Scored in the published criterion's own currency, the number of oncoprotein-target promoters runs 0 to 2282 across 27 KMT2A-rearranged patient samples - 20.01x between the 10th and 90th percentiles - and the spread widens to 61.10x after depth matching
Counting how many gene promoters pass the published test for fusion binding, one child's leukaemia gives a few dozen and another gives a couple of thousand. Making every sample the same sequencing depth does not shrink the gap.
The same thing, for a scientist
**The statistic.** Per sample, the number of TSS +/- 1 kb promoters passing the paper's own criterion - **N/C ratio > 1.75 with binomial upper-tail p < 1e-5** against the within-sample null share TN/(TN+TC). It runs from **0 to 4646** by construction, so it is unbounded in the sense this beat was dispatched to supply [E1]. **Measured across 27 samples: 0 to 2282 called promoters, median 947.00. One sample calls ZERO. The robust spread (p90/p10) is 20.01x and the largest over the smallest NON-ZERO count is 103.73x** [E1]. **It is not a depth artefact, and that was checked rather than assumed.** A binomial threshold has more power in a deeper library, so this was the first thing to break. Spearman of the call count against log10 total fragments is **-0.165 (p = 0.411)**. Thinning every library by seeded binomial down-sampling to a common **6,811,300** fragments per arm leaves the spread at **0 to 1802, p90/p10 = 61.10x** - wider, not narrower [E2]. **This is the magnitude answer the corpus asked for, and its sign is unambiguous.** Whatever else is true, the amount of chromatin a KMT2A oncoprotein occupies, measured the way the people who built the assay measure it, is not a constant of the fusion. It is a property of the patient, and it varies by two orders of magnitude. **What it does NOT say.** There is **no spike-in in this deposit**. Every input is a within-sample share, so this is a statement about how much of a library's signal is N-biased, not about how many oncoprotein molecules are on chromatin per cell. A patient with fewer called promoters may have less oncoprotein, or the same oncoprotein concentrated on fewer sites, and nothing here separates those.
Per-sample call counts, depth-matched
| sample | called promoters (raw) | called promoters (depth-matched) |
|---|---|---|
| TB040576 | 2282 | 1802 |
| p247 | 2095 | 1523 |
| R3652 | 2063 | 1773 |
| p160 | 2060 | 1611 |
| p279 | 2045 | 1677 |
| p454 | 2000 | 1511 |
| p318 | 1894 | 1226 |
| R3595 | 1233 | 805 |
| TB000694 | 1207 | 1068 |
| TB986292 | 1151 | 1061 |
| A93692 | 1087 | 658 |
| A89691 | 1069 | 359 |
| TB051939 | 1048 | 721 |
| p186 | 947 | 540 |
| TB971992 | 893 | 728 |
| TB995291 | 890 | 683 |
| p214 | 767 | 511 |
| p179 | 712 | 546 |
| TB920488 | 429 | 114 |
| A82485 | 400 | 204 |
| 148752 | 345 | 217 |
| A80956 | 332 | 90 |
| A95941 | 237 | 118 |
| A93949 | 147 | 34 |
| A70498 | 37 | 16 |
| A73051 | 22 | 2 |
| 152985 | 0 | 0 |
Why this number and not the amplitude
The per-promoter amplitude statistic pre-registered as primary is voided by its own noise-floor clause (see ana-q144-the-unbounded-statistic-works-and-the-magnitude-test-is-still-void-but-for-the-opposite-reason-to-q142). The call count is a different quantity and is not voided by that clause, because its control is a fusion-negative sample rather than a same-protein reagent pair - and that control exists and was run. The two statistics are reported separately and neither is used to rescue the other.
