PrimeReplace Atlas maps ClinVar pathogenic/likely pathogenic variants onto MANE/GENCODE transcript structures to show how disease-associated variant burden is distributed across exons, exon blocks, and coding-payload units.
It provides a pre-implementation architecture layer for evaluating how public pathogenic variant records are distributed across transcript units relevant to large-fragment genome-writing hypotheses.
The atlas does not predict editing efficiency, safety, therapeutic efficacy, or patient coverage; it provides a pre-implementation target-architecture map.
Browser: https://best916116-crypto.github.io/PrimeReplace-Atlas/
Repository: https://github.com/best916116-crypto/PrimeReplace-Atlas
Zenodo archive: https://doi.org/10.5281/zenodo.20338345
Current release: v1.0.1, 2026-05-22
Release notes: reports/release_notes_v1.0.1.md
Data dictionary: reports/data_dictionary_v1.0.0.md
Validation summary: validation/public_release_checks_v1.0.1.json
The schematic summarizes the release logic: public ClinVar/MANE/GENCODE resources are mapped onto transcript units, converted into architecture labels and payload/context caveats, and exposed through browser pages and downloadable release tables. The claim boundary is explicit: PrimeReplace Atlas is a pre-implementation architecture resource, not an editing-efficiency, safety, patient-coverage, therapeutic-efficacy, or modality-recommendation system.
PrimeReplace Atlas converts public disease-associated variant records into transcript-level architecture summaries.
In practical terms, the atlas helps answer whether ClinVar P/LP records for a gene are:
- concentrated in one exon,
- distributed across an adjacent exon block,
- grouped by a downstream coding-payload unit,
- spread across a large or payload-burdened gene,
- limited by sparse ClinVar record support,
- affected by tumor-predisposition, repeat, noncoding, splice, isoform, or other mechanism-complex contexts.
The core output is an architecture map, not a yes/no feasibility call.
PrimeReplace Atlas does not replace ClinVar, MANE, GENCODE, genome browsers, or editing-design tools. Instead, it adds a transcript-unit architecture layer between public disease-variant records and downstream genome-writing design.
| Resource type | What it provides | What PrimeReplace Atlas adds |
|---|---|---|
| ClinVar | Pathogenic/likely pathogenic variant records | Gene- and condition-level transcript-unit burden architecture |
| MANE / GENCODE | Transcript anchors and exon/CDS structures | Record-level coverage across exon, exon-block, and boundary-CDS units |
| Genome browsers | Locus and transcript visualization | Precomputed architecture labels and payload/context caveats |
| Editing-design tools | Modality-specific design parameters | Upstream pre-implementation architecture review |
Most public variant resources answer what variants or annotations exist for a gene. PrimeReplace Atlas asks how disease-associated ClinVar P/LP records are organized relative to replacement-scale transcript units, and whether apparent record coverage is local, boundary-driven, payload-burdened, sparse, tumor-predisposition-associated, or mechanism-complex.
That derived architecture layer is the main novelty: it makes gene- and condition-level pathogenic-record organization reviewable before any experimental implementation, editing modality choice, construct design, or guide design.
Use PrimeReplace Atlas to ask questions such as:
- For a disease gene, where do ClinVar P/LP records fall across the MANE/GENCODE transcript?
- Do records cluster in a local exon or adjacent exon block?
- Does apparent high coverage depend on a large coding payload or boundary-driven CDS coverage?
- Is the gene record-supported enough for architecture interpretation, or is it low-record-burden?
- Are condition-associated ClinVar record groups available for disease-facing interpretation?
- Which downloadable source tables support the gene or condition summary?
Start here:
https://best916116-crypto.github.io/PrimeReplace-Atlas/
The browser is freely available without login, registration, or password protection. It is a static public site, so the same release can be reviewed through GitHub Pages, the GitHub repository, or the archived Zenodo bundles.
Suggested first-use workflow:
- Open Gene search.
- Search a gene symbol, for example
DMD,F9,ABCA4,CFTR,LDLR, orBRCA1. - Open the gene page.
