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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
Tomas Babak1, Philip Garrett-Engele, Christopher D Armour
1Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA.
BMC Genomics
|August 17, 2010
Summary
Sequencing cDNA to detect allele-specific expression (ASE) is a cost-effective method. This approach accurately identifies cis-acting regulatory variation, offering a practical alternative to traditional expression genetics.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Microarray-based genotype-gene expression association studies are valuable for understanding complex phenotypes.
- High costs associated with genotyping and expression profiling limit the widespread application of these methods.
Purpose of the Study:
- To develop a cost-effective method for identifying regulatory variation.
- To validate allele-specific expression (ASE) as a proxy for expression quantitative trait loci (eQTL).
Main Methods:
- Sequencing complementary DNA (cDNA) to detect allele-specific expression (ASE).
- Profiling gene expression in 500 animals in parallel.
- Comparing ASE data with cis-acting expression quantitative trait loci (cis-eQTL) identified through traditional methods.
Main Results:
- Genomic regions with ASE detected by cDNA sequencing are highly enriched for cis-eQTL.
- Up to 90% agreement was observed between ASE and cis-eQTL in identifying the preferentially expressed allele.
- Widespread noncoding and antisense ASE, along with allele-specific alternative splicing variants, were identified.
Conclusions:
- Monitoring ASE via cDNA sequencing is a practical alternative to expression genetics for mapping cis-acting variation.
- This method can effectively regulate RNA transcription and processing.
- ASE analysis from a single sample provides a cost-efficient approach for genetic variation studies.
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