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Updated: Apr 30, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.

Christopher R Cabanski¹, Vincent Magrini², Malachi Griffith²

¹The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri.

The Journal of Molecular Diagnostics : JMD

|May 13, 2014

Summary

This summary is machine-generated.

This study combines RNA sequencing with exome capture to improve transcriptome analysis from limited, formalin-fixed paraffin-embedded (FFPE) samples. This method enhances RNA yield and preserves expression data for better health and disease insights.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Massively parallel sequencing advances transcriptome analysis.
Clinical samples offer insights into health and disease RNA expression.
RNA degradation and limited yield complicate studies using formalin-fixed paraffin-embedded (FFPE) samples.

Purpose of the Study:

To enhance RNA sequencing yield from limited and degraded clinical samples.
To evaluate the efficacy of exome capture selection in improving transcriptome analysis.
To enable robust differential expression analysis and mutation validation from FFPE material.

Main Methods:

Combined RNA sequencing with exome capture selection.
Utilized cDNA hybrid capture techniques.
Compared sequencing data yield and quality against RNA sequencing alone.

Main Results:

Exome capture significantly enhanced the yield of on-exon sequencing data.
The method preserved the dynamic range of gene expression.
Enabled differential comparisons and validation of expressed mutations from FFPE samples.
Reduced overall data generation requirements.

Conclusions:

Combined RNA sequencing and exome capture improves transcriptome analysis from low-yield FFPE samples.
This approach is valuable for studying RNA expression in clinical settings.
cDNA hybrid capture offers a significant advancement for FFPE material analysis.