Oncofusion

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Explainerunrated confidence 0 of 5: unrated

The eleven-line panel is nine patients, seven of them myeloid, and none an infant

also called eleven lines nine patients · DepMap KMT2A panel composition · effective n of the rearranged panel

Almost every dependency conclusion in this project comes from eleven cancer cell lines. They came from nine people, most of them adults with a different kind of leukaemia from the one we study, and not one of them was a baby.

The same thing, for a scientist

Roughly **138 entries in this graph quantify the DepMap KMT2A-rearranged panel** — 'the 11 Cellosaurus-annotated KMT2A-rearranged lines' — and treat those eleven as eleven samples. Resolved by accession, they are **nine individuals**: SEMK2 is a child record of SEM and MOLM-14 of MOLM-13. **Seven of the nine are myeloid or monocytic**, against a disease that is infant B-lymphoid. **The index-fusion arm is three patients** — a 32-year-old, a 10-year-old with monocytic AML, and a 5-year-old counted twice. Ages run 1Y to 65Y and **none is under one year**.

Go deeper
The panel, resolved by accession
lineaccessionagesexCellosaurus disease term
SEMCVCL_00955YFChildhood B acute lymphoblastic leukemia
SEMK2CVCL_S9065YFchild record of SEM — same patient
RS4;11CVCL_009332YFAdult B acute lymphoblastic leukemia
MV4-11CVCL_006410YMChildhood acute monocytic leukemia
HB11;19CVCL_8227unspecifiedunspecifiedB-ALL with t(v;11q23.3)
THP-1CVCL_00061YMChildhood acute monocytic leukemia
NOMO-1CVCL_160931YFAdult acute monocytic leukemia
OCI-AML-2CVCL_161965YMAdult acute myeloid leukemia
MOLM-13CVCL_211920YMAdult acute monocytic leukemia
MOLM-14CVCL_791620YMsame patient as MOLM-13
SHI-1CVCL_219137YMAdult acute monocytic leukemia

Nine individuals, not eleven. SEMK2 (CVCL_S906) is a Cellosaurus child record of SEM (CVCL_0095); MOLM-14 of MOLM-13. Every per-line statistic computed over the eleven assumes an independence those pairs do not have.

Seven of the nine are myeloid or monocytic. Only SEM/SEMK2, RS4;11 and HB11;19 are B-lineage. The disease this project exists for is infant B-ALL, and the panel that supplies its dependency conclusions is dominated by adult monocytic leukaemia.

The index fusion is three patients: SEM/SEMK2 (5Y), RS4;11 (32Y, whose Cellosaurus disease term is literally Adult B acute lymphoblastic leukemia), and MV4-11 (10Y, monocytic). THP-1 is KMT2A::MLLT3 and HB11;19 is KMT2A::MLLT1.

Why this is one entry and not 138 edits

A sweep found 138 entries that quantify this panel without the patient-count caveat. Appending the same boilerplate to 138 entries would be a bulk mutation that adds noise to every one of them and makes the graph harder to read, not easier — and it would put the correction in 138 places that then drift apart.

So the correction lives here, once, and the entries that carry the most weight point at it. A reader who wants to know what 'the 11 KMT2A-rearranged lines' means has one place to look. The alternative — quietly leaving it uncorrected because correcting it properly is expensive — is the failure mode this project has been auditing itself for.

What the 138 entries say is not wrong: there are eleven lines in the DepMap panel. What is wrong is the inference a reader draws about sample size, lineage and age, and that inference is what this entry exists to block.

A recall error made while writing this entry

Assembling the table, the coordinator mapped NOMO-1 to CVCL_1274 from memory. That accession resolves to HEC-1, a 71-year-old's type II endometrial adenocarcinoma. NOMO-1 is CVCL_1609, a 31-year-old woman's adult acute monocytic leukaemia.

The error was caught because the API returns the primary name and the disease term, and an endometrial adenocarcinoma in a leukaemia panel is conspicuous. Had the recalled accession been another leukaemia line it would have passed. This is the fifth identifier-from-recall error the coordinator has made in four cycles, and it happened inside the check designed to enforce the rule against it. Resolve by accession and read back the primary name; the accession alone is not self-validating.

