jama-peer-review-revision

Peer Review & Revision (jama-peer-review-revision)

When to trigger

• A decision letter arrives: major/minor revision (or a reject-with-encouragement)
• Reviewer or editor comments need a structured, point-by-point reply
• The statistical reviewer has raised analysis questions
• You must revise the manuscript before writing the response — not after

How JAMA review works (durable shape)

• Editorial screening first; manuscripts that pass go to external peer review.
• JAMA applies dedicated statistical review to manuscripts under serious consideration — expect detailed methods/analysis queries.
• Decisions typically come with one or more revision rounds; address every point.

Response-letter structure

1. Open with thanks and a one-paragraph summary of the main changes.
2. Reproduce each comment verbatim, then respond beneath it.
3. For each point: state the change, quote the new manuscript text, and give the page/line. If you disagree, do so respectfully with evidence — do not ignore a comment.
4. Group editor vs reviewer comments; number them (Reviewer 1, Comment 1.1 …).
5. Keep the manuscript and the letter perfectly consistent (numbers, claims, wording).
6. Provide a tracked-changes manuscript alongside a clean copy.

Handling common JAMA comment types

| Comment type | Response approach |

|-------------------------------------------------------|-------------------------------------------------------------|

| "Report effect sizes with CIs, not p-values" | Add estimates + 95% CIs throughout; confirm in the letter |

| "Was this outcome pre-specified?" | Cite the protocol/registry; relabel post hoc as exploratory |

| "Analysis should be intention-to-treat" | Re-run ITT as primary; move per-protocol to sensitivity |

| "Address multiplicity" | Add/justify the correction; downgrade unadjusted subgroups |

| "Conclusions overstate the data (spin)" | Rewrite to the primary outcome; bound the claim |

| "Reporting incomplete (CONSORT/PRISMA item X)" | Add the item; update the checklist locations |

| "Generalizability / limitations" | Strengthen the limitations paragraph honestly |

| "Registration timing" | State the facts transparently; do not obscure |

Checklist

• [ ] Manuscript revised first; letter written from the revised version
• [ ] Every comment reproduced and answered (none skipped)
• [ ] Each response cites new text with page/line
• [ ] Statistical-reviewer points fully resolved (CIs, ITT, multiplicity, missing data)
• [ ] No spin reintroduced; conclusions still bounded by the primary outcome
• [ ] Reporting checklist updated to match the revised text
• [ ] Tracked-changes + clean copies prepared
• [ ] Letter and manuscript numerically consistent

Anti-patterns

• Writing the response before actually revising the manuscript
• Silently skipping an uncomfortable comment
• Claiming a change was made that the manuscript does not reflect
• Defensive or dismissive tone toward reviewers
• Running new post hoc analyses and presenting them as confirmatory
• Reintroducing spin while "addressing" the spin comment
• Leaving the checklist out of sync with the revised text

Operating pass for JAMA

Run this as a concrete capability pass. First lock the clinical question, patient population, estimand or endpoint, safety/ethics issue, and reporting checklist; then test whether the manuscript addresses clinical reviewers who ask whether the evidence changes patient care, policy, or medical decision-making while satisfying reporting standards.

• Primary move: Return a claim-evidence-risk ledger; every recommendation must point to a manuscript location or missing artifact.
• Decision ledger: return claim / evidence / blocker / next edit rows so the next pass can patch the manuscript directly.
• Sibling comparison: compare against NEJM for field-changing clinical medicine, Lancet for global-health breadth, specialty journals for narrower clinical domains; if the neighboring outlet has the stronger audience claim, recommend re-routing before polishing.
• Verification floor: before submission-ready advice, re-open resources/official-source-map.md for volatile rules and name the one unresolved fact that could change the recommendation.

Output format

【Decision】major / minor revision / reject-with-encouragement
【Comments addressed】X of X (none skipped)
【Statistical-review points resolved】yes / remaining: ...
【New text cited with page/line】yes / no
【Spin reintroduced?】no / fixed: ...
【Checklist updated】yes / no
【Files ready】tracked + clean + point-by-point letter