Base by Base18 Sep 2025

141: RetiGene: a gene atlas for inherited retinal diseases

Rivolta C et al., The American Journal of Human Genetics - RetiGene is an expert‑curated, openly accessible atlas integrating variant data, bulk and single‑cell RNA‑seq, and functional annotations for genes linked to inherited retinal diseases to aid diagnosis and research. Key terms: RetiGene, inherited retinal diseases, gene atlas, single-cell RNA-seq, diagnostic genetics.

Study Highlights:
The authors manually curated 470 genes (plus 4 loci) strongly associated with inherited retinal diseases and flagged 196 candidate genes and 17 discarded genes based on evidence strength. They integrated variant annotations, bulk (FANTOM5) and single‑cell RNA‑seq, and Gene Ontology‑based functional classifications to map genotype–phenotype relationships. Ciliary genes form the largest functional category and autosomal recessive inheritance predominates; expression patterns help explain syndromic versus non‑syndromic presentations. The resource is hosted at retigene.erdc.info and is intended for regular updates to support diagnostics, gene prioritization, and therapeutic development.

Conclusion:
RetiGene provides a continuously updated, expert‑curated gene atlas that integrates genetic and expression data to improve molecular diagnosis, panel design, and functional studies of inherited retinal diseases.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
RetiGene, a comprehensive gene atlas for inherited retinal diseases

First author:
Rivolta C

Journal:
The American Journal of Human Genetics

DOI:
10.1016/j.ajhg.2025.08.017

Reference:
Rivolta C., Celik E., Kamdar D., et al., RetiGene, a comprehensive gene atlas for inherited retinal diseases. The American Journal of Human Genetics (2025), https://doi.org/10.1016/j.ajhg.2025.08.017

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/retigene-a-comprehensive-gene-atlas-for-inherited-retinal-diseases

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-18.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive auditing of the transcript sections describing the RetiGene atlas, gene counts (470 genes + 4 loci), functional categorization (with cilium as a leading category), inheritance patterns (68.9% AR), housekeeping paradox and tissue expression (retina-prevalent vs ubiquitous), RNA-seq and scRNA-seq findings, th
- transcript topics: Diagnostic challenges in inherited retinal diseases; RetiGene gene atlas and the 470 genes (plus 4 loci); Functional categorization of IRD genes (cilia, transmembrane transport, lipid metabolism); RNA-seq and single-cell RNA-seq expression patterns; Inheritance patterns and variant effects (LoF vs missense); Clinical impact: discarded genes (UNC119) and diagnostic panels

QC Summary:
- factual score: 8/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- 470 IRD-related genes (including 4 loci) retained as strongly disease-associated
- 196 candidate genes and 17 exc...

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