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10:17
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing
Pierre Fontanillas1, Christian R Landry, Patricia J Wittkopp
1Department of Ecology and Evolution, University of Lausanne, Switzerland. pierre.fontanillas@unil.ch
Molecular Ecology
|March 25, 2010
Summary
Dissecting gene expression variation is key to understanding adaptation. This study determines the minimum sequencing depth needed for accurate allelic expression analysis in heterozygous individuals.
Area of Science:
- Evolutionary genetics
- Genomics
- Molecular biology
Background:
- Phenotypic diversity arises from gene expression differences.
- Allelic expression analysis provides deeper regulatory insights than total gene expression.
- High-throughput sequencing enables genomic-scale allelic transcription studies.
Purpose of the Study:
- To determine the minimum sequencing depth for accurate relative allelic expression measurement.
- To establish the sequencing requirements for detecting allelic imbalance using high-throughput sequencing.
- To apply allelic expression analysis to study cis-regulatory divergence in Drosophila.
Main Methods:
- Mathematical modeling and computer simulations were used to assess statistical power.
- Analysis focused on the influence of sequencing depth and allele assignment accuracy.
- 454 sequencing was employed for a practical application in Drosophila.
Main Results:
- A minimum of 500-1000 sequencing reads per gene are necessary to test for allelic imbalance within a species.
- At least 5-10 million reads are required for genome-wide allelic expression studies of 10,000 genes.
- The study demonstrated the feasibility of detecting cis-regulatory divergence using allelic expression.
Conclusions:
- Accurate allelic expression measurement requires substantial sequencing depth.
- High-throughput sequencing is a powerful tool for studying regulatory variation and evolution.
- This approach can reveal evolutionary differences in gene regulation between species.
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