Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.
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.
Ronald
James
J
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Akey
Joshua M
JM
Whittle
Jacqueline
J
Smith
Erin N
EN
Yvert
Gael
G
Kruglyak
Leonid
L
D000483:Alleles; D004271:DNA, Fungal / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013045:Species Specificity
D004271:DNA, Fungal