Automating sequence-based detection and genotyping of SNPs from diploid samples
Automating sequence-based detection and genotyping of SNPs from diploid samples
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DOI：
10.1038/ng1746
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发表时间：
2006-03-01
期刊：
影响因子：
30.8
通讯作者：
Nickerson, DA
中科院分区：
文献类型：
--
作者：
Stephens, M;Sloan, JS;Nickerson, DA
DNA测序已成为最敏感和自动化的方法，序列变异的检测构成了所有遗传分析的基础。在这里，我们描述和说明了一种算法，准确地检测和基因型SNP基于荧光的序列数据。由于该算法特别关注通过鉴定杂合个体来检测SNP，因此它特别适合于检测DNA扩增后获得的二倍体样品中的SNP。它比现有的方法更准确，特别是，它提供了一个有用的定量测量其在每个潜在的SNP检测和在每个基因型调用的信心。被分配最高置信度的调用足够可靠，从而在若干上下文中消除了手动审查的需要。例如，对于正向和反向链上测序的47-90个个体的序列数据，我们算法的最高置信度调用检测到93%的所有SNP和100%的高频SNP，未发现假阳性SNP，基因分型准确率为99.9%。该算法在软件包PolyPhred 5.0版中实现，该软件包可免费用于学术用途。
The detection of sequence variation, for which DNA sequencing has emerged as the most sensitive and automated approach, forms the basis of all genetic analysis. Here we describe and illustrate an algorithm that accurately detects and genotypes SNPs from fluorescence-based sequence data. Because the algorithm focuses particularly on detecting SNPs through the identification of heterozygous individuals, it is especially well suited to the detection of SNPs in diploid samples obtained after DNA amplification. It is substantially more accurate than existing approaches and, notably, provides a useful quantitative measure of its confidence in each potential SNP detected and in each genotype called. Calls assigned the highest confidence are sufficiently reliable to remove the need for manual review in several contexts. For example, for sequence data from 47-90 individuals sequenced on both the forward and reverse strands, the highest-confidence calls from our algorithm detected 93% of all SNPs and 100% of high-frequency SNPs, with no false positive SNPs identified and 99.9% genotyping accuracy. This algorithm is implemented in a software package, PolyPhred version 5.0, which is freely available for academic use.