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 unrelat...
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| Veröffentlicht in: | Genome research 2005-02, Vol.15 (2), p.284-291 |
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| creator | Ronald, James Akey, Joshua M Whittle, Jacqueline Smith, Erin N Yvert, Gael Kruglyak, Leonid |
| description | 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. |
| doi_str_mv | 10.1101/gr.2850605 |
| format | Article |
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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. 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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. 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| ispartof | Genome research, 2005-02, Vol.15 (2), p.284-291 |
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| subjects | Alleles DNA, Fungal - genetics Gene Expression Profiling - methods Gene Expression Regulation, Fungal - genetics Genes, Fungal - genetics Genome, Fungal Methods Oligonucleotide Array Sequence Analysis - methods Research Design Saccharomyces cerevisiae Saccharomyces cerevisiae - genetics Species Specificity |
| title | Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays |
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