And again, in the same entry. The SEM founding paper's DOI was also typed from memory (...tb04912.x); the real one is 10.1111/j.1365-2141.1994.tb04726.x. Caught by verify-citations.py --strict on the run immediately after. That is two recall errors inside the single entry whose subject is recall errors, which settles the question of whether care is a sufficient control. It is not; the checker is.

The SEM question, asked and not answerable

This entry's own open question was whether the SEM patient was diagnosed in infancy — Cellosaurus records age at sampling and SEM is relapse-derived, so if she had been an infant at diagnosis the most-used index-fusion line in the world would be infant material and the verdict would move.

The founding paper was found and read, and it does not say. PMID 8199015 states the line was "established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia". Age at sampling, at relapse; no age at diagnosis anywhere in the abstract. The full text is unreachable: no PMCID, not in Europe PMC, checked under the corrected rule against both fullTextXML and efetch db=pmc. Same for the companion breakpoint paper.

So the question is bounded-unresolvable by this project's routes, not open. One could reason that infant ALL relapses early and a relapse at five years is unlikely to follow an infant diagnosis — but that is inference, and this graph has a rule about presenting inference as evidence.

The reading returned something better than it was sent for. SEM is biphenotypic: B-lineage CD19, CD22 and CDw75 in the absence of CD20, CD24 and immunoglobulin, together with myeloid CD13, CD15, CD33 and CDw65. That refines this entry's own lineage arithmetic. Calling the panel 'seven myeloid, four B-lineage' overstates how clean the B-lineage arm is: its largest member co-expresses four myeloid antigens. And the companion paper places SEM's crossover in KMT2A intron 7 — the 5' edge of the major breakpoint cluster region, which this graph elsewhere gives as intron 7 to exon 13.

The targeted audit, and how few entries it actually reaches

This entry's own open question was which of the 138 entries actually draw an inference the true composition would change. Audited on 2026-09-20.

A first pass for sample-size and generalisation language returned 20 candidates. Reading three of them showed eighteen were a false positive: they match on the phrase "computed by us from per-line API values", which is a statement about data provenance, not about sample size. A blanket edit would have annotated eighteen entries with an irrelevant caveat.

The answer is one. mechanism-kat8-mof-requirement-is-myeloid-not-fusion-specific E2 computes "n = 11 KMT2A-rearranged versus 42 other leukaemia gives a minimum detectable effect around d = 1" — a power calculation on eleven assumed-independent samples when there are nine patients. It is now corrected, and the correction runs against that entry's own conclusion: a wider detectable effect makes its null weaker, not stronger.

So the proportionate response to 138 matches was one citable entry and one edit. The instinct to bulk-annotate would have been wrong by a factor of 138, and the instinct to stop at 'too many to fix' would have missed the one that mattered.

Still open
  1. SEM's age at diagnosis is bounded-unresolvable by this project's routes: the founding paper gives 5 years at sampling in relapse and no diagnosis age, and its full text is unreachable. Institutional access or a note to the depositing laboratory would settle it.
  2. Re-run the lineage split on effective-n rather than line count for the analyses that report confidence intervals. Any interval computed over 11 assumed-independent lines is too narrow.
  3. Answered: one. A targeted audit found eighteen of twenty candidates were a false match on 'per-line API values', and the single real case was a minimum-detectable-effect calculation, now corrected.
Every source behind this entry (3)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    The eleven DepMap KMT2A-rearranged lines resolve to nine individuals: SEMK2 (CVCL_S906) is a Cellosaurus child record of SEM (CVCL_0095) and MOLM-14 (CVCL_7916) of MOLM-13 (CVCL_2119). Ages are SEM 5Y, SEMK2 5Y, RS4;11 32Y, MV4-11 10Y, THP-1 1Y, NOMO-1 31Y, OCI-AML-2 65Y, MOLM-13 20Y, MOLM-14 20Y, SHI-1 37Y, and HB11;19 unspecified. None is under one year.