| script | analyses/q144-unbounded-magnitude/run.py |
|---|---|
| status | run |
| result summary | Called oncoprotein-target promoters per sample: 0-2282 raw (p90/p10 20.01x), 0-1802 depth-matched (p90/p10 61.10x). |
per sample raw — the numbers behind the chart
{
"148752": 345,
"152985": 0,
"A70498": 37,
"A73051": 22,
"A80956": 332,
"A82485": 400,
"A89691": 1069,
"A93692": 1087,
"A93949": 147,
"A95941": 237,
"R3595": 1233,
"R3652": 2063,
"TB000694": 1207,
"TB040576": 2282,
"TB051939": 1048,
"TB920488": 429,
"TB971992": 893,
"TB986292": 1151,
"TB995291": 890,
"p160": 2060,
"p179": 712,
"p186": 947,
"p214": 767,
"p247": 2095,
"p279": 2045,
"p318": 1894,
"p454": 2000
}per sample depth matched — the numbers behind the chart
{
"148752": 217,
"152985": 0,
"A70498": 16,
"A73051": 2,
"A80956": 90,
"A82485": 204,
"A89691": 359,
"A93692": 658,
"A93949": 34,
"A95941": 118,
"R3595": 805,
"R3652": 1773,
"TB000694": 1068,
"TB040576": 1802,
"TB051939": 721,
"TB920488": 114,
"TB971992": 728,
"TB986292": 1061,
"TB995291": 683,
"p160": 1611,
"p179": 546,
"p186": 540,
"p214": 511,
"p247": 1523,
"p279": 1677,
"p318": 1226,
"p454": 1511
}- If oncoprotein occupancy varies a hundred-fold between patients, a fixed menin-inhibitor dose is targeting very different amounts of substrate in different children, and a pharmacodynamic threshold calibrated on the high-occupancy end will look like non-response at the low end.
- Does the call count track blast percentage? The deposit records none, and a purity column would either explain the spread or make it much stronger.
- Does the same spread appear on the authors' own peak intervals, where the threshold was calibrated?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
Applying the published oncoprotein-site criterion (N/C > 1.75, binomial p < 1e-5) to TSS +/- 1 kb promoters in 27 KMT2A-rearranged patient samples from GSE252378 gives 0 to 2282 called promoters per sample, a 20.01x spread between the 10th and 90th percentiles, with one sample calling zero.
GSE252378 - KMT2A oncoproteins induce epigenetic resistance to targeted therapies (171 GSMs, AutoCUT&RUN / AutoCUT&Tag, hg38 fragment BEDs and bigWigs) · Janssens DH, Henikoff S (Fred Hutchinson Cancer Center / Van Andel Institute) · NCBI Gene Expression Omnibus 2024What this evidence cannot show
refGene promoters, not the authors' peak intervals, and without the CD34+ calibration sample that set the 1.75 threshold - so the absolute counts are not comparable to the paper's 1,692 and are not offered as such. Within-sample shares; no spike-in. The promoter universe is the 4646 promoters clearing n_N+n_C >= 20 in every sample, 14758 of 19404 removed.
Evidence that argues against this (1)
- A large part of the between-sample spread could be tumour purity rather than oncoprotein level: a marrow with 30%% blasts dilutes the fusion signal with normal cells whose N/C ratio is near 1, which lowers the call count without any change in the leukaemic cells. The deposit records no blast percentage, so this cannot be excluded here and it is the single most likely alternative explanation. Janssens DH et al. 2024
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
The between-sample spread in called promoters is not explained by sequencing depth: Spearman of call count against log10 library total is -0.165 (p = 0.411), and after seeded binomial thinning of every library to 6,811,300 fragments per arm the spread is 0 to 1802 (61.10x).
GSE252378 - KMT2A oncoproteins induce epigenetic resistance to targeted therapies (171 GSMs, AutoCUT&RUN / AutoCUT&Tag, hg38 fragment BEDs and bigWigs) · Janssens DH, Henikoff S (Fred Hutchinson Cancer Center / Van Andel Institute) · NCBI Gene Expression Omnibus 2024What this evidence cannot show
Down-sampling is seeded (20260924) and is a single draw, not an average over draws, so the depth-matched counts carry sampling noise of their own. The rank order of samples is unchanged by thinning, which is why the depth correlation is identical before and after.
Evidence that argues against this (1)
- Depth matching controls the number of fragments but not the signal-to-background ratio, which differs between samples for reasons of cell input and antibody batch. A sample with high background has a flatter N/C landscape at any depth, so the spread could still be an assay-quality gradient rather than a biological one. Janssens DH et al. 2024
the 27-sample N/C arm
the companion amplitude statistic, which is voided
supplies the unbounded magnitude number that beat could not compute
- related to →KMT2A / MLL1 — the gene that breaks
KMT2A N-terminal over C-terminal call count
- related to →KMT2A-rearranged acute lymphoblastic leukaemia
between-patient variation in oncoprotein target-site number
sizes the reagent noise the magnitude spread has to beat, and it beats it
the magnitude question clears its noise floor where the ordering question does not
the same call sets, counted rather than intersected
the positive control for the call-count statistic
the between-patient occupancy range this constraint rests on
the occupancy range this partitions
shows why the verdict rests on the call count and not on the amplitude