A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Benjamin Lehne; Alexander W Drong; Marie Loh; Weihua Zhang; William R Scott; Sian-tsung Tan; Uzma Afzal; James Scott; Marjo-riitta Jarvelin; Paul Elliott; Mark I Mccarthy; Jaspal S Kooner; John C Chambers

doi:10.1186/s13059-015-0600-x

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Benjamin Lehne, Alexander W Drong, Marie Loh, Weihua Zhang, William R Scott, Sian-tsung Tan, Uzma Afzal, James Scott, Marjo-riitta Jarvelin, Paul Elliott, Mark I Mccarthy, Jaspal S Kooner, John C Chambers

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Abstract

DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on 2,687 individuals, with 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment and establish a null hypothesis for EWAS using permutation testing. Our analysis pipeline outperforms existing approaches, enabling accurate identification of methylation quantitative trait loci for hypothesis driven follow-up experiments.

Original language	English
Article number	37
Journal	GENOME BIOLOGY
Volume	16
Early online date	15 Feb 2015
DOIs	https://doi.org/10.1186/s13059-015-0600-x
Publication status	Published - 15 Feb 2015

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A coherent approach for analysis_LEHNE_Accepted28Jan2015_GOLD VoRFinal published version, 1.47 MBLicence: CC BY

261 Citations
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Erratum to: A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies
Lehne, B., Drong, A. W., Loh, M., Zhang, W., Scott, W. R., Tan, S.-T., Afzal, U., Schulz, R., Scott, J., Jarvelin, M.-R., Elliott, P., McCarthy, M. I., Kooner, J. S. & Chambers, J. C., 21 Apr 2016, In: GENOME BIOLOGY. 17, 73.
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4 Citations (Scopus)

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Lehne, B., Drong, A. W., Loh, M., Zhang, W., Scott, W. R., Tan, S., Afzal, U., Scott, J., Jarvelin, M., Elliott, P., Mccarthy, M. I., Kooner, J. S., & Chambers, J. C. (2015). A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. GENOME BIOLOGY, 16, Article 37. https://doi.org/10.1186/s13059-015-0600-x

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abstract = "DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on 2,687 individuals, with 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment and establish a null hypothesis for EWAS using permutation testing. Our analysis pipeline outperforms existing approaches, enabling accurate identification of methylation quantitative trait loci for hypothesis driven follow-up experiments.",

author = "Benjamin Lehne and Drong, {Alexander W} and Marie Loh and Weihua Zhang and Scott, {William R} and Sian-tsung Tan and Uzma Afzal and James Scott and Marjo-riitta Jarvelin and Paul Elliott and Mccarthy, {Mark I} and Kooner, {Jaspal S} and Chambers, {John C}",

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Lehne, B, Drong, AW, Loh, M, Zhang, W, Scott, WR, Tan, S, Afzal, U, Scott, J, Jarvelin, M, Elliott, P, Mccarthy, MI, Kooner, JS & Chambers, JC 2015, 'A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies', GENOME BIOLOGY, vol. 16, 37. https://doi.org/10.1186/s13059-015-0600-x

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T1 - A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

AU - Lehne, Benjamin

AU - Drong, Alexander W

AU - Loh, Marie

AU - Zhang, Weihua

AU - Scott, William R

AU - Tan, Sian-tsung

AU - Afzal, Uzma

AU - Scott, James

AU - Jarvelin, Marjo-riitta

AU - Elliott, Paul

AU - Mccarthy, Mark I

AU - Kooner, Jaspal S

AU - Chambers, John C

PY - 2015/2/15

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N2 - DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on 2,687 individuals, with 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment and establish a null hypothesis for EWAS using permutation testing. Our analysis pipeline outperforms existing approaches, enabling accurate identification of methylation quantitative trait loci for hypothesis driven follow-up experiments.

AB - DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on 2,687 individuals, with 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment and establish a null hypothesis for EWAS using permutation testing. Our analysis pipeline outperforms existing approaches, enabling accurate identification of methylation quantitative trait loci for hypothesis driven follow-up experiments.

U2 - 10.1186/s13059-015-0600-x

DO - 10.1186/s13059-015-0600-x

M3 - Article

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VL - 16

JO - GENOME BIOLOGY

JF - GENOME BIOLOGY

M1 - 37

ER -

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

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Erratum to: A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

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