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

BLUEPRINT consortium, Christoph Bock, Florian Halbritter, Francisco J Carmona, Sascha Tierling, Paul Datlinger, Yassen Assenov, María Berdasco, Anke K Bergmann, Keith Booher, Florence Busato, Mihaela Campan, Christina Dahl, Christina M Dahmcke, Dinh Diep, Agustín F Fernández, Clarissa Gerhauser, Andrea Haake, Katharina Heilmann, Thomas Holcomb, Dianna Hussmann, Mitsuteru Ito, Ruth Kläver, Martin Kreutz, Marta Kulis, Virginia Lopez, 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, Jörn Walter, Kun Zhang, BLUEPRINT consortium, Christoph Bock, Florian Halbritter, Francisco J Carmona, Sascha Tierling, Paul Datlinger, Yassen Assenov, María Berdasco, Anke K Bergmann, Keith Booher, Florence Busato, Mihaela Campan, Christina Dahl, Christina M Dahmcke, Dinh Diep, Agustín F Fernández, Clarissa Gerhauser, Andrea Haake, Katharina Heilmann, Thomas Holcomb, Dianna Hussmann, Mitsuteru Ito, Ruth Kläver, Martin Kreutz, Marta Kulis, Virginia Lopez, 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, Jörn Walter, Kun Zhang

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.

References

    1. Forensic Sci Int Genet. 2014 Jul;11:117-25
    1. Nucleic Acids Res. 2007;35(18):e119
    1. Nat Rev Genet. 2012 Oct;13(10):679-92
    1. Science. 1978 Jun 9;200(4346):1153-4
    1. Nat Biotechnol. 2012 Mar 07;30(3):224-6
    1. Epigenetics. 2013 Jul;8(7):765-71
    1. Br J Cancer. 2014 Oct 28;111(9):1802-9
    1. Genome Res. 2010 Sep;20(9):1279-87
    1. Nat Rev Genet. 2012 Jan 04;13(2):97-109
    1. Science. 1998 Jul 17;281(5375):363, 365
    1. Nat Biotechnol. 2010 Oct;28(10):1057-68
    1. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821-6
    1. Epigenetics. 2014 May;9(5):678-84
    1. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4844-9
    1. Cancer Res. 2007 Feb 1;67(3):876-80
    1. Nat Protoc. 2013 Oct;8(10):1841-51
    1. Nucleic Acids Res. 1994 Aug 11;22(15):2990-7
    1. Nat Med. 2011 Apr;17(4):510-3
    1. Nat Protoc. 2006;1(5):2353-64
    1. Nat Rev Mol Cell Biol. 2015 Oct;16(10 ):593-610
    1. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15785-90
    1. Nat Rev Genet. 2011 Jul 12;12(8):529-41
    1. Nat Methods. 2012 Feb 05;9(3):270-2
    1. Leukemia. 2015 Mar;29(3):598-605
    1. Epigenetics. 2009 Apr 1;4(3):176-84
    1. Nat Rev Genet. 2010 Mar;11(3):191-203
    1. Cell Oncol (Dordr). 2012 Aug;35(4):259-67
    1. Biotechniques. 2003 Jul;35(1):152-6
    1. Clin Chem. 2009 Aug;55(8):1471-83
    1. Epigenetics Chromatin. 2013 Oct 11;6(1):33
    1. N Engl J Med. 2012 Jan 5;366(1):44-53
    1. Nat Rev Genet. 2012 Oct;13(10):705-19
    1. Epigenomics. 2009 Oct;1(1):177-200
    1. Expert Rev Mol Diagn. 2012 Jun;12(5):473-87
    1. Bioinformatics. 2005 Oct 15;21(20):3940-1
    1. Clin Chem. 2009 Jul;55(7):1337-46
    1. Nat Protoc. 2008;3(12):1903-8
    1. Nat Biotechnol. 2010 Oct;28(10):1097-105
    1. Blood. 1980 Aug;56(2):265-73
    1. Anal Biochem. 2012 Mar 15;422(2):74-8
    1. J Am Chem Soc. 2013 Jun 26;135(25):9315-7
    1. Forensic Sci Int Genet. 2014 Nov;13:147-53
    1. Nucleic Acids Res. 2000 Apr 15;28(8):E32
    1. Epigenomics. 2010 Aug;2(4):561-73
    1. Nat Rev Cancer. 2011 Sep 23;11(10):726-34
    1. Clin Cancer Res. 2012 Apr 15;18(8):2360-73
    1. Nature. 2007 May 24;447(7143):425-32
    1. Blood. 2014 Jul 3;124(1):42-8
    1. Int J Cancer. 2009 Aug 1;125(3):723-9
    1. Methods Mol Biol. 2009;507:23-34
    1. Nat Protoc. 2007;2(9):2265-75
    1. Nat Biotechnol. 2010 Oct;28(10):1106-14
    1. PLoS One. 2014 Apr 03;9(4):e93933
    1. Cell. 2013 Apr 25;153(3):678-91
    1. Antioxid Redox Signal. 2013 May 20;18(15):1972-86
    1. Genome Res. 2012 Feb;22(2):407-19
    1. Methods Mol Biol. 2009;507:325-37
    1. N Engl J Med. 2005 Mar 10;352(10 ):997-1003
    1. Clin Chem. 2001;47(7):1183-9
    1. Nat Methods. 2013 Oct;10(10):949-55
    1. Nat Biotechnol. 2010 Oct;28(10):1026-8
    1. Cell. 2011 Feb 4;144(3):439-52
    1. Nat Methods. 2014 Nov;11(11):1138-40
    1. Epigenomics. 2009 Dec;1(2):239-59
    1. Epigenomics. 2009 Oct;1(1):99-110
    1. Methods. 2002 Jun;27(2):121-7
    1. Nat Biotechnol. 2010 Oct;28(10):1039-44
    1. J Mol Diagn. 2013 Jan;15(1):17-26
    1. Nat Rev Cancer. 2003 Apr;3(4):253-66
    1. Nucleic Acids Res. 2004 Feb 18;32(3):e38

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