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

Bock, C; Halbritter, F; Carmona, FJ; Tierling, S; Datlinger, P; Assenov, Y; Berdasco, M; ... Zhang, K; + view all (2016) Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. NATURE BIOTECHNOLOGY , 34 (7) pp. 726-737. 10.1038/nbt.3605. Green open access

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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.

Type: Article
Title: Quantitative comparison of DNA methylation assays for biomarker development and clinical applications
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/nbt.3605
Publisher version: http://dx.doi.org/10.1038/nbt.3605
Language: English
Additional information: © 2016 Macmillan Publishers Limited, part of Springer Nature.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, CHRONIC LYMPHOCYTIC-LEUKEMIA, EPIGENOME-WIDE ASSOCIATION, MASS-SPECTROMETRY, EPIGENETIC MODIFICATIONS, COLORECTAL-CANCER, CPG ISLANDS, CELL-LINES, QUANTIFICATION, IDENTIFICATION, CHALLENGES
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/1506393
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