- Inspect the gene-level architecture label.
- Review unit-level record coverage and payload/context caveats.
- Open Condition facets to inspect condition-associated ClinVar P/LP record groups.
- Download source tables from the Downloads page.
PrimeReplace Atlas reports several independent interpretation axes.
| Axis | Meaning |
|---|---|
| Record support | Number of ClinVar P/LP records available for a gene or condition-associated record group |
| Transcript-unit type | Single exon, adjacent exon block, or coding-payload / boundary-driven CDS unit |
| Record-level coverage | Fraction of ClinVar records covered by a transcript unit |
| Payload/context burden | Donor span, coding-payload burden, boundary context, or related caveat |
| Architecture label | Public-facing summary of how the pathogenic-record burden is organized |
| Condition facet | ClinVar condition-associated record group, where available |
The atlas deliberately keeps these axes separate. It does not reduce them to a single suitability score.
PrimeReplace Atlas uses architecture labels to describe how pathogenic records are organized relative to transcript-unit replacement hypotheses.
Primary public-facing groups include:
- Low-record-burden interpretation-limited: genes retained in the atlas but not overinterpreted because record support is sparse.
- Local compact architecture: pathogenic records concentrate in a single exon or adjacent exon block.
- Boundary-driven CDS coverage architecture: records downstream of a transcript boundary can be grouped by a coding-payload hypothesis; this is a burden-aware architecture descriptor, not a functional-rescue claim.
- Donor/payload-burden caveat: high theoretical record coverage may require large or context-burdened payloads.
- Tumor-predisposition control context: high-burden tumor-predisposition genes retained as control/caution contexts.
- Mechanism-complex limitation: repeat, noncoding, splice, isoform, or mechanism-specific biology limits transcript-unit interpretation.
PrimeReplace Atlas is not:
- an editing-efficiency predictor,
- a therapeutic-efficacy predictor,
- a safety predictor,
- a patient-coverage or prevalence estimator,
- a final PA-family or genome-writing modality recommender,
- a global ranking score,
- a clinical decision engine.
PrimeReplace Atlas is a pre-implementation architecture resource for organizing public disease-associated ClinVar records relative to transcript-unit replacement hypotheses.
The current public release is v1.0.1. The biological table baseline is the v1.0.0 static-browser payload; v1.0.1 aligns citation and archival metadata for the deployed browser without changing the count denominators below.
| Layer | Count |
|---|---|
| ClinVar VCF records scanned | 4,403,650 |
| Primary ClinVar P/LP VCF records | 337,682 |
| ClinVar P/LP gene-variant rows | 346,444 |
| Unique genomic coordinates | 336,901 |
| All-mapped genes | 5,738 |
| Transcript-unit opportunity rows | 437,301 |
| Low-record-burden interpretation-limited genes | 3,459 |
| Architecture-interpretable genes | 2,279 |
| High-support condition-associated record groups | 3,389 |
| High-support condition groups with recovered unit coverage | 1,278 |
| Condition-unit coverage rows | 160,125 |
PrimeReplace Atlas uses Zenodo DOI-versioned releases.
| DOI type | DOI | Meaning |
|---|---|---|
| Concept DOI | https://doi.org/10.5281/zenodo.20174921 | Persistent DOI for the PrimeReplace Atlas release series |
| Current release DOI | https://doi.org/10.5281/zenodo.20338345 | v1.0.1 public release |
The current authoritative public release checks are the v1.0.1 files. v1.0.0-named dictionary and inventory files are retained as baseline static-browser payload and prior-release provenance artifacts. Previous release DOI details are recorded in reports/release_notes_v1.0.1.md.
