Metzger Patrick, Hess Maria Elena, Blaumeiser Andreas, Pauli Thomas, Schipperges Vincent, Mertes Ralf, Christoph Jan, Unberath Philipp, Reimer Niklas, Scheible Raphael, Illert Anna L, Busch Hauke, Andrieux Geoffroy, Boerries Melanie
Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany.
Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
Cancers (Basel). 2023 Jul 1;15(13):3456. doi: 10.3390/cancers15133456.
(1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting.
(1) 背景：晚期肿瘤患者的下一代测序（NGS）正成为分子肿瘤委员会中的一种既定方法。然而，体细胞变异检测、解读和报告生成需要生物信息学和肿瘤学方面的深入知识。(2) 方法：MIRACUM-Pipe将许多单独的工具整合到一个无缝工作流程中，用于对NGS数据进行全面分析和注释，包括质量控制、比对、变异调用、拷贝数变异估计、复杂生物标志物评估以及RNA融合检测。(3) 结果：MIRACUM-Pipe提供了一个易于使用的、一键式标准化解决方案，用于分析NGS数据，包括质量控制、变异调用、拷贝数估计、注释、可视化和报告生成。(4) 结论：MIRACUM-Pipe是一种通用的NGS流程，可根据生物信息学和临床需求进行定制，并通过可视化处理和交互式报告支持临床决策。
