Quality scores and SNP detection in sequencing-by-synthesis systems
Quality scores and SNP detection in sequencing-by-synthesis systems
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DOI：
10.1101/gr.070227.107
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发表时间：
2008-05-01
期刊：
影响因子：
7
通讯作者：
Jaffe, David B.
中科院分区：
文献类型：
--
作者：
Brockman, William;Alvarez, Pablo;Jaffe, David B.
基于合成测序（SBS）的新测序技术正开始以极低的成本提供大量的DNA序列。多态性检测是一个关键的应用。我们描述了提高质量分数和准确的自动化多态性检测的一般方法，并将其应用于罗氏（454）基因组测序仪20的数据。我们使用已知真值数据集评估我们的方法，这对评估的有效性至关重要。我们为该测序器开发了信息丰富的碱基误差预测器，并使用phred bin算法的变体将它们组合成一个经验推导的质量评分。这些质量分数比系统软件产生的分数更有用：它们既能更好地预测实际错误率，又能识别出更多高质量的基础。我们开发了一种SNP检测方法，具有低覆盖率、高覆盖率和PCR扩增子应用的变体，并在已知事实数据集上对其进行了评估。我们在单reads中表现出良好的特异性，在高覆盖率数据中表现出优异的特异性（在215kb基因组中没有假阳性）。
Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We describe general methods for improved quality scores and accurate automated polymorphism detection, and apply them to data from the Roche (454) Genome Sequencer 20. We assess our methods using known-truth data sets, which is critical to the validity of the assessments. We developed informative, base-by-base error predictors for this sequencer and used a variant of the phred binning algorithm to combine them into a single empirically derived quality score. These quality scores are more useful than those produced by the system software: They both better predict actual error rates and identify many more high-quality bases. We developed a SNP detection method, with variants for low coverage, high coverage, and PCR amplicon applications, and evaluated it on known-truth data sets. We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data.