MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

(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: MIRAC...

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Published inCancers Vol. 15; no. 13; p. 3456
Main Authors 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
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 01.07.2023
MDPI
Subjects
Annotations
Automation
Bioinformatics
Biomarkers
Copy number
Decision making
DNA sequencing
Gene mutations
Genes
Genetic aspects
Genetic engineering
Genomes
Information processing
Next-generation sequencing
Oncology
Patients
Precision medicine
Proteins
Quality control
Regulatory approval
RNA
Sequence analysis
Tumors
Visual perception
Visualization
Germany
computational biology
pipeline
precision oncology
software
workflow
molecular tumor board
next-generation sequencing
somatic variant calling
bioinformatics
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Summary:(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.
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These authors contributed equally to this work.
ISSN:2072-6694
2072-6694
DOI:10.3390/cancers15133456