Related Experiment Videos
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Beryl B Cummings1,2,3, Jamie L Marshall1,2, Taru Tukiainen1,2
1Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
Science Translational Medicine
|April 21, 2017
Summary
Transcriptome sequencing (RNA-seq) enhances rare disease diagnosis by detecting genetic variants missed by standard methods. This approach identified new causes of muscle disorders, improving the diagnostic rate for undiagnosed patients.
Area of Science:
- Genomics and Transcriptomics
- Rare Disease Diagnostics
- Molecular Medicine
Background:
- Exome and whole-genome sequencing are standard for Mendelian disease diagnosis but have diagnostic rates of only 25-50%.
- Many rare genetic disorders remain undiagnosed despite comprehensive genomic analysis.
- Splice-altering variants, particularly in intronic regions, are challenging to detect with current genomic approaches.
Purpose of the Study:
- To evaluate transcriptome sequencing (RNA-seq) as a complementary diagnostic tool for genetically undiagnosed rare muscle disorders.
- To develop and apply an integrated RNA-seq analysis framework for detecting patient-specific transcript-level changes.
- To identify novel genetic variants and improve diagnostic yield in rare muscle diseases.
Main Methods:
- Analyzed muscle RNA-sequencing data from 50 patients with genetically undiagnosed rare muscle disorders.
- Utilized an analysis framework to detect transcript-level alterations compared to over 180 control skeletal muscle samples.
- Integrated RNA-seq findings with existing genomic data to validate candidate mutations and identify splice-altering variants.
Main Results:
- Achieved an overall diagnostic rate of 35% by identifying splice-disrupting variants in exonic and deep intronic regions.
- Discovered a recurrent de novo intronic mutation in COL6A1 causing a dominant splice-gain event affecting the collagen VI triple helical domain.
- Identified this COL6A1 pathogenic variant in 27 patients with collagen VI-like dystrophy, explaining ~25% of previously unsolved cases.
Conclusions:
- Transcriptome sequencing (RNA-seq) is a powerful complementary tool for rare disease diagnosis, significantly increasing diagnostic yield.
- RNA-seq effectively detects and interprets splice-altering variants, including deep intronic mutations, often missed by standard genomic analyses.
- This study demonstrates the broad utility of systematic RNA-seq application in uncovering genetic causes of rare diseases.