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

@article{citeulike:143676, abstract = {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.}, address = {Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.}, author = {Ronald, J. and Akey, J. M. and Whittle, J. and Smith, E. N. and Yvert, G. and Kruglyak, L.}, citeulike-article-id = {143676}, doi = {10.1101/gr.2850605}, issn = {1088-9051}, journal = {Genome Res}, keywords = {allele, pcr, specific}, month = {February}, number = {2}, pages = {284--291}, posted-at = {2005-03-31 22:19:15}, priority = {0}, title = {Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.}, url = {http://dx.doi.org/10.1101/gr.2850605}, volume = {15}, year = {2005} }

TY - JOUR ID - citeulike:143676 L3 - citeulike-article-id:143676 N2 - 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. IS - 2 JF - Genome Res SN - 1088-9051 AD - Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. EP - 291 TI - Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. VL - 15 SP - 284 KW - allele KW - pcr KW - specific AU - Ronald, J AU - Akey, JM AU - Whittle, J AU - Smith, EN AU - Yvert, G AU - Kruglyak, L PY - 2005/02// UR - http://dx.doi.org/10.1101/gr.2850605 ER -