Low-level processing of Illumina Infinium DNA Methylation BeadArrays
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...
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| Published in: | Nucleic acids research Vol. 41; no. 7; p. e90 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Oxford University Press
01.04.2013
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| Subjects: | |
| ISSN: | 0305-1048, 1362-4962, 1362-4962 |
| Online Access: | Get full text |
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| Abstract | 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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| AbstractList | 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.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. 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. |
| Author | Siegmund, Kimberly D. Triche, Timothy J. Van Den Berg, David Weisenberger, Daniel J. Laird, Peter W. |
| AuthorAffiliation | 1 Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA, 2 USC Epigenome Center, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA, 3 Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA and 4 Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA |
| AuthorAffiliation_xml | – name: 1 Department of Preventive Medicine, USC Keck School of Medicine of USC, Los Angeles, CA 90089, USA, 2 USC Epigenome Center, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA, 3 Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA and 4 Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA |
| Author_xml | – sequence: 1 givenname: Timothy J. surname: Triche fullname: Triche, Timothy J. organization: Department 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, Department 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 – sequence: 2 givenname: Daniel J. surname: Weisenberger fullname: Weisenberger, Daniel J. organization: Department 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, Department 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 – sequence: 3 givenname: David surname: Van Den Berg fullname: Van Den Berg, David organization: Department 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, Department 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 – sequence: 4 givenname: Peter W. surname: Laird fullname: Laird, Peter W. organization: Department 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, Department 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, Department 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 – sequence: 5 givenname: Kimberly D. surname: Siegmund fullname: Siegmund, Kimberly D. organization: Department 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 |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23476028$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | DNA Methylation Fluorescent Dyes HapMap Project Humans Methods Online Oligonucleotide Array Sequence Analysis - methods |
| Title | Low-level processing of Illumina Infinium DNA Methylation BeadArrays |
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