Transcriptome-wide outlier approach identifies individuals with minor spliceopathies

Area of Science:

• Genomics
• Molecular Biology
• Rare Diseases

Background:

• RNA sequencing enhances rare disease diagnosis, but current methods miss trans-acting variants affecting splicing.
• Focusing on cis-acting variants overlooks spliceosome function disruptions.
• A new transcriptomics-first strategy is needed to capture these overlooked variants.

Purpose of the Study:

• To develop and apply a transcriptomics-first method for diagnosing rare diseases by analyzing transcriptome-wide splicing outliers.
• To identify causal variants with trans-acting effects on splicing, particularly those impacting the minor spliceosome.
• To increase the diagnostic yield for individuals with rare and undiagnosed diseases.

Main Methods:

• Utilized FRASER and FRASER2 splicing outlier detection methods on whole blood RNA sequencing data.
• Analyzed 385 individuals from the GREGoR and Undiagnosed Diseases Network (UDN) consortia.
• Specifically examined for excess intron retention outliers in minor intron-containing genes (MIGs).

Main Results:

• Identified five individuals with excess intron retention outliers in MIGs.
• All five individuals harbored rare, bi-allelic variants in minor spliceosome small nuclear RNAs (snRNAs).
• Discovered compound heterozygous variants in RNU4ATAC (four individuals) and RNU6ATAC (one individual), aiding variant reclassification and suggesting RNU6ATAC as a Mendelian disease gene.

Conclusions:

• Analyzing RNA sequencing data for transcriptome-wide splicing signatures increases rare disease diagnostic yield.
• This approach provides variant-to-function interpretation for spliceopathies.
• Uncovers novel gene-disease associations, particularly for genes involved in spliceosome function.