The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Low-level processing of Illumina Infinium DNA Methylation BeadArrays
Open accessAbstract
We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.
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Cites
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
Du, P., Zhang, X., Huang, C.-C., Jafari, N., Kibbe, W. A., Hou, L., & Lin, S. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-587 · Cited by 2,136
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., et al. (2012) · Nature · doi:10.1038/nature10738 · Cited by 1,993
Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
Sandoval, J., Heyn, H., Moran, S., Serra-Musach, J., Pujana, M. A., Bibikova, M., & Esteller, M. (2011) · Epigenetics · doi:10.4161/epi.6.6.16196 · Cited by 990
A comparison of background correction methods for two-colour microarrays
Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., & Smyth, G. K. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm412 · Cited by 907
Akalin, A., Garrett-Bakelman, F. E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., Milne, T. A., Huang, Y., Biswas, D., Hess, J. L., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002781 · Cited by 296
Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression Beadchips
Shi, W., Oshlack, A., & Smyth, G. K. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq871 · Cited by 225
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Oncogenic Signaling Pathways in The Cancer Genome Atlas
Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.035 · Cited by 3,201
“…Level 1 IDAT files to calculate out-of-band (‘oob’) probe intensities as a surrogate for background intensity, superior to internal negative controls (Triche et al., 2013). cg13601799 is a Type I probe with both methylated (M) and unmethylated (U) versions in the red color channel, and therefore…”
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Lu, A. T., Quach, A., Wilson, J. G., Reiner, A. P., Aviv, A., Raj, K., Hou, L., Baccarelli, A. A., Li, Y., Stewart, J. D., et al. (2019) · Aging · doi:10.18632/aging.101684 · Cited by 2,540
Integrated genomic characterization of pancreatic ductal adenocarcinoma
Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., Robertson, A. G., Cherniack, A. D., Gupta, M., Getz, G., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.007 · Cited by 2,019
Self-citationFunctional normalization of 450k methylation array data improves replication in large cancer studies
Fortin, J.-P., Labbe, A., Lemire, M., Zanke, B. W., Hudson, T. J., Fertig, E. J., Greenwood, C. M., & Hansen, K. D. (2014) · Genome Biology · doi:10.1186/s13059-014-0503-2 · Cited by 892
DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis
Joubert, B. R., Felix, J. F., Yousefi, P., Bakulski, K. M., Just, A. C., Breton, C., Reese, S. E., Markunas, C. A., Richmond, R. C., Xu, C.-J., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.02.019 · Cited by 886
Metadata
- Authors
- Triche, T. J., Weisenberger, D. J., Van Den Berg, D., Laird, P. W., & Siegmund, K. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-03-09
- Volume
- 41
- Issue
- 7
- Pages
- e90-e90
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2081182312
- Cited by
- 905
- References
- 7
- FWCI
- 10.49
- Type
- journal article
- Language
- en
- Open access
- gold
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- Triche, T. J., Weisenberger, D. J., Van Den Berg, D., Laird, P. W., & Siegmund, K. D. (2013). Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt090
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