    What this evidence cannot show

    Every line resolved by accession through the Cellosaurus API by the coordinator on 2026-09-20, with the primary name read back to confirm the accession. Cellosaurus records **age at sampling**, not age at diagnosis, and several of these lines are relapse-derived — so a line listed at 5Y may come from a patient diagnosed earlier, possibly in infancy. That distinction is unresolved for SEM and matters.

    Evidence that argues against this (1)
    • Age at sampling is the wrong variable for the question this entry is usually asked to answer. SEM is relapse-derived, so if that patient was diagnosed in infancy the most-used index-fusion line in the world is infant material and the headline changes. The Cellosaurus record does not say, and nobody in this project has checked the founding paper. Oncofusion knowledge graph (internal analysis) 2026
  2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    Seven of the nine individuals in the panel are myeloid or monocytic by Cellosaurus disease term - MV4-11, THP-1, NOMO-1, OCI-AML-2, MOLM-13/14 and SHI-1 - against a target disease that is infant B-lymphoid. Only SEM/SEMK2, RS4;11 and HB11;19 are B-lineage, and of those RS4;11's term is 'Adult B acute lymphoblastic leukemia'. The index fusion KMT2A::AFF1 is carried by three patients.

    What this evidence cannot show

    Lineage taken from the Cellosaurus disease term rather than from immunophenotype in the founding papers; terms are curated and occasionally coarse. THP-1 carries KMT2A::MLLT3 and HB11;19 carries KMT2A::MLLT1, so the panel is also partner-heterogeneous, which several analyses in this graph already split on.

    Evidence that argues against this (2)
    • A myeloid-dominated panel is not automatically the wrong instrument. This graph's own lineage-split analyses exist precisely to separate myeloid from lymphoid effects, and several of its findings - the MEN1 correlation in the Fanconi work, for one - were explicitly reported as myeloid-carried with the lymphoid arm non-significant. The panel's composition is a limitation that has sometimes been handled rather than one that is always ignored. Oncofusion knowledge graph (internal analysis) 2026
    • Counting patients rather than lines cuts both ways. Two lines from one patient at different timepoints are not independent samples, but they are also not redundant: SEM and SEMK2 differ in subclonal composition and drug history, and treating them as one datum discards real variance. 'Effective n = 9' is a better default than 11, not a correct number. SIB Swiss Institute of Bioinformatics 2026
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    The SEM founding paper reports the line was established from the peripheral blood of a 5-year-old girl in relapse and does not state her age at diagnosis. SEM is biphenotypic: CD19, CD22 and CDw75 positive, CD20, CD24 and surface immunoglobulin negative, and simultaneously positive for the myeloid antigens CD13, CD15, CD33 and CDw65. The companion paper localises the SEM crossover to intron 7 of KMT2A and a large intron of AFF1, and detects transcripts from both derivative chromosomes.

    What this evidence cannot show

    Both abstracts fetched from NCBI efetch and read by the coordinator on 2026-09-20; neither full text is reachable — no PMCID, not in Europe PMC, and both `fullTextXML` and `efetch db=pmc` were tried per the corrected unreadable rule. Age at diagnosis may well appear in the full text and is simply not available here. These are 1994-1995 immunophenotyping and cloning methods.

    Evidence that argues against this (2)
    • The biphenotypic result undercuts this entry's own lineage tally. Describing the panel as seven myeloid and four B-lineage treats SEM as cleanly B-lymphoid when its founding paper's title calls it biphenotypic and it carries four myeloid antigens. The lineage split this graph performs on the panel is therefore coarser than the arithmetic implies, and SEM sits on the boundary rather than inside one arm. British Journal of Haematology 1994
    • Biphenotypic immunophenotype in 1994 is not the same claim as mixed-phenotype acute leukaemia by current WHO criteria, which require specific lineage-defining markers at defined thresholds. CD13/CD15/CD33 co-expression on a KMT2A-rearranged B-ALL blast is common and by itself does not reassign lineage — so the counter-evidence above should temper the tally rather than overturn it. SIB Swiss Institute of Bioinformatics 2026
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