An optimized algorithm for detecting and annotating regional differential methylation

BMC Bioinformatics

Volumn 14, Issue SUPPL.5, 2013, Pages

  Li, Sheng ^a   Garrett Bakelman, Francine E ^a   Akalin, Altuna ^a   Zumbo, Paul ^a   Levine, Ross ^b   To, Bik L ^c   Lewis, Ian D ^c   Brown, Anna L ^d   D'Andrea, Richard J ^d   Melnick, Ari ^a   Mason, Christopher E ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^c ROYAL ADELAIDE HOSPITAL   (Australia)

^d QUEEN ELIZABETH HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE MYELOID LEUKEMIA; BIMODAL DISTRIBUTION; EPIGENETIC MODIFICATION; METHYLATION ANALYSIS; OPTIMIZATION ALGORITHMS; OPTIMIZED ALGORITHMS; REGIONAL ANALYSIS; WEIGHTED COST FUNCTIONS;

ALGORITHMS; ALKYLATION; DATA HANDLING; GENES; OPTIMIZATION; REGIONAL PLANNING;

METHYLATION;

ALGORITHM; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENETICS; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; LEUKEMIA; MOLECULAR GENETICS; PROCEDURES; ARTICLE; METHODOLOGY;

ALGORITHMS; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA;

EID: 84876130617     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S5-S10     Document Type: Article

References (26)

1. Chi P, Allis CD, Wang GG. Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 2010, 10(7):457-469. 10.1038/nrc2876, 3262678, 20574448.
2. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature 2007, 447(7143):433-440. 10.1038/nature05919, 17522677.
3. Sorensen AL, Timoskainen S, West FD, Vekterud K, Boquest AC, Ahrlund-Richter L, Stice SL, Collas P. Lineage-specific promoter DNA methylation patterns segregate adult progenitor cell types. Stem Cells Dev 2010, 19(8):1257-1266. 10.1089/scd.2009.0309, 19886822.
4. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005, 37(8):853-862. 10.1038/ng1598, 16007088.
5. Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood 2010, 116(20):81-89. 10.1182/blood-2010-05-285320, 2993635, 20610814.
6. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Löwenberg B, Delwel R, Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 2010, 17(1):13-27. 10.1016/j.ccr.2009.11.020, 3008568, 20060365.
7. Bullinger L, Ehrich M, Döhner K, Schlenk RF, Döhner H, Nelson MR, van den Boom D. Quantitative DNA methylation predicts survival in adult acute myeloid leukemia. Blood 2010, 115(3):636-42. 10.1182/blood-2009-03-211003, 19903898.
8. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452(7184):215-219. 10.1038/nature06745, 2377394, 18278030.
9. 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, 2860480, 20062050.
10. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011, 6(4):468-481. 10.1038/nprot.2010.190, 21412275.
11. 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, 1258174, 16224102.
12. Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 2012, 8(6):e1002781. 10.1371/journal.pgen.1002781, 3380828, 22737091.
13. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol 2012, 13(10):R92. 10.1186/gb-2012-13-10-r92, 3491420, 23034176.
14. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010, 28(10):1097-1105. 10.1038/nbt.1682, 2955169, 20852635.
15. Jacinto FV, Ballestar E, Esteller M. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. BioTechniques 2008, 44(1). 35, 37, 39 passim.
16. Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010, 38(2):391-399. 10.1093/nar/gkp992, 2811030, 19906696.
17. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 2012, 13(10):R87. 10.1186/gb-2012-13-10-r87, 3491415, 23034086.
18. Team RC. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2012, ISBN 3-900051-07-0, URL., http://www.R-project.org/
19. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:r80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
20. Benaglia T, Chauveau D, Hunter DR, Young DS. mixtools: An R Package for Analyzing Finite Mixture Models. Journal of Statistical Software 2009, 32(6).
21. Wickham H. ggplot2: elegant graphics for data analysis 2009, New York: Springer.
22. Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics 2012, 28(22):2986-2988. 10.1093/bioinformatics/bts545, 22954632.
23. Kechris KJ, Biehs B, Kornberg TB. Generalizing moving averages for tiling arrays using combined p-value statistics. Stat Appl Genet Mol Biol 2010, 9. Article29, 2942027, 20812907.
24. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behavioural brain research 2001, 125(1-2):279-284. 10.1016/S0166-4328(01)00297-2, 11682119.
25. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society, Series B (Methodological) 1995, 57(1):289-300.
26. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009, 27(4):361-368. 10.1038/nbt.1533, 3566772, 19329998.