The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array

BMC Biotechnology

JiHoon E Joo²  Ee Ming Wong²  Laura Baglietto¹  Chol-Hee Jung⁴  Helen Tsimiklis²  Daniel J Park²  Nicholas C Wong³  Dallas R English¹  John L Hopper¹  Gianluca Severi¹  Graham G Giles¹  Melissa C Southey² 

[1] Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Victoria, 3010, Australia

[2] Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Victoria, 3010, Australia

[3] Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Department of Paediatrics, The University of Melbourne, Royal Children’s Hospital, Victoria, 3052, Australia

[4] Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative Carlton, Victoria, 3010, Australia

关键词: Genome-wide DNA methylation;    Guthrie cards;    Dried blood spots;    Infinium HumanMethylation450;    Epigenetics;    DNA methylation;   

Others  :  1123207
DOI  :  10.1186/1472-6750-13-23

 received in 2012-11-16, accepted in 2013-03-01,  发布年份 2013

【 摘 要 】

Background

Dried blood (Guthrie card) spots provide an efficient way to collect and store blood specimens. DNA from this source has been utilised for a number of molecular analyses including genome-wide association studies, but only few studies have tested the feasibility of using it for epigenetic applications, particularly at a genome-wide level.

Results

In this study, we demonstrate the successful use of DNA isolated from archived dried blood spots for the Infinium HumanMethylation450 Beadchip, along with DNA from matched frozen buffy coats. We obtained high quality and reproducible genome-wide DNA methylation profiles using both sample types. We also report high correlations (r > 0.9907) between DNA obtained from matched dried blood spots and frozen buffy coats, sufficient to distinguish between unrelated individuals.

Conclusions

We, thus, demonstrate that DNA from archived dried blood spots is suitable for genome-wide DNA methylation profiling.

【 授权许可】

   
2013 Joo et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Audrezet MP, Costes B, Ghanem N, Fanen P, Verlingue C, Morin JF, Mercier B, Goossens M, Ferec C: Screening for cystic fibrosis in dried blood spots of newborns. Mol Cell Probes 1993, 7(6):497-502.
• [2]Mei JV, Alexander JR, Adam BW, Hannon WH: Use of filter paper for the collection and analysis of human whole blood specimens. J Nutr 2001, 131(5):1631S-1636S.
• [3]Giles GG, English DR: The Melbourne Collaborative Cohort Study. IARC Sci Publ 2002, 156:69-70.
• [4]John EM, Hopper JL, Beck JC, Knight JA, Neuhausen SL, Senie RT, Ziogas A, Andrulis IL, Anton-Culver H, Boyd N: The breast cancer family registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Res 2004, 6(4):R375-389. BioMed Central Full Text
• [5]Hollegaard MV, Grove J, Grauholm J, Kreiner-Moller E, Bonnelykke K, Norgaard M, Benfield TL, Norgaard-Pedersen B, Mortensen PB, Mors O: Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source. BMC Genet 2011, 12:58.
• [6]Hollegaard MV, Grove J, Thorsen P, Norgaard-Pedersen B, Hougaard DM: High-throughput genotyping on archived dried blood spot samples. Genet Test Mol Biomarkers 2009, 13(2):173-179.
• [7]Feinberg AP, Tycko B: The history of cancer epigenetics. Nat Rev Cancer 2004, 4(2):143-153.
• [8]Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, Jager N, Gnirke A, Stunnenberg HG, Meissner A: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28(10):1106-1114.
• [9]Morris T, Lowe R: Report on the infinium 450 k methylation array analysis workshop: April 20,UCL, London, UK. Epigenetics 2012, 2012:7(8).
• [10]Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL: High density DNA methylation array with single CpG site resolution. Genomics 2011, 98(4):288-295.
• [11]Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M: DNA methylation: bisulphite modification and analysis. Nat Protoc 2006, 1(5):2353-2364.
• [12]Wong N, Morley R, Saffery R, Craig J: Archived guthrie blood spots as a novel source for quantitative DNA methylation analysis. Biotechniques 2008, 45(4):423-424. 426
• [13]Xu H, Zhao Y, Liu Z, Zhu W, Zhou Y, Zhao Z: Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples. Forensic Sci Int Genet 2012, 6(3):306-309.
• [14]Clark SJ, Millar DS, Molloy P: Bisulfite methylation analysis of tumor suppressor genes in prostate cancer from fresh and archival tissue samples. Methods Mol Med 2003, 81:219-240.
• [15]Beyan H, Down TA, Ramagopalan SV, Uvebrant K, Nilsson A, Holland ML, Gemma C, Giovannoni G, Boehm BO, Ebers GC: Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans. Genome Res 2012, 22(11):2138-2145.
• [16]Makowski GS, Davis EL, Hopfer SM: The effect of storage on Guthrie cards: implications for deoxyribonucleic acid amplification. Ann Clin Lab Sci 1996, 26(5):458-469.
• [17]Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F: Evaluation of the infinium methylation 450 K technology. Epigenomics 2011, 3(6):771-784.
• [18]Rakyan VK, Down TA, Balding DJ, Beck S: Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011, 12(8):529-541.
• [19]Cruickshank MN, Pitt J, Craig JM: Going back to the future with Guthrie-powered epigenome-wide association studies. Genome medicine 2012, 4(10):83. BioMed Central Full Text
• [20]Hansen KD, Aryee M: Minfi: analyze Illumina’s 450 k methylation arrays. R package version 1.2.0
• [21]Maksimovic J, Gordon L, Oshlack A: SWAN: subset quantile within-array normalization for illumina infinium human Methylation450 BeadChips. Genome Biol 2012, 13(6):R44. BioMed Central Full Text
• [22]Du P, Kibbe WA, Lin SM: lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008, 24(13):1547-1548.