Journal Article

DKFZ-2025-02184

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.

Lin, Y.-Y. (First author)DKFZ* ; Breuer, K.DKFZ* ; Weichenhan, D.DKFZ* ; Lafrenz, P.DKFZ* ; Sarnataro, A. ; Wilk, A.DKFZ* ; Chepeleva, M. ; Mücke, O.DKFZ* ; Schönung, M.DKFZ* ; Petermann, F.DKFZ* ; Kensche, P. R.DKFZ* ; Weiser, L.DKFZ* ; Thommen, F.DKFZ* ; Giacomelli, G. ; Nordstroem, K. ; Gonzalez-Avalos, E. ; Merkel, A. ; Kretzmer, H. ; Fischer, J. ; Krämer, S.DKFZ* ; Iskar, M.DKFZ* ; Wolf, S.DKFZ* ; Buchhalter, I.DKFZ* ; Esteller, M. ; Lawerenz, C. ; Twardziok, S. ; Zapatka, M.DKFZ* ; Hovestadt, V. ; Schlesner, M. ; Schulz, M. H. ; Hoffmann, S. ; Gerhäuser, C.DKFZ* ; Walter, J. ; Hartmann, M.DKFZ* ; Lipka, D.DKFZ* ; Assenov, Y. ; Bock, C. ; Plass, C.DKFZ* ; Toth, R. (Last author)DKFZ* ; Lutsik, P. (Last author)DKFZ*

2025
Oxford Univ. Press Oxford

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Please use a persistent id in citations: doi:10.1093/nar/gkaf970

Abstract: DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five whole-genome profiling protocols. As an evaluation reference, we employed accurate locus-specific measurements from our previous benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and multiple performance metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To ensure the long-term utility of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and readily expandable to future software.

Keyword(s): DNA Methylation (MeSH) ; Workflow (MeSH) ; Software (MeSH) ; Benchmarking (MeSH) ; Humans (MeSH) ; Whole Genome Sequencing: methods (MeSH) ; Whole Genome Sequencing: standards (MeSH) ; Sequence Analysis, DNA: methods (MeSH) ; Sequence Analysis, DNA: standards (MeSH) ; Computational Biology: methods (MeSH) ; Epigenesis, Genetic (MeSH) ; Epigenomics: methods (MeSH)

Note: ISSN 1362-4962 / #EA:B370#LA:B370#

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Contributing Institute(s):

1. Epigenomik (B370)
2. Translationale Medizinische Onkologie (B340)
3. Hochdurchsatz-Sequenzierung (W190)
4. Core Facility Omics IT (W610)
5. B060 Molekulare Genetik (B060)
6. DKTK HD zentral (HD01)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2025

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Database coverage:
; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DOAJ Seal ; Essential Science Indicators ; Fees ; IF >= 10 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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