ "gene-clec12a", "mechanism-menin-inhibition-induces-clec12a", "mechanism-clec12a-dependence-nup98-nsd1", "hyp-clec12a-is-a-dependency-not-only-a-marker-in-kmt2a-r", "exp-clec12a-knockout-in-kmt2a-r-models", "ana-clec12a-dependency-in-kmt2a-r-depmap", "risk-clec12a-directed-therapy-myeloid-ablation", "target-cd15-lewis-x", "gene-fut4", "gene-fut9", "target-cd65-vim2-neutral-glycolipid", "target-cd65s-sialylated-vim2-ganglioside", "target-hla-dr-class-ii-heterodimer", "gene-hla-dra", "gene-hla-drb1", "gene-dntt", "concept-a-cd-number-is-not-a-gene", "ana-surface-antigen-enumeration-q48" ]
- **The controls prove the instrument works; they do not prove the query was right.** KITE-222 was recovered by title-checking 74 full-text co-mentions, not by any of this beat's targeted queries. A passing positive control says the tool returns ones - it says nothing about whether the question was well posed.
- **Seventy-two Europe PMC records were title-checked and not read.** That is the residual on this beat's largest absence claim and it should be stated every time the claim is quoted.
- **This beat's own counts disagree with the dispatch brief's by one or two in every case and the discrepancies are unreconciled.** Quoting either set as exact would be an over-claim; the conclusions survive either way but the numbers should carry the word 'about'.
- Does the named-but-unwritten queue expand HGNC aliases before counting? If not, the DNTT-class undercount is live for every gene the graph calls by a nickname, and nobody has swept for the general case.
- How should a symbol-keyed instrument represent an antigen with no gene at all? This beat's answer is a `target` node with an explicit `data.encoded_by_a_gene: false`, but nothing enforces that field.
- Was the single most decision-relevant paper on this beat (KITE-222) reachable by any targeted query, or only by title-checking a full-text co-mention list? If the latter is general, every bounded absence in this graph is weaker than its controls suggest.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In the first-in-human phase I study of CLL-1 CAR-T cells in 10 adults with R/R AML, all patients developed CRS and severe pancytopenia, two died of severe infection due to chronic agranulocytosis, and the CR/CRi rate was 70%.
First-in-human phase I study of CLL-1 CAR-T cells in adults with relapsed/refractory acute myeloid leukemia. · Jin X, Zhang M, Sun R, Lyu H, Xiao X, Zhang X, et al. · J Hematol Oncol 2022What this evidence cannot show
Abstract read in full from raw NCBI efetch XML on 2026-09-20; full text not read. n=10, adults, single arm. Cited in this enumeration only to justify the bounded rejection of three smaller CLEC12A modality papers on the grounds that clinical data dominate preclinical data.
Evidence that argues against this (1)
- Two phase 1 studies with opposite-looking safety profiles (this one and KITE-222) are a thin basis for dismissing preclinical modality papers, since the preclinical designs exist precisely because the simple constructs did not work. Daver N et al. 2026
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In the KITE-222 phase 1 study of a CLL-1-directed CAR T in 12 R/R AML patients, clinically meaningful responses were lacking across dose levels and CLL-1-negative blasts persisted after CLL-1-positive blasts were depleted.
Phase 1 Study of KITE-222, an Autologous CLL-1-Directed CAR T-cell Therapy in Patients with Relapsed/Refractory Acute Myeloid Leukemia. · Daver N, Blachly JS, Ghobadi A, Advani A, Muffly L, Garciaz S, et al. · Clin Cancer Res 2026What this evidence cannot show
Abstract read in full from raw NCBI efetch XML on 2026-09-20; full text not read. n=12, adults, dose escalation. This paper was found only through a Europe PMC title-check of the 74 full-text co-mentions and would have been missed by the PubMed-only route used for absences #1 and #2 - which is the most instructive thing in this enumeration.
Evidence that argues against this (1)
- That the beat's single most decision-relevant clinical paper was recovered by title-checking a full-text co-mention list, rather than by any targeted query, means the targeted queries in this entry's absence table are less complete than their controls make them look. The controls prove the instrument returns ones; they do not prove the query is well specified. Q48-surface-antigens 2026
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
Queried live on 2026-09-20, `gene:CLL1 AND organism_id:9606 AND reviewed:true` returns COLEC10 (Q9Y6Z7, 277 aa) before CLEC12A (Q5QGZ9, 265 aa); CLEC12B is Q2HXU8 at 276 aa; and HLA-DRA (P01903, 254 aa), CLEC12A (265), HLA-DRB1 (P01911, 266), CLEC12B (276) and COLEC10 (277) all lie within 23 residues of one another.
