Author Correction: Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓The central claim held under reproduction
- 🟡A deviation arose in the data or preprocessing
- 🟡A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough to reproduce 1:1 from PUBLIC data. PMID 40555819 is the author correction of the TRANSLATE-NAMSE study (orig PMID 39039281); reproduced its pipeline-derived results by running the authors' own Snakemake (Ax-Sch/TNAMSE_geno_pheno @6877589) on the public medRxiv supplement on «our HPC» («job»). Headline numbers reproduce exactly/within-tol: cohort N=1577 (exact), diagnostic yield 31.6%~=32% (within-tol), distinct molecular causes 363 vs 370 (within-tol), YieldPred LASSO AUC 0.6875 (CI 0.6244-0.7506) vs reported 0.67 (0.61-0.74) (within-tol, CIs overlap), held-out test N=321 (exact). Two adaptations were required because the authors' code hard-codes skip=2 for a supplement layout that differs from the public file (needed skip=0) plus one dplyr-version fix - a real out-of-the-box friction, independently confirmed by the sibling room. Partial: the 34-novel/23-candidate SPLIT reproduces only approximately (31/33 from public supplement flags vs paper's manually-curated 34/23). NOT attempted (restricted/licence, recorded not down-ranked): raw exome variant calling (raw reads not public), PEDIA/GestaltMatcher facial-image arm (images restricted, separate repo), OMIM-gated rules. All grades provisional - human signs off.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
-
v1 current initial assessment Score 76assessed: 2026-06-19 ⛓ c92217eb1767
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-19
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-20no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnet- ★ This document is a publisher author correction notice for the article 'Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings' (Nature Genetics, 10.1038/s41588-024-01836-1, published 22 July 2024) resource
- ★ The surname of author Meghna Ahuja Bhasin was incorrectly printed as 'Basin' in the originally published version and has been amended in the HTML and PDF versions finding
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-40555819
What this RU actually is
- PMID 40555819 is an Author Correction (Nat Genet 2025;57(7):1790-1791, DOI 10.1038/s41588-025-02271-6) to the original article PMID 39039281 (Nat Genet 2024;56(8):1644-1653, DOI 10.1038/s41588-024-01836-1), the TRANSLATE-NAMSE study.
- The correction itself only fixes an author surname spelling ("Basin" → "Meghna Ahuja Bhasin") in the HTML/PDF. It contains no scientific or computational content → nothing to reproduce in the correction.
- We therefore assess reproducibility of the underlying study's pipeline-derived
results, exactly as the original article reports them. (A sibling room
pmid-39039281is reproducing the same study in parallel; we reuse its prebuilt conda env but produce our own outputs.)
Code artifact (P16 — third-party/authors' own both valid)
- Authors' own analysis code: https://github.com/Ax-Sch/TNAMSE_geno_pheno (R scripts in a Snakemake pipeline; named per manuscript figure).
- PEDIA (facial-image arm) code: separate repo https://github.com/igsb/PEDIA-TNAMSE.
- YieldPred web service: https://translate-namse.de/
Data
- Primary analysis input = a public de-identified case/variant table shipped as
the medRxiv supplement (media-3.xlsx), hard-coded in
config/config.yaml:https://www.medrxiv.org/content/medrxiv/early/2023/04/25/2023.04.19.23288824/DC3/embed/media-3.xlsx→ openly obtainable; the core genotype-phenotype analysis is reproducible. - Patient-level exome reads / VCFs and facial photographs: NOT public (clinical, GDPR; consent only for in-study use) → out of scope.
- External reference resources shipped in
resources/: HGNC, CCDS, ClinVar (2017 + current), HPO obo + HPO grouping, Turro 2020 supplement. OMIM files are licence-gated (not shipped) → the two OMIM-dependent rules are excluded from the defaultrule all.
IN SCOPE (reproducible from public data + shipped resources)
Pipeline = Ax-Sch/TNAMSE_geno_pheno Snakemake, run on the public supplement table:
| Result | Snakemake rule / script | Reported value to compare |
|---|---|---|
| Cohort / case counts parsed from supplement | parse_table |
N exome-analysed cases (1,577) |
| Diagnostic-yield predictor (YieldPred) AUC | figure5 (LASSO + pROC) |
AUC 0.67 (95% CI 0.61–0.74), test N≈321 |
| Inheritance / variant-type breakdown | figure3 |
Fig 3 proportions |
| Solved-case / phenotype structure | figure2 |
Fig 2 |
| New-disease-gene novelty over years (ClinVar/Turro/TN) | figure4 |
Fig 4 gene counts |
| Population / autozygosity / VUS-vs-solving supporting analyses | supporting_* |
suppl figs |
OUT OF SCOPE (not attempted — recorded, not down-ranked)
- Exome variant calling / annotation from raw reads — raw patient genomic data
not public (
data_restricted). The shipped pipeline starts from the already- curated variant table, not from FASTQ/BAM. - PEDIA / GestaltMatcher facial-gestalt arm (224 consented patients) — facial images are restricted patient data; separate repo. Not reproducible without images.
- OMIM-dependent rules (
figure1_part2,supporting_ccds_length) — OMIM licence required; excluded from default targets.figure1_part1attempted best-effort (needs webr/moonBook). supporting2_annotate_w_VEP— needs Ensembl VEP + live ClinVar download; heavier, not part of the headline claims; deferred.- Wet-lab / clinical / MDT-process results (diagnostic workflow, secondary findings curation) — manual/clinical, non-pipeline.
Honesty note
Reported values are taken from the original Nature Genetics 2024 article and its
medRxiv preprint (the supplement is the 2023 preprint version). Where the preprint
and final paper differ slightly, both are noted in claims.tsv. Every grade is
PROVISIONAL — a human signs off.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Re-running the authors' own Snakemake on the public medRxiv supplement reproduces every headline result 1:1 or within tolerance: cohort N=1577 (exact), yield 31.6%≈32%, distinct genes 363 vs 370, YieldPred AUC 0.6875 vs 0.67 (overlapping CIs), test set 321 (exact) — the central conclusions hold. The only substantive deviations are the secondary novel (31 vs 34) and candidate (33 vs 23) counts, which rest on a manual evidence classification not encoded in the public supplement — a definition/specification gap on the data-availability side, not a fabrication signal. Two documented code adaptations (skip=2→0, dplyr fix) reflect genuine out-of-the-box friction in the authors' repo but do not affect the verdict. Overall: a solid reproduction with explainable, bounded deviations → yellow.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.