title: FastDMA: an infinium humanmethylation450 beadchip analyzer.
abstract: DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than 480,000 CpG sites and a few CHG sites with high data quality. To analyze the data of this promising platform, we developed FastDMA which can be used to identify significantly differentially methylated probes. Besides single probe analysis, FastDMA can also do region-based analysis for identifying the differentially methylated region (DMRs). A uniformed statistical model, analysis of covariance (ANCOVA), is used to achieve all the analyses in FastDMA. We apply FastDMA on three large-scale DNA methylation datasets from The Cancer Genome Atlas (TCGA) and find many differentially methylated genomic sites in different types of cancer. On the testing datasets, FastDMA shows much higher computational efficiency than current tools. FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/.
authors.affiliation: Bioinformatics Division/Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology (TNLIST), Department of Automation, Tsinghua University, Beijing, China.
authors.forename: Dingming
authors.initials: D
authors.lastname: Wu
authors.forename: Jin
authors.initials: J
authors.lastname: Gu
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D001271:Atlases as Topic; D001943:Breast Neoplasms / Q000235:genetics*; D002277:Carcinoma / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D015894:Genome, Human; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics*; D012984:Software
references.citation: Br J Cancer. 2008 Mar 25;98(6):1147-56
references.pmid: 18283316
references.citation: Cancer Res. 2010 Oct 15;70(20):8015-24
references.pmid: 20736368
references.citation: PLoS Genet. 2012 Feb;8(2):e1002517
references.pmid: 22346766
references.citation: Am J Hum Genet. 2012 Oct 5;91(4):760-2
references.pmid: 23040498
references.citation: Cancer Res. 2011 Oct 1;71(19):6195-207
references.pmid: 21825015
references.citation: Int J Epidemiol. 2012 Feb;41(1):200-9
references.pmid: 22422453
references.citation: Science. 2009 May 15;324(5929):929-30
references.pmid: 19372393
references.citation: Epigenomics. 2009 Oct;1(1):177-200
references.pmid: 22122642
references.citation: Science. 1975 Jan 24;187(4173):226-32
references.pmid: 1111098
references.citation: Cell. 2008 May 2;133(3):523-36
references.pmid: 18423832
references.citation: Nucleic Acids Res. 2005 Oct 13;33(18):5868-77
references.pmid: 16224102
references.citation: Epigenomics. 2011 Dec;3(6):771-84
references.pmid: 22126295
references.citation: Nucleic Acids Res. 2010 Jan;38(2):391-9
references.pmid: 19906696
references.citation: Epigenetics. 2013 Jan;8(1):34-43
references.pmid: 23208076
references.citation: Nat Biotechnol. 2011 Jan;29(1):24-6
references.pmid: 21221095
references.citation: Bioinformatics. 2012 Mar 1;28(5):729-30
references.pmid: 22253290
references.citation: Science. 2011 Nov 11;334(6057):799-802
references.pmid: 22076376
references.citation: Am J Hum Genet. 2012 Feb 10;90(2):260-72
references.pmid: 22305529
references.citation: Nat Rev Genet. 2012 May 29;13(7):484-92
references.pmid: 22641018
references.citation: Bioinformatics. 2003 Jan 22;19(2):185-93
references.pmid: 12538238
references.citation: Epigenetics. 2013 Feb;8(2):203-9
references.pmid: 23314698
references.citation: Genome Biol. 2012 Jun 15;13(6):R44
references.pmid: 22703947