Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the Hu...
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| Vydáno v: | Bioinformatics (Oxford, England) Ročník 33; číslo 4; s. 558 - 560 |
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| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
England
Oxford University Press
15.02.2017
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| Témata: | |
| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
| On-line přístup: | Získat plný text |
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| Abstract | The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.
The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project.
khansen@jhsph.edu.
Supplementary data are available at Bioinformatics online. |
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| AbstractList | The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.SummaryThe minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project.Availability and ImplementationThe minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project.khansen@jhsph.edu.Contactkhansen@jhsph.edu.Supplementary data are available at Bioinformatics online.Supplementary informationSupplementary data are available at Bioinformatics online. The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data. The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project. khansen@jhsph.edu. Supplementary data are available at Bioinformatics online. |
| Author | Fortin, Jean-Philippe Hansen, Kasper D Triche, Timothy J. |
| AuthorAffiliation | 2 Jane Anne Nohl Division of Hematology, Keck School of Medicine of USC, Los Angeles, CA, USA 3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA 1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA |
| AuthorAffiliation_xml | – name: 1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA – name: 2 Jane Anne Nohl Division of Hematology, Keck School of Medicine of USC, Los Angeles, CA, USA – name: 3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA |
| Author_xml | – sequence: 1 givenname: Jean-Philippe surname: Fortin fullname: Fortin, Jean-Philippe – sequence: 2 givenname: Timothy J. surname: Triche fullname: Triche, Timothy J. – sequence: 3 givenname: Kasper D surname: Hansen fullname: Hansen, Kasper D |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28035024$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.12688/f1000research.4680.2 10.1186/gb-2004-5-10-r80 10.1016/j.ygeno.2011.07.007 10.1186/s13059-015-0741-y 10.4161/epi.23924 10.1371/journal.pone.0041361 10.1186/s13059-014-0503-2 10.1186/1471-2105-13-86 10.2217/epi.15.114 10.1080/15592294.2016.1161875 10.1038/nmeth.3252 10.1093/nar/gkt090 10.1186/gb-2014-15-2-r31 10.1186/gb-2012-13-6-r44 10.1093/bioinformatics/btu049 |
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| References | Bakulski (2023020204420044200_btw691-B2) 2016; 11 Fortin (2023020204420044200_btw691-B5) 2014; 15 Jaffe (2023020204420044200_btw691-B11) 2014; 15 Guintivano (2023020204420044200_btw691-B8) 2013; 8 Triche (2023020204420044200_btw691-B15) 2013; 41 Aryee (2023020204420044200_btw691-B1) 2014; 30 Moran (2023020204420044200_btw691-B13) 2016; 8 Huber (2023020204420044200_btw691-B10) 2015; 12 Houseman (2023020204420044200_btw691-B9) 2012; 13 Fortin (2023020204420044200_btw691-B4) 2015; 16 Reinius (2023020204420044200_btw691-B14) 2012; 7 Fortin (2023020204420044200_btw691-B6) 2014; 3 Bibikova (2023020204420044200_btw691-B3) 2011; 98 Gentleman (2023020204420044200_btw691-B7) 2004; 5 Maksimovic (2023020204420044200_btw691-B12) 2012; 13 |
| References_xml | – volume: 3 start-page: 175. year: 2014 ident: 2023020204420044200_btw691-B6 article-title: shinymethyl: interactive quality control of illumina 450k DNA methylation arrays in R publication-title: F1000Research doi: 10.12688/f1000research.4680.2 – volume: 5 start-page: R80. year: 2004 ident: 2023020204420044200_btw691-B7 article-title: Bioconductor: open software development for computational biology and bioinformatics publication-title: Genome Biol doi: 10.1186/gb-2004-5-10-r80 – volume: 98 start-page: 288 year: 2011 ident: 2023020204420044200_btw691-B3 article-title: High density DNA methylation array with single CpG site resolution publication-title: Genomics doi: 10.1016/j.ygeno.2011.07.007 – volume: 16 start-page: 180. year: 2015 ident: 2023020204420044200_btw691-B4 article-title: Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data publication-title: Genome Biol doi: 10.1186/s13059-015-0741-y – volume: 8 start-page: 290 year: 2013 ident: 2023020204420044200_btw691-B8 article-title: A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression publication-title: Epigenetics doi: 10.4161/epi.23924 – volume: 7 start-page: e41361. year: 2012 ident: 2023020204420044200_btw691-B14 article-title: Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility publication-title: Plos One doi: 10.1371/journal.pone.0041361 – volume: 15 start-page: 503. year: 2014 ident: 2023020204420044200_btw691-B5 article-title: Functional normalization of 450k methylation array data improves replication in large cancer studies publication-title: Genome Biol doi: 10.1186/s13059-014-0503-2 – volume: 13 start-page: 86. year: 2012 ident: 2023020204420044200_btw691-B9 article-title: DNA methylation arrays as surrogate measures of cell mixture distribution publication-title: BMC Bioinform doi: 10.1186/1471-2105-13-86 – volume: 8 start-page: 389 year: 2016 ident: 2023020204420044200_btw691-B13 article-title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences publication-title: Epigenomics doi: 10.2217/epi.15.114 – volume: 11 start-page: 354 year: 2016 ident: 2023020204420044200_btw691-B2 article-title: DNA methylation of cord blood cell types: applications for mixed cell birth studies publication-title: Epigenetics doi: 10.1080/15592294.2016.1161875 – volume: 12 start-page: 115 year: 2015 ident: 2023020204420044200_btw691-B10 article-title: Orchestrating high-throughput genomic analysis with bioconductor publication-title: Nat. Methods doi: 10.1038/nmeth.3252 – volume: 41 start-page: e90. year: 2013 ident: 2023020204420044200_btw691-B15 article-title: Low-level processing of Illumina Infinium DNA Methylation BeadArrays publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt090 – volume: 15 start-page: R31. year: 2014 ident: 2023020204420044200_btw691-B11 article-title: Accounting for cellular heterogeneity is critical in epigenome-wide association studies publication-title: Genome Biol doi: 10.1186/gb-2014-15-2-r31 – volume: 13 start-page: R44. year: 2012 ident: 2023020204420044200_btw691-B12 article-title: SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips publication-title: Genome Biol doi: 10.1186/gb-2012-13-6-r44 – volume: 30 start-page: 1363 year: 2014 ident: 2023020204420044200_btw691-B1 article-title: Minfi: a flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu049 |
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| Title | Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi |
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