Put three descriptions of the same address on one hg38 axis - the exon-11 CTCF site, the intron-10/exon-11 functional cut point, and the region that breaks more in patients who got a KMT2A fusion - and find out whether they are one element

[
  "GSE210480 - the 4 CTCF ChIP-seq samples plus matched inputs (Homo sapiens, RPE); the ONLY route to a coordinate for the exon-11 CTCF site",
  "hg38 KMT2A exon coordinates from a named, versioned Ensembl or RefSeq transcript",
  "hg38 chr11:118,488,500-800 (PMID 34405474, build to be reconfirmed from the paper)",
  "the DCAL exon convention's transcript basis, to be established"
]

[
  "the hg38 coordinate of the exon-11 CTCF peak summit and the peak width",
  "base-pair distance from that summit to the intron-10/exon-11 junction",
  "base-pair distance from that summit to the midpoint and both edges of chr11:118,488,500-800",
  "which HALF of the BCR the site sits in - centromeric (de novo-skewed) or telomeric (t-AML-skewed)",
  "a table of the three exon conventions against the chosen transcript, so the corpus has one"
]

{
  "all_three_within_~500bp": "one element. The boundary deciding whether a break is oncogenic is also the element whose chromatin state decides whether it happens and the region that breaks more in people who developed the disease - the most important 300 bp in this graph's genesis model.",
  "ctcf_and_cut_point_coincide_but_not_the_patient_window": "the molecular convergence stands; the patient-level link is dropped.",
  "scattered_across_subregion_C": "the convergence was an artefact of a 5 kb window and three coordinate conventions. THIS IS THE MOST LIKELY OUTCOME and genome-kmt2a-exon-11-ctcf-site must be rewritten to say so."
}

[
  "BUILD MISMATCH - the commonest way this class of analysis fails silently. Reconfirm the build of every coordinate from its own source, and state it.",
  "transcript choice - exon numbering depends on the transcript, and the DCAL convention's basis is not recorded in this graph",
  "CONTAINMENT REPORTED AS COINCIDENCE - subregion C is 5,026 bp wide, so 'in subregion C' is not 'at the cut point'. Report distances in base pairs, never containment.",
  "the CTCF peak summit is a peak in RPE cells; it may not be where CTCF sits in a haematopoietic cell"
]

{
  "headline": "NONE of the three pre-registered readings occurred, and the result is the MIRROR IMAGE of reading 2. Reading 2 expected the CTCF site and the functional cut point to coincide while the patient window did not. The opposite is true: the patient window and the CTCF site are ONE element, and the cut point is the outlier.",
  "the_measurements": {
    "canonical exon 11 (ENST00000534358, GRCh38)": "chr11:118,488,614-118,488,760, 147 bp",
    "Atkin patient break window (PMID 34405474)": "chr11:118,488,500-800 - CONTAINS all 147 bp of canonical exon 11",
    "ENCODE CTCF+RAD21+SMC3 cluster": "chr11:118,488,159-118,489,206 - contains both of the above",
    "DCAL functional cut point (canonical intron 9/exon 10)": "chr11:118,484,861|118,484,862",
    "distance, cut point to canonical exon 11 start": "3,752 bp",
    "distance, cut point to the CTCF anchor's near edge": "3,297 bp"
  },
  "most_likely_outcome_did_not_occur": "The pre-registered MOST LIKELY reading was 'scattered across subregion C - the convergence was an artefact of a 5 kb window and three coordinate conventions'. It is wrong in both directions at once: two of the three features are not scattered but identical, and the third is not scattered either, it is cleanly and measurably 3.7 kb away. The conventions WERE the problem, but they had concealed a real coincidence as well as manufacturing a false one.",
  "secondary_test_answered": "AFFIRMATIVE. The element sits at 70.4% along the Broeker BCR, in the telomeric, t-AML-skewed half (75% versus 26%), and inside DCAL subregion C which holds 39.5% of 3,401 breakpoints. This is the prediction breakpoint-kmt2a-bcr-architecture's aetiology skew implies for a therapy-related mechanism, and it holds.",
  "the_deliverable_that_was_asked_for": "The table of exon conventions against one transcript now exists as a registry row: DCAL = Ensembl canonical + 1, on three exact bp identities (canonical e8+i8 = 74+1,687 = 1,761 matching Meyer 'exon 9 - intron 9 = 1761'; canonical e9+i9 = 132+547 = 679 matching 'exon 10 - intron 10 = 679'; canonical e10 start to e12 end = 5,026 matching 'exon 11 ... exon 13 = 5026'). A FOURTH convention was found and is deliberately not reconciled - Canela 2017's 'near exon 10' and 'at exon 12' are MOUSE Kmt2a exons.",
  "the_listed_input_was_not_needed_and_could_not_have_worked": "This analysis named the GSE210480 CTCF ChIP-seq samples as 'the ONLY route to a coordinate for the exon-11 CTCF site'. That was wrong twice over. The series deposits COVERAGE bigWigs only, with no narrowPeak or BED peak calls in the supplement, so it could not have yielded a summit without peak calling the raw signal. And the coordinate was obtained without it, from ENCODE TFBS clusters plus a versioned Ensembl transcript - a desk job, not the costed cluster job. 'No coordinates published' was really 'no coordinates deposited either', and the route around it was cheaper than the route through it."
}