Low-level processing of Illumina Infinium DNA Methylation BeadArrays

Nucleic Acids Research - Tập 41 Số 7 - Trang e90-e90 - 2013
Timothy J. Triche1, Daniel J. Weisenberger1, David Van Den Berg1, Peter W. Laird1, Kimberly D. Siegmund1
1Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA, 2USC Epigenome Center, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA, 3Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA and 4Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA

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Tài liệu tham khảo

Bird, 2002, DNA methylation patterns and epigenetic memory, Genes Dev., 16, 6, 10.1101/gad.947102

Sandoval, 2011, Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome, Epigenetics, 6, 692, 10.4161/epi.6.6.16196

Siegmund, 2011, Statistical approaches for the analysis of DNA methylation microarray data, Hum. Genet., 129, 585, 10.1007/s00439-011-0993-x

Xie, 2009, Statistical methods of background correction for Illumina BeadArray data, Bioinformatics, 25, 751, 10.1093/bioinformatics/btp040

Verdugo, 2009, Importance of randomization in microarray experimental designs with Illumina platforms, Nucleic Acids Res., 37, 5610, 10.1093/nar/gkp573

Teschendorff, 2009, An epigenetic signature in peripheral blood predicts active ovarian cancer, PLoS One, 4, 10.1371/journal.pone.0008274

Ritchie, 2007, A comparison of background correction methods for two-colour microarrays, Bioinformatics, 23, 2700, 10.1093/bioinformatics/btm412

Chen, 2011, An exponential-gamma convolution model for background correction of Illumina BeadArray data, Commun. Stat. Theory Methods, 40, 3055, 10.1080/03610921003797753

Ritchie, 2009, R/bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips, Bioinformatics, 25, 2621, 10.1093/bioinformatics/btp470

Chen, 2009, A distribution-free convolution model for background correction of oligonucleotide microarray data, BMC Genomics, 10, S19, 10.1186/1471-2164-10-S1-S19

Shi, 2010, Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips, Nucleic Acids Res., 38, 10.1093/nar/gkq871

Du, 2010, Comparison of beta-value and m-value methods for quantifying methylation levels by microarray analysis, BMC Bioinformatics, 11, 587, 10.1186/1471-2105-11-587

Raby, 2011, Asthma bridge: the asthma biorepository for integrative genomic exploration, Am. J. Respir. Crit. Care Med., 183

Figueroa, 2010, DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia, Cancer Cell, 17, 13, 10.1016/j.ccr.2009.11.020

Byun, 2009, Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns, Hum. Mol. Genet., 18, 4808, 10.1093/hmg/ddp445

Bell, 2011, DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines, Genome Biol., 12, R10, 10.1186/gb-2011-12-1-r10

Ding, 2012, Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing, Nature, 481, 506, 10.1038/nature10738

Akalin, 2012, Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia, PLoS Genet., 8, 10.1371/journal.pgen.1002781

Dedeurwaerder, 2011, Evaluation of the Infinium methylation 450K technology, Epigenomics, 3, 771, 10.2217/epi.11.105

Maksimovic, 2012, SWAN: subset-quantile within array normalization for Illumina Infinium HumanMethylation450 BeadChips, Genome Biol., 13, R44, 10.1186/gb-2012-13-6-r44

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Nucleic Acids Research

Tập 41 Số 7

e90-e90

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