title: High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot.
abstract: The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach.
authors: Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA. kaaberg@vcu.edu
authors: Karolina A
authors: KA
authors: Aberg
authors: Lin Y
authors: LY
authors: Xie
authors: Srilaxmi
authors: S
authors: Nerella
authors: William E
authors: WE
authors: Copeland
authors: E Jane
authors: EJ
authors: Costello
authors: Edwin J C G
authors: EJ
authors: van den Oord
mesh_terms: D001771:Blood Banks; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D059788:Dried Blood Spot Testing; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans
chemical_list: D004247:DNA
keywords: DNA extraction; MBD-seq; archived blood spots; methylation; next-generation sequencing
references: FASEB J. 2012 Jun;26(6):2712-8
references: 22426120
references: Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1302-6
references: 7877972
references: Trends Genet. 2012 Mar;28(3):118-27
references: 22226176
references: Genome Biol. 2008;9(9):R137
references: 18798982
references: BMC Med Genet. 2011 Feb 09;12:22
references: 21306642
references: Nucleic Acids Res. 2010 Jan;38(2):391-9
references: 19906696
references: Science. 2006 Apr 14;312(5771):279-83
references: 16614226
references: Electrophoresis. 2009 Jul;30(14):2532-5
references: 19639574
references: Nat Rev Genet. 2009 Apr;10(4):241-51
references: 19293820
references: BMC Genet. 2011 Jul 04;12:58
references: 21726430
references: Science. 2005 Apr 15;308(5720):385-9
references: 15761122
references: Growth Dev Aging. 1993 Winter;57(4):261-73
references: 8300279
references: Nucleic Acids Res. 1991 Oct 25;19(20):5771-5
references: 1945854
references: Am J Hum Genet. 2008 Mar;82(3):696-711
references: 18319075
references: Epigenomics. 2009 Oct;1(1):177-200
references: 22122642
references: Forensic Sci Int Genet. 2012 May;6(3):306-9
references: 21737370
references: Nat Rev Genet. 2010 Mar;11(3):191-203
references: 20125086
references: Epigenetics. 2011 Jan;6(1):34-44
references: 20818161
references: Nature. 1978 Aug 24;274(5673):775-80
references: 355893
references: Genome Res. 2012 Aug;22(8):1407-18
references: 22684279
references: Nat Genet. 2000 Jan;24(1):88-91
references: 10615135
references: Epigenetics. 2012 Jan 1;7(1):20-8
references: 22207355
references: Epigenomics. 2012 Dec;4(6):605-21
references: 23244307
references: Nat Biotechnol. 2010 Oct;28(10):1097-105
references: 20852635
references: Science. 2008 Nov 7;322(5903):881-8
references: 18988837
references: Nutrition. 2004 Jan;20(1):63-8
references: 14698016
references: Ann N Y Acad Sci. 2003 Mar;983:151-60
references: 12724220
references: BMC Res Notes. 2012 Sep 13;5:503
references: 22974252
references: Mol Genet Metab. 2013 Apr;108(4):225-31
references: 23422032
references: Trends Mol Med. 2011 Dec;17(12):714-24
references: 21885342
references: Nat Rev Genet. 2011 Jul 12;12(8):529-41
references: 21747404
references: Nature. 2010 Jun 10;465(7299):721-7
references: 20535201
references: Methods. 2010 Nov;52(3):203-12
references: 20430099
references: PLoS One. 2011;6(7):e22226
references: 21779396
references: Arch Gen Psychiatry. 1996 Dec;53(12):1129-36
references: 8956679
references: Genome Res. 2012 Nov;22(11):2138-45
references: 22919074
references: Nat Methods. 2009 Nov;6(11 Suppl):S22-32
references: 19844228
references: Nature. 2007 May 24;447(7143):433-40
references: 17522677
references: Nat Rev Cardiol. 2010 Sep;7(9):510-9
references: 20603647
references: Epigenomics. 2010 Oct;2(5):671-82
references: 22122050
references: BMC Bioinformatics. 2013 Feb 12;14:50
references: 23398781
references: Am J Phys Anthropol. 1997 Sep;104(1):1-21
references: 9331450
references: J Nutr. 2001 May;131(5):1631S-6S
references: 11340130