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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.pdf | Published version | 1.51 MB | Adobe PDF | View/Open |
Title: | A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies |
Authors: | Lehne, B Drong, AW Loh, M Zhang, W Scott, WR Tan, S-T Afzal, U Scott, J Jarvelin, M-R Elliott, P McCarthy, MI Kooner, JS Chambers, JC |
Item Type: | Journal Article |
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. |
Issue Date: | 15-Feb-2015 |
Date of Acceptance: | 28-Jan-2015 |
URI: | http://hdl.handle.net/10044/1/28695 |
DOI: | 10.1186/s13059-015-0600-x |
ISSN: | 1474-760X |
Publisher: | BioMed Central |
Journal / Book Title: | Genome Biology |
Volume: | 16 |
Issue: | 1 |
Copyright Statement: | © 2015 Lehne et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
Sponsor/Funder: | Medical Research Council (MRC) Medical Research Council (MRC) Medical Research Council (MRC) National Institute for Health Research Imperial College Healthcare NHS Trust- BRC Funding National Institute for Health Research Action on Hearing Loss Wellcome Trust British Heart Foundation Medical Research Council (MRC) Medical Research Council (MRC) |
Funder's Grant Number: | G0700931 G0601966 MR/L01341X/1 NF-SI-0611-10136 RDC01 79560 RTJ6219303-1 G51_Chambers 084723/Z/08/Z SP/04/02 G0801056B MR/K002414/1 |
Keywords: | Science & Technology Life Sciences & Biomedicine Biotechnology & Applied Microbiology Genetics & Heredity METHYLATION ARRAY DATA DNA METHYLATION QUANTILE NORMALIZATION PANCREATIC-ISLETS PERIPHERAL-BLOOD SUBSET-QUANTILE GENE-EXPRESSION MICROARRAY PIPELINE CANCER Science & Technology Life Sciences & Biomedicine Biotechnology & Applied Microbiology Genetics & Heredity DNA METHYLATION QUANTILE NORMALIZATION SUBSET-QUANTILE GENE-EXPRESSION ARRAY PIPELINE CpG Islands DNA Methylation Epigenesis, Genetic Epigenomics Genome, Human Genome-Wide Association Study Humans Oligonucleotide Array Sequence Analysis Quantitative Trait Loci Software Humans Oligonucleotide Array Sequence Analysis DNA Methylation Epigenesis, Genetic CpG Islands Quantitative Trait Loci Genome, Human Software Genome-Wide Association Study Epigenomics 05 Environmental Sciences 06 Biological Sciences 08 Information and Computing Sciences Bioinformatics |
Publication Status: | Published |
Article Number: | ARTN 37 |
Appears in Collections: | Institute of Clinical Sciences Faculty of Medicine School of Public Health |