What this beat searched, read and set aside - including one cell line the accession database has not caught up with, and one query that returns a clean zero

[
  {
    "q": "t(9;11) AND (leukemia)",
    "count": 0,
    "translation": "\"t\"[All Fields] AND 9,11[UID] AND (...)",
    "warninglist": "No items found",
    "verdict": "parser trap; unusable"
  },
  {
    "q": "t 9 11 AND leukemia",
    "count": 610,
    "verdict": "usable bare-token form"
  },
  {
    "q": "KMT2A-MLLT3",
    "count": 92
  },
  {
    "q": "MLL-AF9",
    "count": 623,
    "verdict": "retired symbol returns 6.8x the current symbol"
  },
  {
    "q": "AF9 AND YEATS AND leukemia",
    "count": 20
  },
  {
    "q": "MLLT3 AND menin",
    "count": 3
  },
  {
    "q": "MLL-AF9 AND (CBX8 OR BCOR)",
    "count": 7
  },
  {
    "q": "MLL-AF9 subnuclear",
    "count": 1
  },
  {
    "q": "MLL-AF9 immunofluorescence nuclear",
    "count": 1
  },
  {
    "q": "(MLL-AF9 OR KMT2A-MLLT3) AND (nuclear speckle OR nuclear body OR nucleolus)",
    "count": 3
  },
  {
    "q": "MLLT3 nucleolus",
    "count": 0,
    "warninglist": "No items found"
  },
  {
    "q": "AF9 nuclear localization signal MLLT3",
    "count": 4,
    "verdict": "none on point"
  },
  {
    "q": "MLL-AF9 YEATS domain transformation",
    "count": 0,
    "warninglist": "No items found",
    "verdict": "no published in-cis add-back"
  },
  {
    "q": "MLL-AF9 condensate phase separation",
    "count": 1
  },
  {
    "q": "MI-503 menin MLL small molecule leukemia",
    "count": 4
  },
  {
    "q": "Menin-MLL inhibitor MI-503 MLL-AF9 MOLM-13 leukemia",
    "count": 0,
    "verdict": "over-specified AND-chain manufactures an absence"
  }
]

[
  {
    "pmid": "42063817",
    "reason": "MD simulation only; stability ordering conflicts with measured affinities",
    "would_change": "experimental validation of the metastable intermediates",
    "title": "Mechanism of AF9 (MLLT3)-Partner Dissociation in Mixed-Lineage Leukemia-Rearranged Leukemia.",
    "authors": "Sharma S, Joshi K, Saha A",
    "venue": "JACS Au",
    "year": 2026,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  },
  {
    "pmid": "40964345",
    "reason": "preprint about wild-type ENL/AF9 YEATS inhibition; the t(9;11) fusion has no YEATS domain",
    "would_change": "evidence that YEATS inhibition acts on the fusion rather than on wild-type protein in t(9;11) cells",
    "title": "A chemical-genetic interaction between PAF1 and ENL/AF9 YEATS inhibition.",
    "authors": "Barta PA, Garnar-Wortzel L, Bishop TR, et al.",
    "venue": "bioRxiv",
    "year": 2025,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  },
  {
    "pmid": "38747396",
    "reason": "AHD peptidomimetic structures with no cellular or in vivo data; this beat's druggability position rests on paralogue cross-reactivity",
    "would_change": "a selectivity profile distinguishing AF9 from ENL",
    "title": "Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors.",
    "authors": "Yang Y, Ahmad E, Premkumar V, et al.",
    "venue": "Protein Sci",
    "year": 2024,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  },
  {
    "pmid": "42020782",
    "reason": "zebrafish transgene; architecture is chosen, so it cannot inform human breakpoint distribution",
    "would_change": "extraction of the construct's MLLT3 boundary",
    "title": "A transgenic zebrafish leukemia model driven by KMT2A::MLLT3 (MLL-AF9).",
    "authors": "Saberi M, Delfi O, Hall CJ, et al.",
    "venue": "Leukemia",
    "year": 2026,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  },
  {
    "pmid": "42613434",
    "reason": "co-mutation and progression, out of this beat's scope",
    "would_change": "a beat on RAS co-mutation in the t(9;11) cell-line panel",
    "title": "Modeling KRAS mutations in KMT2A::MLLT3 acute myeloid leukemia promotes leukemic progression and transcriptional rewiring.",
    "authors": "Esparza N, Defrêne J, Bresson E, et al.",
    "venue": "Leukemia",
    "year": 2026,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  },
  {
    "pmid": "41656387",
    "reason": "new human KMT2A::MLLT3 line with no Cellosaurus accession; this project resolves lines by accession",
    "would_change": "a Cellosaurus entry, or direct reading of the establishment paper",
    "title": "A novel human acute myeloid leukemia cell line SDEY-AML1 with KMT2A: MLLT3, IKZF1: EVX1 fusions exhibits high tumorigenicity in NSG mice.",
    "authors": "Yang C, Zhang W, Wu Y, et al.",
    "venue": "Sci Rep",
    "year": 2026,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  }
]

[
  {
    "pmid": "16239140",
    "routes_tried": [
      "EPMC core record: pmcid none, isOpenAccess N"
    ],
    "note": "no PMCID, so routes 2-4 have no target; used from abstract only",
    "title": "The menin tumor suppressor protein is an essential oncogenic cofactor for MLL-associated leukemogenesis.",
    "authors": "Yokoyama A, Somervaille TC, Smith KS, et al.",
    "venue": "Cell",
    "year": 2005,
    "title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
  }
]

[
  {
    "trap": "success-shaped PMC HTML stub",
    "detail": "PMC7810303 (a guessed PMCID) returned HTTP 200, 21,303 HTML characters, 165 characters of stripped text; the correct PMCID PMC7497807 strips to 74,855"
  },
  {
    "trap": "parenthesised karyotype",
    "detail": "t(9;11) AND (leukemia) -> 0 with 9,11[UID]"
  },
  {
    "trap": "Europe PMC fullTextXML HTTP 500",
    "detail": "PMC11246743 returned 500; the PMC HTML page returned 61,252 characters of stripped text"
  },
  {
    "trap": "Cellosaurus fielded query undercounts",
    "detail": "a query restricted to ca:'Cancer cell line' returned 2 of 11 lines; paging the unfielded query and filtering on the structured fusion comment returned all 11"
  },
  {
    "trap": "shared scratchpad",
    "detail": "a helper script and a citations file written by this agent were overwritten by a concurrently running agent in the same session scratchpad; citation identifiers were re-fetched into a uniquely named file before any were used"
  }
]

{
  "endpoint": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11687943/supplementaryFiles",
  "result": "HTTP 200, valid PK zip, 1,261,425 bytes, six figure files, no Table S3"
}

[
  "partner-side breakpoint distribution in t(9;11) stratified by therapy-induced status",
  "whether the 2 spliced and the 2 YEATS-retaining KMT2A::MLLT3 cases are the same patients",
  "the exon-level composition of the unaccounted ~1.1% of the 442 t(9;11) breakpoints"
]