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Journal Articles Nature Biotechnology Year : 2016

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications

Florian Halbritter
  • Function : Author
Francisco J Carmona
  • Function : Author
Sascha Tierling
  • Function : Author
Paul Datlinger
  • Function : Author
Yassen Assenov
  • Function : Author
María Berdasco
  • Function : Author
Keith Booher
  • Function : Author
Mihaela Campan
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Christina Dahl
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Christina M Dahmcke
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Dinh Diep
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Agustín F Fernández
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Clarissa Gerhauser
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Andrea Haake
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Katharina Heilmann
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Thomas Holcomb
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Dianna Hussmann
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Ruth Kläver
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Martin Kreutz
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Shalima S Nair
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Dirk S Paul
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Nongluk Plongthongkum
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Wenjia Qu
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Ana C Queirós
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Frank Reinicke
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Guido Sauter
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Thorsten Schlomm
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Aaron Statham
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Clare Stirzaker
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Ruslan Strogantsev
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Rocío G Urdinguio
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Kimberly Walter
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Dieter Weichenhan
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Daniel J Weisenberger
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Stephan Beck
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Susan J Clark
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Manel Esteller
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Anne C Ferguson-Smith
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Mario F Fraga
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Per Guldberg
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Lise Lotte Hansen
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Peter W Laird
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José I Martín-Subero
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Anders O H Nygren
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Ralf Peist
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Christoph Plass
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David S Shames
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Reiner Siebert
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Xueguang Sun
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Jörn Walter
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Kun Zhang
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Abstract

DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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cea-04551223 , version 1 (18-04-2024)

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Attribution - NonCommercial - ShareAlike

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Christoph Bock, Florian Halbritter, Francisco J Carmona, Sascha Tierling, Paul Datlinger, et al.. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology, 2016, 34 (7), pp.726 - 737. ⟨10.1038/nbt.3605⟩. ⟨cea-04551223⟩
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