31: Non-canonical FBN1 splicing in the 100k Genomes Project

Walker S et al., Genetics in Medicine - Genome sequencing of 78,195 participants in the 100,000 Genomes Project identified ultra-rare non-canonical FBN1 splice variants enriched among individuals recruited with familial thoracic aortic aneurysm disease (FTAAD). Experimental RNA assays confirmed aberrant splicing for most candidates, including multiple deep intronic pseudoexon events, indicating a measurable diagnostic contribution from intronic variants beyond standard clinical testing windows. Key terms: Marfan syndrome, FBN1, splicing, pseudoexon, genome sequencing.

Study Highlights:
A systematic screen of FBN1 singleton variants using SpliceAI found 20 unique candidate non-canonical splice variants in 23 families, with significant enrichment in the FTAAD cohort (OR=84, p=9.7x10^-14). Experimental validation (RT-PCR, RNAseq, minigene assays) confirmed splicing abnormalities for 16/20 variants, and nine events involved pseudoexon inclusion. Seventy percent of validated variants lay beyond the ±8 bp regions typically interrogated in clinical testing, and the authors estimate a ~3% additional diagnostic yield for unsolved FTAAD families.

Conclusion:
Expanded intronic analysis using genome sequencing combined with refined splice prediction and confirmatory RNA testing reveals non-canonical FBN1 splice variants as an important, actionable cause of previously undiagnosed Marfan/FTAAD cases and supports incorporating intronic analysis and RNA assays into clinical workflows.

Music:
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Article title:
Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome

First author:
Walker S

Journal:
Genetics in Medicine

DOI:
10.1016/j.gim.2025.101477

Reference:
Walker S, Bunyan DJ, Thomas HB, Kesim Y, Kershaw CJ, Holloway J, Wai H, Day M, Smith CL, Hawkes G, Wood AR, Weedon MN, Blair E, Curtis SL, Fielden C, Evans J, Whittington R, Smithson SF, Cox H, Clift P, McEntagart M, Prapa M, Alsters S, Morris-Rosendahl D, Dean J, Morrison PJ, Dixit A, Sarkar A, Prescott K, Riazat Kesh LA, Tharakan R, Turner C, Ellard S, Shaw-Smith C, Fasham J, Clowes V, Holden S, Somarathi S, Mercer C, Berry I, O’Keefe RT, Banka S, Baralle D, Thomas NS, Baple EL, Taylor JC, Pagnamenta AT. Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome. Genetics in Medicine (2025). DOI: https://doi.org/10.1016/j.gim.2025.101477

License:
© 2025 Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.

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Episode link: https://basebybase.com/episodes/decoding-hidden-signals-genome-sequencing-reveals-cryptic-splicing-variants-in-marfan-syndrome

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-05.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive audit of the transcript’s coverage of study rationale, methods (genome sequencing, SpliceAI, RNA validation), key findings (20 variants in 23 families, 3% yield, 16/20 validations), extended analyses (windows/absolute scores), and clinical implications including cascade testing and UK Biobank replication.
- transcript topics: Marfan syndrome and FBN1 genetics; 100k Genomes Project dataset and FTAAD enrichment; SpliceAI-based variant prioritization and thresholds; Non-canonical intronic FBN1 splice variants (pseudoexon...