DISCOVER · PROGRAM
02Which molecular programs are shared, allele-specific, and direct?
A differentially expressed pathway can be direct, compensatory, secondary to cell-state composition, or specific to one allele or laboratory context. Bulk histone-mark abundance cannot identify the regulatory loci that matter.
POPULATION / COMPARATOR
Who or what should be compared?
Molecularly distinct patient alleles with independent donors or independently engineered lines so donor and allele are not confounded, their isogenic corrections, engineered dosage controls, and matched reference lines assayed in the same cell identity and time course.
STUDY DESIGN
How could the question be tested?
Integrate ASH1L occupancy, locus-resolved H3K36me1/2, H3K27me3 and H3K4me3, accessibility, transcription, splicing, and protein or functional readouts across multiple alleles, correction controls, dosage levels, cell identities, and ordered timepoints.
EVIDENCE GATE
What would support the proposed link?
the mechanism-appropriate direct molecular anchor precedes or explains the downstream change, repeats independently, and shows concordant attenuation with correction or rescue. Chromatin-mediated claims require locus- and time-matched chromatin evidence; splicing, localization, complex-assembly, catalytic, or scaffolding claims require the corresponding direct assay and perturbation.
STOP RULE
What would weaken it?
the program appears only in bulk enrichment, follows rather than precedes the outcome, disappears after cell-composition control, lacks the direct anchor required by the proposed mechanism, or does not respond to a validated correction or rescue.