SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
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DOI：
10.1186/1471-2105-10-131
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发表时间：
2009-05-06
影响因子：
3
通讯作者：
Kurata, Nori
中科院分区：
文献类型：
--
作者：
Fujisawa, Hironori;Horiuchi, Youko;Kurata, Nori
背景资料：高密度短寡核苷酸芯片是研究生物多样性的有用工具，因为它们可以用于研究核苷酸和表达多态性。然而，当不同的菌株（或物种）在mRNA杂交后产生不同的信号强度时，不容易确定信号强度是否受核苷酸或表达多态性的影响。为了克服这一困难，核苷酸和表达多态性目前examinedseparately.Results：我们已经开发出SNEP，一种新的方法，允许同时检测核苷酸和表达多态性。SNEP涉及一种稳健的统计程序，其基于这样的想法，即在探针水平观察到的核苷酸多态性可以被视为离群值，因为核苷酸多态性可以降低杂交信号强度。为了研究SNEP的性能，我们使用了三个物种：大麦，水稻和小鼠。除了公开的大麦数据外，我们还从具有可用基因组序列的品系中获得了新的水稻和小鼠数据。根据序列信息估计核苷酸多态性检测的灵敏度和假阳性率。对nucleotide polymorphisms.Conclusion：SNEP表现良好，无论基因组大小，并表现出更好的性能，为核苷酸多态性检测，与其他先前提出的方法相比。R软件“SNEP”可从http://www.ism.ac.jp/similar下载到fujisawa/SNEP/。
Background: High-density short oligonucleotide microarrays are useful tools for studying biodiversity, because they can be used to investigate both nucleotide and expression polymorphisms. However, when different strains (or species) produce different signal intensities after mRNA hybridization, it is not easy to determine whether the signal intensities were affected by nucleotide or expression polymorphisms. To overcome this difficulty, nucleotide and expression polymorphisms are currently examined separately.Results: We have developed SNEP, a new method that allows simultaneous detection of both nucleotide and expression polymorphisms. SNEP involves a robust statistical procedure based on the idea that a nucleotide polymorphism observed at the probe level can be regarded as an outlier, because the nucleotide polymorphism can reduce the hybridization signal intensity. To investigate the performance of SNEP, we used three species: barley, rice and mice. In addition to the publicly available barley data, we obtained new rice and mouse data from the strains with available genome sequences. The sensitivity and false positive rate of nucleotide polymorphism detection were estimated based on the sequence information. The robustness of expression polymorphism detection against nucleotide polymorphisms was also investigated.Conclusion: SNEP performed well regardless of the genome size and showed a better performance for nucleotide polymorphism detection, when compared with other previously proposed methods. The R-software 'SNEP' is available at http://www.ism.ac.jp/similar to fujisawa/SNEP/.