Allele-specific expression assays using Solexa

Bradley Main, Ryan D. Bickel, Lauren M. McIntyre, Rita M. Graze, Peter P. Calabrese, Sergey V. Nuzhdin

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

Background: Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts. Results: We introduce a Solexa-based method to perform large numbers of ASE assays using only a single lane of a Solexa flowcell. In brief, transcripts of interest, which contain a known SNP, are PCR enriched and barcoded to enable multiplexing. Then high-throughput sequencing is used to estimate allele-specific expression using sequencing counts. To validate this method, we measured the allelic bias in a dilution series and found high correlations between measured and expected values (r>0.9, p < 0.001). We applied this method to a set of 5 genes in a Drosophila simulans parental mix, F1 and introgression and found that for these genes the majority of expression divergence can be explained by cis-regulatory variation. Conclusion: We present a new method with the capacity to measure ASE for large numbers of assays using as little as one lane of a Solexa flowcell. This will be a valuable technique for molecular and population genetic studies, as well as for verification of genome-wide data sets.

Original languageEnglish (US)
Article number1471
Number of pages1
JournalBMC Genomics
Volume10
DOIs
StatePublished - Sep 9 2009
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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    Main, B., Bickel, R. D., McIntyre, L. M., Graze, R. M., Calabrese, P. P., & Nuzhdin, S. V. (2009). Allele-specific expression assays using Solexa. BMC Genomics, 10, [1471]. https://doi.org/10.1186/1471-2164-10-422