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

Patrick Metzger; Maria Elena Hess; Andreas Blaumeiser; Thomas Pauli; Vincent Schipperges; Ralf Mertes; Jan Christoph; Philipp Unberath; Niklas Reimer; Raphael Scheible; Anna L. Illert; Hauke Busch; Geoffroy Andrieux; Melanie Boerries

doi:10.3390/cancers15133456

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

Patrick Metzger^*, Maria Elena Hess, Andreas Blaumeiser, Thomas Pauli, Vincent Schipperges, Ralf Mertes, Jan Christoph, Philipp Unberath, Niklas Reimer, Raphael Scheible, Anna L. Illert, Hauke Busch, Geoffroy Andrieux, Melanie Boerries^*

^*Korrespondierende/r Autor/-in für diese Arbeit

14 Zitate (Scopus)

Abstract

(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.

Originalsprache	Englisch
Aufsatznummer	3456
Zeitschrift	Cancers
Jahrgang	15
Ausgabenummer	13
ISSN	2072-6694
DOIs	https://doi.org/10.3390/cancers15133456
Publikationsstatus	Veröffentlicht - 07.2023

Fördermittel

This work was funded by the German Federal Ministry of Education and Research (BMBF) by MIRACUM within the Medical Informatics Funding Scheme (01ZZ1801B to P.M. and M.B., 01ZZ1801A to J.C. and P.U.). EkoEstMed–FKZ 01ZZ2015 to G.A. A.L.I. is supported by a Mildred-Scheel-Professorship Grant by the German Cancer Aid (#70114112). H.B. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 22167-390884018.

Träger	Trägernummer
MIRACUM	FKZ 01ZZ2015, 01ZZ1801A, 01ZZ1801B
Deutsche Forschungsgemeinschaft (DFG)	EXC 22167-390884018
Bundesministerium für Bildung und Forschung
Deutsche Krebshilfe	70114112

UN SDGs

Dieser Output leistet einen Beitrag zu folgendem(n) Ziel(en) für nachhaltige Entwicklung

SDG 3 – Gesundheit und Wohlergehen
SDG 6 – Sauberes Wasser und sanitäre Einrichtungen
SDG 9 – Industrie, Innovation und Infrastruktur

Dokumente

10.3390/cancers15133456

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Metzger, P., Hess, M. E., Blaumeiser, A., Pauli, T., Schipperges, V., Mertes, R., Christoph, J., Unberath, P., Reimer, N., Scheible, R., Illert, A. L., Busch, H., Andrieux, G., & Boerries, M. (2023). MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making. Cancers, 15(13), Artikel 3456. https://doi.org/10.3390/cancers15133456

@article{1dc32268b5314f4782c7c5cf42137fc7,

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

abstract = "(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.",

author = "Patrick Metzger and Hess, \{Maria Elena\} and Andreas Blaumeiser and Thomas Pauli and Vincent Schipperges and Ralf Mertes and Jan Christoph and Philipp Unberath and Niklas Reimer and Raphael Scheible and Illert, \{Anna L.\} and Hauke Busch and Geoffroy Andrieux and Melanie Boerries",

note = "Publisher Copyright: {\textcopyright} 2023 by the authors.",

year = "2023",

month = jul,

doi = "10.3390/cancers15133456",

language = "English",

volume = "15",

journal = "Cancers",

issn = "2072-6694",

publisher = "MDPI",

number = "13",

}

Metzger, P, Hess, ME, Blaumeiser, A, Pauli, T, Schipperges, V, Mertes, R, Christoph, J, Unberath, P, Reimer, N, Scheible, R, Illert, AL, Busch, H, Andrieux, G & Boerries, M 2023, 'MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making', Cancers, Jg. 15, Nr. 13, 3456. https://doi.org/10.3390/cancers15133456

TY - JOUR

T1 - MIRACUM-Pipe

T2 - An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

AU - Metzger, Patrick

AU - Hess, Maria Elena

AU - Blaumeiser, Andreas

AU - Pauli, Thomas

AU - Schipperges, Vincent

AU - Mertes, Ralf

AU - Christoph, Jan

AU - Unberath, Philipp

AU - Reimer, Niklas

AU - Scheible, Raphael

AU - Illert, Anna L.

AU - Busch, Hauke

AU - Andrieux, Geoffroy

AU - Boerries, Melanie

PY - 2023/7

Y1 - 2023/7

N2 - (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.

AB - (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.

UR - https://www.scopus.com/pages/publications/85164939368

U2 - 10.3390/cancers15133456

DO - 10.3390/cancers15133456

M3 - Journal articles

AN - SCOPUS:85164939368

SN - 2072-6694

VL - 15

JO - Cancers

JF - Cancers

IS - 13

M1 - 3456

ER -

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

Abstract

Fördermittel

UN SDGs

Dokumente

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