SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
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DOI：
10.1093/bioinformatics/btm154
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发表时间：
2007-07-01
期刊：
影响因子：
5.8
通讯作者：
Lien, Sigbjorn
中科院分区：
文献类型：
--
作者：
Hayes, Ben J.;Nilsen, Kjetil;Lien, Sigbjorn
动机：单核苷酸多态性（SNP）检测利用表达序列标签（EST）集合中的冗余性，该集合源于来自不同个体的同一基因的转录本，已被用于生成许多物种的大量SNP集合。冗余的第二个来源，即EST集合可以包含来自同一个体的同一基因的多个转录本，可以用来区分真正的snp和测序错误。在本文中，我们用大西洋鲑鱼和猪的EST集合演示了将EST集合分成两部分，检测两个子集中的snp，然后只接受交叉验证的snp，从而提高验证率。结果：在猪数据集中，在160 689个ESTs中检测到676个交叉验证的假定snp。当在MassARRAY上通过基因分型验证其中的一个子集时，85.1%的snp在成功的分析中是多态性的。在鲑鱼数据集中，在243 674个ESTs中检测到856个交叉验证的假定snp。基因分型验证表明，81.0%的交叉验证的推测snp在成功的分析中是多态性的。
Motivation: Single nucleotide polymorphism ( SNP) detection exploiting redundancy in expressed sequence tag ( EST) collections that arises from the presence of transcripts of the same gene from different individuals has been used to generate large collections of SNPs for many species. A second source of redundancy, namely that EST collections can contain multiple transcripts of the same gene from the same individual, can be exploited to distinguish true SNPs from sequencing error. In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates. Results: In the pig data set, 676 cross-validated putative SNPs were detected in a collection of 160 689 ESTs. When validating a subset of these by genotyping on MassARRAY 85.1% of SNPs were polymorphic in successful assays. In the salmon data set, 856 cross-validated putative SNPs were detected in a collection of 243 674 ESTs. Validation by genotyping showed that 81.0% of the cross-validated putative SNPs were polymorphic in successful assays.