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?