Reliable variant calling during runtime of Illumina sequencing
Reliable variant calling during runtime of Illumina sequencing
复制标题
DOI：
10.1038/s41598-019-52991-z
复制
发表时间：
2019-11-11
影响因子：
4.6
通讯作者：
Renard, Bernhard Y.
中科院分区：
文献类型：
--
作者：
Loka, Tobias P.;Tausch, Simon H.;Renard, Bernhard Y.
在下一代测序中，数据采集和分析的顺序范例导致产生可解释结果的高周转时间。我们将一种新的实时读段映射算法与快速变异识别相结合，以在测序过程中获得可靠的变异识别。因此，我们的新算法允许中间循环的准确读取映射结果，并支持大型参考基因组，例如完整的人类参考。这使得实时读取映射结果与复杂的后续分析相结合。在这项研究中，我们通过将实时读取映射和变体调用应用于七个公开的人类全外显子组测序数据集来展示我们方法的准确性和可扩展性。因此，在40个测序循环后，已经鉴定了高达89%的所有检测到的SNP，同时显示出与测序结束时相似的精度。最终结果显示与传统事后分析方法相似的准确性。与标准程序相比，我们的实时方法可以在临床应用和传染病爆发中实现更快的干预。除了变体调用，我们的方法可以适用于大量其他基于映射的分析。
The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby, our new algorithm allows for accurate read mapping results for intermediate cycles and supports large reference genomes such as the complete human reference. This enables the combination of real-time read mapping results with complex follow-up analysis. In this study, we showed the accuracy and scalability of our approach by applying real-time read mapping and variant calling to seven publicly available human whole exome sequencing datasets. Thereby, up to 89% of all detected SNPs were already identified after 40 sequencing cycles while showing similar precision as at the end of sequencing. Final results showed similar accuracy to those of conventional post-hoc analysis methods. When compared to standard routines, our live approach enables considerably faster interventions in clinical applications and infectious disease outbreaks. Besides variant calling, our approach can be adapted for a plethora of other mapping-based analyses.