MRSD

MRSD estimates the sequencing depth required to achieve user-specified RNA-seq coverage for genes, transcripts, or gene sets across tissues to enable detection of mis-splicing events in Mendelian disease studies.

Key Features:

• Minimum Required Sequencing Depth (MRSD) metric: Estimates the necessary sequencing depth to achieve user-specified coverage for genes, transcripts, or groups of genes.
• Precision and bias mitigation: Demonstrates precision rates of 90.1%–98.2% and mitigates transcript region-specific sequencing biases that can skew interpretation.
• Cross-biosample application: Applied to whole blood, lymphoblastoid cell lines (LCLs), skeletal muscle, and cultured fibroblasts to evaluate RNA-seq feasibility across tissues.
• Diagnostic yield optimization: Application to established disease gene panels identified fibroblasts as the optimal RNA source for 63.1% of panels.
• VUS assessment: Indicates that up to 67.8% of variants of uncertain significance predicted to impact splicing are assayable by RNA-seq in at least one studied biosample.

Scientific Applications:

• Functional genomics: Informs selection of samples and sequencing depth to study gene expression and splicing.
• Clinical diagnostics for Mendelian diseases: Supports investigation of mis-splicing events to improve diagnostic interpretation.
• Variant interpretation: Prioritizes RNA-seq assays to test variants of uncertain significance predicted to affect splicing.
• Sample selection and sequencing strategy: Guides choice of biosample and sequencing depth to maximize detection of splice aberrations.

Methodology:

Computes the MRSD metric by estimating the sequencing depth required to meet user-specified coverage thresholds for genes, transcripts, or gene groups.