Genome Sequencing Reveals the Impact of Pseudoexons in Rare Genetic Disease

Authors

Georgia Pitsava
Megan Hawley
Light Auriga
Ivan de Dios
Arthur Ko
Sofia Marmolejos
Miguel Almalvez
Ingrid Chen
Kaylee Scozzaro
Jianhua Zhao
Rebekah Barrick
Nicholas Ah Mew
Vincent A Fusaro
Jonathan LoTempio
Matthew Taylor
Luisa Mestroni
Sharon Graw
Dianna Milewicz
Dongchuan Guo
David R Murdock
Kinga M Bujakowska
Changrui Xiao
Emmanuèle C Délot
Seth I Berger
Eric Vilain

Language

English

Publication Date

11-1-2025

Journal

Genetics in Medicine

DOI

10.1016/j.gim.2025.101574

PMID

40927908

PMCID

PMC12501780

PubMedCentral® Posted Date

10-8-2025

PubMedCentral® Full Text Version

Author MSS

Abstract

Purpose: Advancements in sequencing technologies have significantly improved clinical genetic testing; yet, the diagnostic yield remains around 30% to 40%. Emerging technologies are now being deployed to address the remaining diagnostic gap.

Methods: We tested whether short-read genome sequencing could increase the diagnostic yield in individuals enrolled into the UCI-GREGoR research study, who had suspected Mendelian conditions and prior inconclusive testing. Two other collaborative research cohorts, focused on aortopathy and dilated cardiomyopathy, consisted of individuals who were undiagnosed but had not undergone harmonized prior testing.

Results: We sequenced 353 families (754 participants) and found a molecular diagnosis in 54 (15.3%) of them. Of these diagnoses, 55.5% were previously missed because the causative variants were in regions not originally interrogated. In 5 cases, they were deep intronic variants, all of which led to abnormal splicing and pseudoexons, as directly shown by RNA sequencing. All 5 of these variants had inconclusive spliceAI scores. In 26% of newly diagnosed cases, the causal variant could have been detected by exome sequencing reanalysis.

Conclusion: Genome sequencing can overcome limitations of clinical genetic testing, such as the inability to call intronic variants. Our findings highlight pseudoexons as a common mechanism via which deep intronic variants cause Mendelian disease.

Keywords

Humans, Genetic Testing, Rare Diseases, Whole Genome Sequencing, Male, Female, Exons, Genome, Human, Introns, Cardiomyopathy, Dilated, Genetic Diseases, Inborn, Exome Sequencing, High-Throughput Nucleotide Sequencing, Genetic Predisposition to Disease, Sequence Analysis, DNA, Aortic Diseases, genome sequencing, RNA sequencing, rare disease, intronic variants, pseudoexon

Published Open-Access

yes

Recommended Citation

Pitsava, Georgia; Hawley, Megan; Auriga, Light; et al., "Genome Sequencing Reveals the Impact of Pseudoexons in Rare Genetic Disease" (2025). Faculty, Staff and Student Publications. 6276.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/6276