Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays

Journal Article

Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to perform genotyping on genomic DNA. Here, we show that in segregants from a cross between two unrelated strains of Saccharomyces cerevisiae, high-quality genotype data can also be obtained when mRNA is hybridized to an oligonucleotide-expression array. We were able to identify and genotype nearly 1000 polymorphisms at an error rate close to 3% in segregants and at an error rate of 7% in diploid strains, a performance comparable to methods using genomic DNA. In addition, we demonstrate how simultaneous genotyping and gene-expression profiling can reveal cis-regulatory variation by screening hundreds of genes for allele-specific expression. With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two S. cerevisiae strains.

Full Text

Duke Authors

Cited Authors

  • Ronald, J; Akey, JM; Whittle, J; Smith, EN; Yvert, G; Kruglyak, L

Published Date

  • February 2005

Published In

Volume / Issue

  • 15 / 2

Start / End Page

  • 284 - 291

Published By

International Standard Serial Number (ISSN)

  • 1088-9051

Digital Object Identifier (DOI)

  • 10.1101/gr.2850605


  • en