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

Christoph Bock (1) , Florian Halbritter , Francisco J Carmona , Sascha Tierling , Paul Datlinger , Yassen Assenov , María Berdasco , Anke K Bergmann (2) , Keith Booher , Florence Busato (3, 4) , Mihaela Campan , Christina Dahl , Christina M Dahmcke , Dinh Diep , Agustín F Fernández , Clarissa Gerhauser , Andrea Haake , Katharina Heilmann , Thomas Holcomb , Dianna Hussmann , Mitsuteru Ito (5) , Ruth Kläver , Martin Kreutz , Marta Kulis (6) , Virginia Lopez (7) , Shalima S Nair , Dirk S Paul , Nongluk Plongthongkum , Wenjia Qu , Ana C Queirós , Frank Reinicke , Guido Sauter , Thorsten Schlomm , Aaron Statham , Clare Stirzaker , Ruslan Strogantsev , Rocío G Urdinguio , Kimberly Walter , Dieter Weichenhan , Daniel J Weisenberger , Stephan Beck , Susan J Clark , Manel Esteller , Anne C Ferguson-Smith , Mario F Fraga , Per Guldberg , Lise Lotte Hansen , Peter W Laird , José I Martín-Subero , Anders O H Nygren , Ralf Peist , Christoph Plass , David S Shames , Reiner Siebert , Xueguang Sun , Jörg Tost (4, 3) , Jörn Walter , Kun Zhang

1 CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences [Vienna, Austria]
2 CAU - Christian-Albrechts-Universität zu Kiel = Christian-Albrechts University of Kiel = Université Christian-Albrechts de Kiel
3 LEE - Laboratoire Epigénétique et environnement​​
4 CNG - Centre National de Génotypage
5 CAM - University of Cambridge [UK]
6 IDIBAPS - Institut d'Investigacions Biomèdiques August Pi i Sunyer
7 SGCSR (U_1274 / UMR_E_008) - Stabilité génétique, cellules souches et radiations

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.

Domaines: Sciences du Vivant [q-bio]; Biotechnologie; Génétique

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⟩