The release includes public validation artifacts so users can inspect the files, counts, and claim-boundary checks supporting the browser.
| Artifact | Purpose |
|---|---|
| validation/public_release_checks_v1.0.1.json | Current machine-readable v1.0.1 release check summary |
| validation/public_release_checks_v1.0.1.tsv | Current tabular v1.0.1 release check summary |
| validation/public_language_audit_v1.0.1.tsv | Current v1.0.1 public-language, local-link, and DOI-lock audit |
| reports/table_inventory_v1.0.0.tsv | Baseline public table inventory retained in v1.0.1 |
| reports/data_dictionary_v1.0.0.md | Baseline field-level data dictionary retained in v1.0.1 |
The validator also writes validation/checksum_manifest_v1.0.1.tsv during local release checks. Full checksum manifests, larger validation bundles, and archival payloads are preserved through the Zenodo archive.
PrimeReplace Atlas contains public source-derived records and derived transcript-architecture summaries. It does not contain user-submitted data, protected individual-level human subject data, or private clinical records.
The public browser is intended to be maintained at its current URL for at least five years, while immutable release snapshots are archived through Zenodo DOI-versioned records. Future releases should remain versioned through GitHub and Zenodo when the upstream ClinVar/MANE/GENCODE resource stack, data schema, browser, or claim-boundary audit changes.
- Overview:
index.html - Start here:
start_here.html - Gene search:
gene_search.html - All-gene index:
all_gene_index.html - Opportunity units:
opportunity_units.html - Architecture classes:
architecture_classes.html - Condition facets:
condition_facets.html - Methods:
methods.html - Limitations:
limitations.html - Citation:
citations.html - Glossary:
glossary.html - Downloads:
downloads.html
The browser provides source tables and validation-linked summaries, including:
all_mapped_gene_semantic_summary.tsvall_mapped_low_burden_interpretation_flags.tsvall_mapped_semantic_class_summary.tsvall_mapped_unit_type_summary.tsvallmapped_unique_variant_coordinate_sensitivity.tsvgene_condition_record_groups_v1.tsvgene_condition_record_architecture_recovered_v1.tsvgene_condition_unit_coverage_recovered_v1.tsvcondition_architecture_class_summary_recovered_v1.tsvcondition_facet_representative_examples_v1.tsv
Large archival payloads, validation manifests, checksums, and release bundles are available through the Zenodo archive.
PrimeReplace Atlas uses a frozen public resource stack:
| Layer | Resource |
|---|---|
| Genome build | GRCh38 / GRCh38.p14 |
| Transcript anchor | MANE Select |
| Transcript structure | GENCODE v49 |
| Variant records | ClinVar GRCh38 pathogenic/likely pathogenic VCF |
ClinVar, MANE, GENCODE, and other third-party public resources remain subject to their original provider terms.
The browser is a static site and can also be opened locally.
git clone https://github.com/best916116-crypto/PrimeReplace-Atlas.git
cd PrimeReplace-Atlas
python -m http.server 8000 --directory docsThen open:
http://localhost:8000/
data/small_tables/
Compact release tables
docs/
Static browser pages and browser-downloadable source tables
figures/
Public release figures and browser-supporting visual assets
reports/
Release notes, data dictionary, table inventory, and reviewer-facing release documentation
scripts/
Source scripts used to generate and validate the release
validation/
Current v1.0.1 release summaries and public-language audit output
If you use PrimeReplace Atlas in your work, please cite the archived release:
Park J, Cho SI. PrimeReplace Atlas: a transcript-unit architecture database for disease-associated large-fragment genome writing. Zenodo. https://doi.org/10.5281/zenodo.20338345
A manuscript describing the atlas is in preparation. Until the manuscript is available, please cite the Zenodo DOI for the release used in your analysis.
This repository uses separate licenses for software and generated data:
- Code and static browser source: MIT License. See
LICENSE. - Generated atlas tables, figures, browser-downloadable data files, and archived release materials: Creative Commons Attribution 4.0 International (CC BY 4.0). See
LICENSE-DATA.md.
ClinVar, MANE, GENCODE, and other third-party public resources are not relicensed by this repository and remain subject to their original provider terms.
For public questions, bug reports, or feature requests, please use GitHub Issues.
For release correspondence, contact the release maintainer:
Junjae Park
best9161@korea.ac.kr