Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

Nakao M: Epigenetics: interaction of DNA methylation and chromatin. Gene. 2001, 278 (1–2): 25-31.

Reik W, Dean W, Walter J: Epigenetic reprogramming in mammalian development. Science. 2001, 293 (5532): 1089-1093. 10.1126/science.1063443.

Chen ZX, Riggs AD: DNA methylation and demethylation in mammals. J Biol Chem. 2011, 286 (21): 18347-18353. 10.1074/jbc.R110.205286.

Robertson KD: DNA methylation and human disease. Nat Rev Genet. 2005, 6 (8): 597-610.

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. 10.1038/nbt.1681.

Laird PW: Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010, 11 (3): 191-203. 10.1038/nrg2732.

Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL: A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA. 1992, 89 (5): 1827-1831. 10.1073/pnas.89.5.1827.

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D: DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011, 480 (7378): 490-495.

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J: Dynamic changes in the human methylome during differentiation. Genome Res. 2010, 20 (3): 320-331. 10.1101/gr.101907.109.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009, 462 (7271): 315-322. 10.1038/nature08514.

Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R: Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005, 33 (18): 5868-5877. 10.1093/nar/gki901.

Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010, 7 (2): 133-136. 10.1038/nmeth.1414.

Pan H, Chen L, Dogra S, Teh AL, Tan JH, Lim YI, Lim YC, Jin S, Lee YK, Ng PY: Measuring the methylome in clinical samples: improved processing of the Infinium Human Methylation450 BeadChip Array. Epigenetics. 2012, 7 (10): 1173-1187. 10.4161/epi.22102.

Rakyan VK, Down TA, Balding DJ, Beck S: Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011, 12 (8): 529-541. 10.1038/nrg3000.

Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8 (3): 186-194.

illumina: Quality Scores for Next-Generation Sequencing. Technical Note: Sequencing. 2011

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): R25-10.1186/gb-2009-10-3-r25.