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

Autor: Bock, Christoph, Halbritter, Florian, Carmona, Francisco J., Tierling, Sascha, Datlinger, Paul, Assenov, Yassen, Berdasco, María, Bergmann, Anke K., Booher, Keith, Busato, Florence, Campan, Mihaela, Dahl, Christina, Dahmcke, Christina M., Diep, Dinh, Fernández, Agustín F., Gerhauser, Clarissa, Haake, Andrea, Heilmann, Katharina, Holcomb, Thomas, Hussmann, Dianna, Ito, Mitsuteru, Kläver, Ruth, Kreutz, Martin, Kulis, Marta, López, Virginia, Nair, Shalima S., Paul, Dirk S., Plongthongkum, Nongluk, Qu, Wenjia, Queirós, Ana C., Reinicke, Frank, Sauter, Guido, Schlomm, Thorsten, Statham, Aaron, Stirzaker, Clare, Strogantsev, Ruslan, Urdinguio, Rocío G., Walter, Kimberly, Weichenhan, Dieter, Weisenberger, Daniel J., Beck, Stephan, Clark, Susan J., Esteller, Manel, Ferguson-Smith, Anne C., Fraga, Mario F., Guldberg, Per, Lotte Hansen, Lise, Laird, Peter W., Martín, José Ignacio, Nygren, Anders O. H., Peist, Ralf, Plass, Christoph, Shames, David S., Siebert, Reiner, Sun, Xueguang, Tost, Jörg, Walter, Jörn, Zhang, Kun
Přispěvatelé: Biotechnology and Biological Sciences Research Council (UK), Federal Ministry of Education and Research (Germany), National Institute on Mental Health (US), European Commission, Deutsches Krebsforschungszentrum, Universitat de Barcelona
Rok vydání: 2015
Předmět:
Zdroj: Recercat. Dipósit de la Recerca de Catalunya
instname
Dipòsit Digital de la UB
Universidad de Barcelona
Bock, C; Halbritter, F; Carmona, FJ; Tierling, S; Datlinger, P; Assenov, Y; et al.(2016). Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology, 34(7), 726-737. doi: 10.1038/nbt.3605. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/7tf2342w
Digital.CSIC. Repositorio Institucional del CSIC
Bock, C, Halbritter, F, Carmona, F J, Tierling, S, Datlinger, P, Assenov, Y, Berdasco, M, Bergmann, A K, Booher, K, Busato, F, Campan, M, Dahl, C, Dahmcke, C M, Diep, D, Fernández, A F, Gerhauser, C, Haake, A, Heilmann, K, Holcomb, T, Hussmann, D, Ito, M, Kläver, R, Kreutz, M, Kulis, M, Lopez, V, Nair, S S, Paul, D S, Plongthongkum, N, Qu, W, Queirós, A C, Reinicke, F, Sauter, G, Schlomm, T, Statham, A, Stirzaker, C, Strogantsev, R, Urdinguio, R G, Walter, K, Weichenhan, D, Weisenberger, D J, Beck, S, Clark, S J, Esteller, M, Ferguson-Smith, A C, Fraga, M F, Guldberg, P, Hansen, L L, Laird, P W, Martín-Subero, J I, Nygren, A O H, Peist, R, Plass, C, Shames, D S, Siebert, R, Sun, X, Tost, J, Walter, J & Zhang, K 2016, ' Quantitative comparison of DNA methylation assays for biomarker development and clinical applications ', Nature Biotechnology, vol. 34, no. 7, pp. 726-737 . https://doi.org/10.1038/nbt.3605
ISSN: 1546-1696
DOI: 10.1038/nbt.3605.
Popis: The BLUEPRINT consortium
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.
This work was performed in the context of the BLUEPRINT project (European Union’s Seventh Framework Programme grant agreement 282510), which funded the study logistics and the integrative data analysis. The assay costs were paid by the contributing laboratories using institutional funds and the following grants: BBSRC BB/G020930/1, BBSRC BB/G020930/1, BMBF 01KU1001A, BMBF 01KU1002A, BMBF 01KU1216F, EU-FP7 282510, FWF I 1575-B19, NHMRC 1063559, NHMRC 1088144 and the DKFZ Graduate School.
Databáze: OpenAIRE
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