a simple optimization can improve the performance of single feature polymorphism detection by affymetrix expression arrays一个简单的优化可以提高单一功能多态性检测的性能通过affymetrix表达式数组.pdfVIP

Horiuchi et al. BMC Genomics 2010, 11:315 /1471-2164/11/315 RESEARCH ARTICLE Open Access A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays 1,3 1,3* 2,3 1 2,4 Youko Horiuchi , Yoshiaki Harushima , Hironori Fujisawa , Takako Mochizuki , Masanori Kawakita , Takayuki Sakaguchi2,3,5, Nori Kurata1,3 Abstract Background: 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. Results: 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 stat