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

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A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. / Lehne, Benjamin; Drong, Alexander W; Loh, Marie et al.

In: GENOME BIOLOGY, Vol. 16, 37, 15.02.2015.

Research output: Contribution to journalArticlepeer-review

Harvard

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

APA

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, [37]. https://doi.org/10.1186/s13059-015-0600-x

Vancouver

Lehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan S et al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. GENOME BIOLOGY. 2015 Feb 15;16. 37. https://doi.org/10.1186/s13059-015-0600-x

Author

Lehne, Benjamin ; Drong, Alexander W ; Loh, Marie et al. / A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. In: GENOME BIOLOGY. 2015 ; Vol. 16.

Bibtex Download

@article{aa86a58031244df5919a57940a24d07f,
title = "A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies",
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}",
year = "2015",
month = feb,
day = "15",
doi = "10.1186/s13059-015-0600-x",
language = "English",
volume = "16",
journal = "GENOME BIOLOGY",
issn = "1465-6906",
publisher = "BioMed Central",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

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

Y1 - 2015/2/15

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

VL - 16

JO - GENOME BIOLOGY

JF - GENOME BIOLOGY

SN - 1465-6906

M1 - 37

ER -

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