title: Allele-specific expression assays using Solexa.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA. bmain@usc.edu
authors.forename: Bradley J
authors.initials: BJ
authors.lastname: Main
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Bickel
authors.forename: Lauren M
authors.initials: LM
authors.lastname: McIntyre
authors.forename: Rita M
authors.initials: RM
authors.lastname: Graze
authors.forename: Peter P
authors.initials: PP
authors.lastname: Calabrese
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
mesh_terms: D000483:Alleles; D000818:Animals; D004330:Drosophila / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D017344:Genes, Insect; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide