Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

Area of Science:

• Genomics
• Molecular Biology
• Medical Genetics

Background:

• Whole-exome sequencing (WES) fails to diagnose over 50% of suspected Mendelian disorders.
• The contribution of non-coding variants, unaddressed by WES, to this diagnostic gap is largely unknown.
• Large-scale empirical data on RNA analysis for Mendelian disease diagnosis are limited.

Purpose of the Study:

• To evaluate the diagnostic yield of transcript-deleterious variants (TDVs) in Mendelian diseases.
• To assess the utility of RNA sequencing as a supplement to WES.
• To determine the feasibility of RNA analysis in a clinical diagnostic setting.

Main Methods:

• Analysis of a cohort of 5647 families with suspected Mendelian diseases.
• Identification and characterization of TDVs.
• Comparison of RT-PCR results with in silico predictions for variant pathogenicity.
• RNA analysis using blood, skin fibroblast, and urine-derived RNA.

Main Results:

• TDVs contributed to 18.9% of Mendelian cases mapped to a single locus and 15% of all "solved" cases.
• RNA analysis successfully diagnosed 13.5% of patients with previously negative WES reports.
• RT-PCR provided definitive results for 84.1% of variants, with a low failure rate across all RNA sources (2.6%).
• TDVs may influence penetrance in highly penetrant Mendelian disorders.

Conclusions:

• RNA sequencing, particularly for TDVs, significantly enhances diagnostic yield in Mendelian disorders.
• RNA analysis is a viable and effective tool for clinical diagnosis, complementing WES.
• These findings provide essential empirical data for integrating diagnostic RNA sequencing with genome sequencing.