Transcriptome-wide outlier approach identifies individuals with minor spliceopathies

Area of Science:

• Genomics and Transcriptomics
• Rare Disease Diagnostics
• Molecular Biology

Background:

• RNA sequencing enhances rare disease diagnosis, but current methods often miss trans-acting variants affecting splicing transcriptome-wide.
• Existing analyses primarily focus on cis-acting variants, overlooking spliceosome function disruptions.
• Rare diseases require novel diagnostic strategies to identify causative genetic variants.

Purpose of the Study:

• To develop and apply a transcriptomics-first method for diagnosing rare diseases by detecting transcriptome-wide splicing outliers.
• To investigate the role of minor introns and the minor spliceosome in rare disease pathogenesis.
• To identify novel gene-disease associations through comprehensive splicing analysis.

Main Methods:

• Utilized FRASER and FRASER2 splicing outlier detection methods on whole blood RNA sequencing data from 390 individuals (GREGoR and UDN consortia).
• Focused on identifying excess intron retention outliers specifically in minor intron-containing genes (MIGs).
• Analyzed identified variants for their impact on minor spliceosome small nuclear RNAs (snRNAs).

Main Results:

• Identified five individuals with excess intron retention outliers in MIGs, all harboring rare, biallelic variants in minor spliceosome snRNAs.
• Discovered compound heterozygous variants in RNU4ATAC in four individuals, leading to reclassification of four variants.
• Found rare, conserved compound heterozygous variants in RNU6ATAC in one individual, suggesting a novel disease candidate.

Conclusions:

• Analyzing RNA sequencing data for transcriptome-wide splicing signatures significantly increases rare disease diagnostic yield.
• This approach provides crucial variant-to-function interpretation for spliceopathies.
• The study successfully uncovered novel gene-disease associations by examining splicing patterns.