A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.
A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.
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DOI：
10.1186/1471-2164-11-315
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发表时间：
2010-05-20
期刊：
影响因子：
4.4
通讯作者：
Kurata N
中科院分区：
文献类型：
--
作者：
Horiuchi Y;Harushima Y;Fujisawa H;Mochizuki T;Kawakita M;Sakaguchi T;Kurata N
高密度寡核苷酸阵列是同时对多个基因座进行基因分型的有效工具。在小基因组物种（基因组大小：< ~300 Mb）中，全基因组DNA杂交到表达阵列已用于各种应用。在大基因组物种中，转录物杂交到表达阵列已被用于基因分型。虽然水稻是一个中等基因组大小（~400 Mb）的完整测序模式植物，但使用水稻寡核苷酸阵列作为基因分型工具的例子不多。利用Affymetrix GeneChip®水稻基因组阵列，以具有全基因组序列的粳稻品种“Nipponbare”和籼稻品种93-11为研究对象，比较了全基因组和转录本杂交的单特征多态性（SFP）检测性能。对两个基因组的所有探针靶序列进行了调查。只提取了完全匹配的Nipponbare基因组的25-mer单拷贝探针，并预测了它们与93-11个序列之间的SFPs。我们利用非多态性靶点的完全匹配和不匹配探针强度之间的差异，研究了全基因组和转录本杂交中SFP检测的最佳条件，假设这些差异代表了不匹配和完美靶点之间的差异。在优化条件下，比较了几种全基因组杂交检测SFP的统计方法。分析了两种杂交中SFP检测假阳性和假阴性的原因。优化后的全基因组杂交的SFP检测率提高了20%以上，转录本杂交的SFP检测性能也有了很大的提高。微阵列对PM探针对数转换原始强度的显著性分析在全基因组杂交中表现最佳，全基因组杂交检测出22,936个真SFPs，假阳性23.58%。在转录本杂交中，对高表达基因实现了稳定的SFP检测，在茎部和幼穗转录本中均以高灵敏度（bbb50 %）检测到约3500个SFP。基因组和转录本杂交的高SFP检测性能表明，复杂基因组（如Oryza sativa）的微阵列可以有效地用于全基因组基因分型，进行突变定位和基因表达水平等数量性状的分析。
High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (~400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool. We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip® Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated. The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50%) in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.
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影响因子：
4.5
作者：
Demogines, Ann;Smith, Erin;Kruglyak, Leonid;Alani, Eric
通讯作者：
Alani, Eric
影响因子：
9.5
作者：
Lister, Ryan;Gregory, Brian D.;Ecker, Joseph R.
通讯作者：
Ecker, Joseph R.
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
DOI：
10.1073/pnas.0404780101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Gong, JM;Waner, DA;Schroeder, JI
通讯作者：
Schroeder, JI