Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Warton, Kristina ^a   Lin, Vita ^a   Navin, Tina ^a   Armstrong, Nicola J ^a,b   Kaplan, Warren ^a   Ying, Kevin ^a   Gloss, Brian ^a   Mangs, Helena ^c   Nair, Shalima S ^a   Hacker, Neville F ^c   Sutherland, Robert L ^a   Clark, Susan J ^a,c   Samimi, Goli ^a,c  

^a GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Biobanking; Blood; Free circulating DNA; Methylation; Next Generation Sequencing

Indexed keywords

DNA; DNA FRAGMENT; FREE CIRCULATING DNA; GENOMIC DNA; UNCLASSIFIED DRUG;

ARTICLE; BLOOD LEVEL; BLOOD SAMPLING; BLOOD STORAGE; CONTROLLED STUDY; CYTOLYSIS; DNA DETERMINATION; DNA EXTRACTION; DNA ISOLATION; DNA LIBRARY; DNA METHYLATION; DNA PURIFICATION; DNA SEQUENCE; FEMALE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MALE; NON INVASIVE MEASUREMENT; PLASMA; POLYMERASE CHAIN REACTION; PROCESS OPTIMIZATION; SERUM; VALIDATION PROCESS; AGED; BLOOD; CHEMISTRY; DNA BASE COMPOSITION; DNA CONTAMINATION; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; MIDDLE AGED; NORMAL HUMAN; REPRODUCIBILITY; RISK FACTOR;

AGED; BASE COMPOSITION; DNA; DNA CONTAMINATION; DNA METHYLATION; FEMALE; GENE LIBRARY; HEALTHY VOLUNTEERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MIDDLE AGED; REPRODUCIBILITY OF RESULTS; RISK FACTORS; SEQUENCE ANALYSIS, DNA;

EID: 84902057701     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-476     Document Type: Article

References (29)

1. Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, Hesch RD, Knippers R. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 2001, 61(4):1659-1665.
2. Suzuki N, Kamataki A, Yamaki J, Homma Y. Characterization of circulating DNA in healthy human plasma. Clin Chim Acta 2008, 387(1-2):55-58.
3. Lui YY, Chik KW, Chiu RW, Ho CY, Lam CW, Lo YM. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem 2002, 48(3):421-427.
4. Lo YM, Tein MS, Lau TK, Haines CJ, Leung TN, Poon PM, Wainscoat JS, Johnson PJ, Chang AM, Hjelm NM. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet 1998, 62(4):768-775.
5. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. Clin Chem 2010, 56(8):1279-1286.
6. Nygren AO, Dean J, Jensen TJ, Kruse S, Kwong W, van den Boom D, Ehrich M. Quantification of fetal DNA by use of methylation-based DNA discrimination. Clin Chem 2010, 56(10):1627-1635.
7. Tsui DW, Chiu RW, Lo YD. Epigenetic approaches for the detection of fetal DNA in maternal plasma. Chimerism 2010, 1(1):30-35.
8. Rykova EY, Morozkin ES, Ponomaryova AA, Loseva EM, Zaporozhchenko IA, Cherdyntseva NV, Vlassov VV, Laktionov PP. Cell-free and cell-bound circulating nucleic acid complexes: mechanisms of generation, concentration and content. Expert Opin Biol Ther 2012, 12(Suppl 1):S141-S153.
9. Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011, 11(6):426-437.
10. Sorenson GD, Pribish DM, Valone FH, Memoli VA, Bzik DJ, Yao SL. Soluble normal and mutated DNA sequences from single-copy genes in human blood. Cancer Epidemiol Biomarkers Prev 1994, 3(1):67-71.
11. Frattini M, Gallino G, Signoroni S, Balestra D, Battaglia L, Sozzi G, Leo E, Pilotti S, Pierotti MA. Quantitative analysis of plasma DNA in colorectal cancer patients: a novel prognostic tool. Ann N Y Acad Sci 2006, 1075:185-190.
12. Kimura T, Holland WS, Kawaguchi T, Williamson SK, Chansky K, Crowley JJ, Doroshow JH, Lenz HJ, Gandara DR, Gumerlock PH. Mutant DNA in plasma of lung cancer patients: potential for monitoring response to therapy. Ann N Y Acad Sci 2004, 1022:55-60.
13. Shinozaki M, O'Day SJ, Kitago M, Amersi F, Kuo C, Kim J, Wang HJ, Hoon DS. Utility of circulating B-RAF DNA mutation in serum for monitoring melanoma patients receiving biochemotherapy. Clin Cancer Res 2007, 13(7):2068-2074.
14. Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA, Velculescu VE. Sci Transl Med 2012, 4(162). 162ra154.
15. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010, 11(10):685-696.
16. 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.
17. Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, Bonneville R, Xu M, Wang J, Huang TH, Meredith G, Jin VX. High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PLoS One 2011, 6(7):e22226.
18. Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 2011, 6(1):34-44.
19. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25.
20. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013, 14(2):178-192.
21. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137.
22. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010, 38(4):576-589.
23. Jung M, Klotzek S, Lewandowski M, Fleischhacker M, Jung K. Changes in concentration of DNA in serum and plasma during storage of blood samples. Clin Chem 2003, 49(6 Pt 1):1028-1029.
24. Thijssen MA, Swinkels DW, Ruers TJ, de Kok JB. Difference between free circulating plasma and serum DNA in patients with colorectal liver metastases. Anticancer Res 2002, 22(1A):421-425.
25. Lee TH, Montalvo L, Chrebtow V, Busch MP. Quantitation of genomic DNA in plasma and serum samples: higher concentrations of genomic DNA found in serum than in plasma. Transfusion 2001, 41(2):276-282.
26. Napirei M, Ludwig S, Mezrhab J, Klockl T, Mannherz HG. Murine serum nucleases-contrasting effects of plasmin and heparin on the activities of DNase1 and DNase1-like 3 (DNase1l3). FEBS J 2009, 276(4):1059-1073.
27. De Meyer T, Mampaey E, Vlemmix M, Denil S, Trooskens G, Renard JP, De Keulenaer S, Dehan P, Menschaert G, Van Criekinge W. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One 2013, 8(3):e59068.
28. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2012, 22(9):1813-1831.
29. Ma W, Wong WH. The analysis of ChIP-Seq data. Methods Enzymol 2011, 497:51-73.