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首页> 外文会议>2012 ASE International Conference on BioMedical Computing >Affymetrix#x00AE; Mismatch (MM) Probes: Useful after All
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Affymetrix#x00AE; Mismatch (MM) Probes: Useful after All

机译：Affymetrix®不匹配（MM）探针：毕竟有用

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Affymetrix® GeneChip® micro array design defines probe sets consisting of 11, 16, or 20 distinct 25 base pair (BP) probes for determining mRNA expression for a specific gene, which may be covered by one or more probe sets. Each probe has a corresponding perfect match (PM) and mismatch (MM) set. Traditional analytical techniques have either used the MM probes to determine the level of cross-hybridization or reliability of the PM probe, or have been completely ignored. Given the availability of reference genome sequences, we have reanalyzed the mapping of both PM and MM probes to reference genomes in transcript regions. Our results suggest that depending of the species of interest, 66%-93% of the PM probes can be used reliably in terms of single unique matches to the genome, while a small number of the MM probes (typically less than 1%) could be incorporated into the analysis. In addition, we have examined the mapping of PM and MM probes to five different human genome projects, resulting in approximately a 70% overlap of uniquely mapping PM probes, and a subset of 51 uniquely mapping MM probes commonly found in all five projects, 24 of which are found within annotated exonic regions. These results suggest that individual variation in transcriptome regions provides an additional complexity to micro array data analysis. Given these results, we conclude that the development of custom chip definition files (CDFs) should include MM probe sequences to provide the most effective means of transcriptome analysis of Affymetrix® GeneChip® arrays.
机译：Affymetrix®GeneChip®微阵列设计定义了由11个，16个或20个不同的25个碱基对（BP）探针组成的探针组，用于确定特定基因的mRNA表达，该探针组可能覆盖一个或多个探针组。每个探头都有对应的完美匹配（PM）和不匹配（MM）集。传统的分析技术要么使用MM探针确定交叉杂交的水平或PM探针的可靠性，要么被完全忽略。给定参考基因组序列的可用性，我们已经重新分析了PM和MM探针到转录本区域中参考基因组的映射。我们的结果表明，根据感兴趣的物种，就基因组的单个唯一匹配而言，可以可靠地使用66％-93％的PM探针，而少数MM探针（通常少于1％）可以被纳入分析。此外，我们已经检查了PM和MM探针到五个不同的人类基因组计划的映射，导致唯一映射的PM探针和所有五个项目中常见的51个唯一映射MM探针的子集大约有70％重叠24其中发现于带注释的外显子区域内。这些结果表明，转录组区域中的个体变异为微阵列数据分析提供了额外的复杂性。根据这些结果，我们得出结论，定制芯片定义文件（CDF）的开发应包括MM探针序列，以提供最有效的Affymetrix®GeneChip®阵列转录组分析方法。

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