Positional effects revealed in Illumina methylation array and the impact on analysis

Epigenomics
Chuan JiaoChunyu Liu

Abstract

We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.

References

Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Jul 21, 2005·Nutrition Reviews·Dale C McCabe, Marie A Caudill
Sep 2, 2005·Nature Reviews. Genetics·Keith D Robertson
Feb 2, 2006·Genome Research·Marina BibikovaJian-Bing Fan
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Oct 19, 2006·Biochimica Et Biophysica Acta·Ann S WilsonPeter Molloy
Oct 23, 2008·Nucleic Acids Research·Tanya BarrettRon Edgar
Mar 28, 2009·Cellular and Molecular Life Sciences : CMLS·Igor P Pogribny, Frederick A Beland
Jul 21, 2009·Nucleic Acids Research·Ricardo A VerdugoGary A Churchill
Mar 11, 2010·American Journal of Human Genetics·Dandan ZhangChunyu Liu
Sep 15, 2010·Nature Reviews. Genetics·Jeffrey T LeekRafael A Irizarry
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
Apr 1, 2010·Epigenomics·Stefan T BoernoMichal-Ruth Schweiger
Oct 1, 2009·Epigenomics·Marina BibikovaKevin L Gunderson
Dec 1, 2011·Epigenomics·Sarah DedeurwaerderFrançois Fuks
Dec 17, 2011·BMC Medical Genomics·Zhifu SunJean-Pierre A Kocher
Apr 5, 2012·Current Alzheimer Research·David A BennettRobert S Wilson
May 30, 2012·Nature Reviews. Genetics·Peter A Jones
Jun 13, 2012·Proceedings of the National Academy of Sciences of the United States of America·Holger HeynManel Esteller
Aug 2, 2012·Briefings in Bioinformatics·Cosmin LazarAnn Nowé
Jan 15, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Yi-an ChenRosanna Weksberg
Feb 21, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Francesco MarabitaDavid Gomez-Cabrero
Mar 12, 2013·Nucleic Acids Research·Timothy J TricheKimberly D Siegmund
May 8, 2013·Journal of Agricultural and Food Chemistry·Jay M HarrisonRussell D Wolfinger
Aug 31, 2013·Briefings in Bioinformatics·Sarah DedeurwaerderFrançois Fuks
Apr 16, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Sebastian MoranManel Esteller
Aug 19, 2014·Nature Neuroscience·Philip L De JagerDavid A Bennett
Oct 5, 2014·Gene·Tachapol MuangsubApiwat Mutirangura
Dec 30, 2014·International Journal of Epidemiology·Golareh AghaEric B Loucks
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Feb 5, 2015·Genome Research·Helen SpiersJonathan Mill
Apr 19, 2015·BMC Bioinformatics·E Andres HousemanCarmen J Marsit
Jun 24, 2015·Human Molecular Genetics·Hemant KulkarniMelanie A Carless
Jan 21, 2016·Epigenetics : Official Journal of the DNA Methylation Society·Ai Ling TehNeerja Karnani
Aug 26, 2016·PloS One·Ruslan AkulenkoVolkhard Helms

Related Concepts

Genome, Human
Truncation Biases
CpG Clusters
DNA Methylation
Cdna Microarrays
Methylation
CpG Islands
Genetic Loci
Genetic Analysis
Molecular Array

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