Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays
Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays
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DOI：
10.1101/gr.2850605
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发表时间：
2005-02-01
期刊：
影响因子：
7
通讯作者：
Kruglyak, L
中科院分区：
文献类型：
--
作者：
Ronald, J;Akey, JM;Kruglyak, L
寡核苷酸微阵列为探索基因组提供了一种高通量方法。除了用于基因表达分析外，寡核苷酸表达阵列还被用于对基因组DNA进行基因分型。在这里，我们表明，在两个不相关的酿酒酵母菌株之间杂交的分离物中，当mRNA与寡核苷酸表达阵列杂交时，也可以获得高质量的基因型数据。我们能够在分离株中以接近3%的错误率识别近1000个多态并对其进行分型，在二倍体品系中的错误率为7%，这一性能与使用基因组DNA的方法相当。此外，我们通过筛选数百个等位基因特异性表达的基因，展示了同时进行基因分型和基因表达谱分析如何揭示顺式调控变异。用这种方法，我们在两个酿酒酵母菌株的二倍体杂交中发现了70个ORF，其中一个等位基因有优先表达的证据。
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 ail 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.