Application of microdroplet PCR for large-scale targeted bisulfite sequencing

Genome Research

Volumn 21, Issue 10, 2011, Pages 1738-1745

  Komori, H Kiyomi ^a   LaMere, Sarah A ^a   Torkamani, Ali ^a   Hart, G Traver ^a   Kotsopoulos, Steve ^b   Warner, Jason ^b   Samuels, Michael L ^b   Olson, Jeff ^b   Head, Steven R ^a   Ordoukhanian, Phillip ^a   Lee, Pauline L ^a   Link, Darren R ^b   Salomon, Daniel R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b RainDance Technologies   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE;

AMPLICON; ARTICLE; CD4+ T LYMPHOCYTE; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; DNA SEQUENCE; GENE LIBRARY; HUMAN; HUMAN CELL; MICRODROPLET POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; START CODON; TRANSCRIPTION REGULATION;

BASE SEQUENCE; CPG ISLANDS; DNA; DNA METHYLATION; DNA PRIMERS; EPIGENESIS, GENETIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; JURKAT CELLS; MICROCHEMISTRY; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 80053520872     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.116863.110     Document Type: Article

References (22)

1. Cheung HH, Lee TL, Rennert OM, Chan WY. 2009. DNA methylation of cancer genome. Birth Defects Res C Embryo Today 87: 335-350.
2. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, et al. 2009. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27: 353-360.
3. Ehrlich M. 2009. DNA hypomethylation in cancer cells. Epigenomics 1: 239-259.
4. Fouse SD, Nagarajan RP, Costello JF. 2010. Genome-scale DNA methylation analysis. Epigenomics 2: 105-117.
5. Geiman TM, Muegge K. 2010. DNA methylation in early development. Mol Reprod Dev 77: 105-113.
6. Grolleau-Julius A, Ray D, Yung RL. 2010. The role of epigenetics in aging and autoimmunity. Clin Rev Allergy Immunol 39: 42-50.
7. Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. 2010. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7: 133-136.
8. Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, et al. 2009. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res 19: 1593-1605.
9. Hori M, Fukano H, Suzuki Y. 2007. Uniform amplification of multiple DNAs by emulsion PCR. Biochem Biophys Res Commun 352: 323-328. (Pubitemid 44838491)
10. Huang HC, Zheng S, VanBuren V, Zhao Z. 2010. Discovering disease-specific biomarker genes for cancer diagnosis and prognosis. Technol Cancer Res Treat 9: 219-230.
11. Jones B, Chen J. 2006. Inhibition of IFN-gamma transcription by sitespecific methylation during T helper cell development. EMBO J 25: 2443-2452. (Pubitemid 44012227)
12. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, et al. 2010. Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
13. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
14. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
15. Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
16. Schubeler D, Lorincz MC, Cimbora DM, Telling A, Feng YQ, Bouhassira EE, GroudineM. 2000. Genomic targeting of methylated DNA: Influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol Cell Biol 20: 9103-9112. (Pubitemid 32246099)
17. Schuler GD. 1997. Sequence mapping by electronic PCR. Genome Res 7: 541-550. (Pubitemid 27232016)
18. Shapiro R, Servis R, Welcher M. 1970. Reactions of uracil and cytosine derivatives with sodium bisulfite. J Am Chem Soc 92: 422-424.
19. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, et al. 2009. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27: 1025-1031.
20. Varley KE, Mitra RD. 2010. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res 20: 1279-1287.
21. Villeneuve LM, Natarajan R. 2010. The role of epigenetics in the pathology of diabetic complications. Am J Physiol Renal Physiol 299: F14-F25.
22. Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919.