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Updated: Dec 21, 2025
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
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ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.
Gloria M Sheynkman1,2,3, Katharine S Tuttle4,5,6,7,8,9, Florent Laval4,5,6,10,11
1Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA. gloriam_sheynkman@dfci.harvard.edu.
Nature Communications
|May 13, 2020
Summary
We developed ORF Capture-Seq (OCS), a new method to sequence full-length RNA isoforms. OCS significantly increases the discovery of alternative isoforms, especially for transcription factor genes.
Area of Science:
- Molecular Biology
- Genomics
- Transcriptomics
Background:
- Most human protein-coding genes generate multiple isoforms, expanding proteome diversity.
- Characterizing alternative isoforms is challenging due to expression level differences and difficulties in obtaining full-length sequences.
Purpose of the Study:
- To present ORF Capture-Seq (OCS), a novel method for targeted full-length isoform sequencing.
- To address challenges in isoform detection, including low expression levels and incomplete transcript sequences.
Main Methods:
- Developed ORF Capture-Seq (OCS), a flexible method utilizing cloned open reading frames (ORFs) as probes.
- Applied OCS to targeted sequencing applications for full-length transcript analysis.
Main Results:
- Demonstrated OCS's effectiveness in a proof-of-concept study focusing on transcription factor genes.
- Achieved an order-of-magnitude increase in isoform detection compared to unenriched samples.
Conclusions:
- OCS enables rapid discovery of novel isoforms from custom-selected genes.
- This method will accelerate the comprehensive mapping of the human transcriptome.
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