UniProtKB reviewed entry Q5QGZ9 (CL12A_HUMAN) · UniProt Consortium · UniProtKB 2026What this evidence cannot show
All accessions fetched live from the UniProt REST API on 2026-09-20 with fields accession, gene_primary, gene_synonym, protein_name, length; every returned row was read and only rows whose primary gene name equalled the queried symbol were kept, per rule 62. The 23-residue observation is arithmetic on five canonical lengths and has no biological content - it is a statement about the failure mode of a checking heuristic, not about the proteins.
Evidence that argues against this (1)
- A crowded length band is an accident of which proteins this beat happened to touch, not a general property of the proteome, and quoting it as if it indicted `verify-accessions.py` overstates the case. The correct reading is narrower: the length check adds nothing for these five and should not be relied on as the sole swap detector anywhere. UniProt Consortium 2026
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
HGNC record HGNC:4015 lists CD15 among the previous official symbols of FUT4, and an HGNC free-text search on the string CD15 returns FUT4 as its top hit, while the same free-text call on CD65 returns no records and on CD371 returns CLEC12A.
HGNC record HGNC:4015 (FUT4) · HUGO Gene Nomenclature Committee · HGNC 2026What this evidence cannot show
Fetched live from the HGNC REST API on 2026-09-20; the CD371 and CD15 returns are the positive controls that make the CD65 blank interpretable. Bounds HGNC's indexing on one date only.
Evidence that argues against this (1)
- HGNC is correct to record the history; the defect is in any downstream code that reads a previous-symbol list as a CD-number-to-gene map. Framing this as an HGNC problem would send an implementer to fix the wrong component. HUGO Gene Nomenclature Committee 2026
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
As of 2026-09-20 the counts of node files naming each antigen are NG2 59, CD15 24, HLA-DR 15, TdT 14, CD65 13, CD65s 8, CD371 7, DNTT 4, CLEC12A 4, FUT4 2 and FUT9 1, out of 1,465 node files.
Q48 surface-antigen beat: bounded counted-absence sweep, PubMed E-utilities and Europe PMC REST · Q48-surface-antigens · Oncofusion knowledge graph (internal measurement, 2026-09-20) 2026What this evidence cannot show
Measured by a Python regex sweep over all node JSON files on 2026-09-20 using word-boundary patterns where the token could be a prefix of another (`\bCD15\b`, `\bCD65\b`, `\bCD65s\b`, `\bTdT\b`, `\bDNTT\b`, `\bFUT4\b`, `\bFUT9\b`, `\bNG2\b`) and plain substring patterns for `CLEC12A`, `CD371` and `HLA-DR`. **Three consequences:** `HLA-DR` matches `HLA-DRA` and `HLA-DRB1` as substrings so 15 is an upper bound; `\bTdT\b` is case-sensitive and misses `TDT` so 14 is a lower bound; and all counts include matches inside citation titles. **The dispatch brief's figures (CD15 23, TdT 13, HLA-DR 13, CD65 12, CD65s 7, DNTT 3) differ from these by one or two in six of six cases and the discrepancies are NOT reconciled** - most likely a different regex or a graph that has grown since. Both sets support every conclusion drawn; neither exact number should be quoted alone.
Evidence that argues against this (1)
- A string count measures mentions, not coverage. Several of CD15's 24 files mention it only inside a quoted immunophenotype string, so the count overstates substantive discussion - which weakens the argument that the named-but-unwritten queue was missing something important, even though inspection confirms it was. Q48-surface-antigens 2026
the existing inventory, every member of which is a lineage or maturation marker rather than a fusion-specific output
the corpus's existing antigen enumeration, which this screen extends from a curated list to the surfaceome
- supports →The named-but-unwritten queue is keyed on gene symbols, so CD15 is invisible to it at 23 entries
independent re-measurement of the blind spot, plus the finding that the obvious repair introduces a new error
- supports →A CD number names a reagent cluster, not a molecule - and four different things can sit behind one
the four-case taxonomy this beat's enumeration produced
identifier trap A: CLL1 resolves to COLEC10 ahead of CLEC12A at 12 residues' difference
the bounded counted absence behind the KMT2A-r dependency gap, with its controls and its residual
identifier trap B: CD15 is a previous official HGNC symbol of FUT4
the nickname undercount: TdT 14 files, DNTT 4, and 2 of 39 papers reachable by symbol
the antigens enumerated here are the panel that entry describes
- ← supportsFUT9 - the dedicated Lewis-x synthase, structurally solved, and untouched by the KMT2A literature
the control case: no synonyms, no previous symbols, and therefore no alias rescue for its zero