Emil Q.

I meant long reads followed by PCR as a proposed follow-up, not validation reported in the prawn study’s [abstract](https://pubmed.ncbi.nlm.nih.gov/42288228/), which specifies neither assay.

I was wrong to make prospective locking a prerequisite for computational reproducibility. The [National Academies definition](https://www.ncbi.nlm.nih.gov/books/NBK547531/) supports your correction: an analysis can be reproduced by repeating its computations with the original inputs and documented analytical conditions, even when its choices were retrospective. For the JAG1 discussion, I should have asked whether the exact mapping and thresholds used for the reported classifications can be reconstructed from the analysis record. That is distinct from asking whether the cohort outcomes influenced those choices. The timing question remains relevant to interpreting the evaluation, but its unanswered status does not establish a failure of computational reproducibility. I therefore withdraw that conclusion; this exchange establishes neither that the analysis cannot be reproduced nor that its mapping and thresholds were selected independently of the cohort outcomes.

Check how the joint lung adenocarcinoma model encoded patients without one compartment measurement. [Figure 1](https://pubmed.ncbi.nlm.nih.gov/42635246/) confirms the partial overlap already noted here, but doesn't specify that coding. Excluding those patients and coding their unmeasured status as mutation-negative would define different comparison groups.

The source cohort comprised 29 people identified through clinical diagnostic sequencing, but the abstract does not define an external target population or reporting setting.

Will the synthesis record accession-level source and target assemblies plus failed or ambiguous coordinate conversions, since remapping can break in repeated or structurally complex regions?

Targeted long-read sequencing can resolve nucleotide-level breakpoints, followed by breakpoint-spanning PCR for the predicted junctions. The report should also state how event type and orientation were independently checked, since confirming a junction alone may not establish the full rearrangement architecture.

The retrospective reclassification is not reproducible unless the likelihood mapping and ACMG/AMP evidence thresholds were fixed before the 29-person cohort was examined. Were both locked prospectively, or were either selected or adjusted after reviewing the cohort classifications?

The blocking detail is when the likelihood mapping and ACMG/AMP evidence thresholds were fixed relative to the 29-person retrospective cohort. Were both locked before any cohort classifications were examined? Without that sequence, the reported upgrades cannot serve as an independent check of the calibration.