GSM8006584 names its antibody KMT2A-C1 in its title, its characteristics field and its own filename, and KMT2A-C2 in its description - so keying the antibody off the free-text description gives patient TB-92-0488 two C2 libraries and no C1
One sample record in this public dataset contradicts itself about which antibody was used. Three of its four fields say one thing and the free-text sentence says another, and trusting the sentence would quietly delete half of that patient's control.
The same thing, for a scientist
Audited by comparing the antibody named in `!Sample_title` against the antibody named in `!Sample_description` for all 171 records. **Fifteen records differ; fourteen of the fifteen are formatting only** (`AFF1_1` vs `AFF1-1`, `K4me3` vs `H3K4me3`, a double space). **One is a content disagreement** [E1]: ``` GSM8006584 title TB920488_KMT2A_C1_(220412_JS_Hs_032922_JS2165) desc AutoCUTnRUN for KMT2A-C2 in TB-92-0488... chars sample: Mouse KMT2A-C1 SantaCruz H10; TB-92-0488; KMT2A-AFF1... file GSM8006584_TB920488_KMT2A_C1.hg38.bw ``` **Three independent fields say C1, one says C2, and the adjacent record GSM8006585 is a genuine C2** with the matching `Mouse KMT2A-C2 Millipore 05-765` reagent. The description is the typo. **What it would cost.** TB-92-0488 is one of the eight KMT2A::AFF1 patients. A pipeline keying the antibody off `!Sample_description` assigns it two C2 libraries and no C1, so the N-over-C denominator for that patient is built from one reagent instead of two - and **nothing errors**, because two C libraries are still present. The oncoprotein score for one of eight index-fusion patients would quietly become a different measurement from the other seven. **The generalisable half:** when a deposit's fields disagree, **count how many independent fields support each reading before choosing**. Here the vote is 3-1 and the losing field is the only free-text one. A single-field read - in either direction - would have been a coin flip dressed as a lookup.
Reported, not edited
This is an error in a third-party deposit, not in this corpus. It is recorded here so that any future beat touching GSE252378 knows to resolve the antibody from !Sample_characteristics_ch1, which names the vendor and catalogue number and is the only field in the record that is unambiguous.
| script | analyses/q144-unbounded-magnitude/run.py |
|---|---|
| status | run |
| result summary | 1 content-level title/description antibody disagreement in 171 records; 14 further differences are formatting only. |
| affected gsm | GSM8006584 |
| affected patient | TB-92-0488 (KMT2A-AFF1, infant pre-B-ALL, St Jude) |
- Does the published analysis of this deposit use the description field anywhere to assign antibodies, and if so does TB-92-0488's oncoprotein score differ in character from the other seven KMT2A::AFF1 patients?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
GSM8006584 in GSE252378 is labelled KMT2A-C1 by its title, its !Sample_characteristics_ch1 antibody string (Mouse KMT2A-C1 SantaCruz H10) and its own supplementary filename, and KMT2A-C2 by its !Sample_description.
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
A single record in one deposit. The 3-1 field vote is the whole basis for calling the description wrong rather than the other three; no independent evidence (e.g. re-deriving which antibody produced the data) was obtained, and in principle the title and filename could have been generated from the same erroneous source as each other.
Evidence that argues against this (1)
- The characteristics field is arguably not independent of the title, since both may be generated from one submission spreadsheet column. If so the vote is 2-1 or even 1-1 rather than 3-1. The reading is still that the description is wrong, because the characteristics string carries a vendor and catalogue number that the description does not, and the neighbouring record GSM8006585 carries the matching C2 reagent - but the independence of the three supporting fields is an assumption, stated here rather than hidden. Janssens DH et al. 2024
record-level labelling error in the same deposit
- related to →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)
the affected patient TB-92-0488 is one of eight KMT2A::AFF1 samples in the N/C arm
second labelling defect found in the same deposit, by a different beat