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Updated: Jun 9, 2026
09:58
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.
Tzu-Hung Hsiao1, Chien-Hong Lin, Te-Tsui Lee
1Departmant of Electrical Engineering, National Taiwan University, Taipei, Taiwan 106, ROC.
Nucleic Acids Research
|August 28, 2010
Summary
This study introduces a new system for analyzing gene splicing events and identifying transcript variants. The integrated pipeline enables high-throughput analysis, variant validation, and expression level measurement.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Understanding gene splicing and transcript variants is crucial for deciphering gene function.
- Existing methods for analyzing splicing events can be low-throughput and labor-intensive.
- Accurate identification and characterization of transcript variants are essential for disease research.
Purpose of the Study:
- To develop and validate an integrated system for high-throughput analysis of splicing events.
- To enable the identification and characterization of diverse transcript variants.
- To facilitate the semi-quantitative measurement of transcript variant expression levels.
Main Methods:
- Development of a pipeline combining bioinformatic analysis, high-throughput transcript variant amplification, and capillary electrophoresis.
- Design of minimal primer sets for amplifying all transcript variants of known human genes, archived in the ASprimerDB database.
- Utilized a high-throughput thermocycler (GenTank) and new software (AmpliconViewer, VariantAssembler) for data analysis.
Main Results:
- The system successfully resolves individual splicing events and elucidates transcript variants.
- It facilitates the validation of putative transcript variants and the detection of novel ones.
- The system enables semi-quantitative measurement of transcript variant expression levels for each gene.
Conclusions:
- The described integrated system offers a powerful, high-throughput solution for splicing event analysis and transcript variant identification.
- This novel approach aids in validating known and discovering new transcript variants, advancing genomic research.
- The system's ability to measure expression levels provides deeper insights into gene regulation and function.
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