Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

Bioinformatics
Jean-Philippe FortinKasper D Hansen

Abstract

The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob ( ssNoob ) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data. The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project. khansen@jhsph.edu. Supplementary data are available at Bioinformatics online.

References

Oct 6, 2004·Genome Biology·Robert GentlemanJianhua Zhang
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
May 10, 2012·BMC Bioinformatics·Eugene Andres HousemanKarl T Kelsey
Feb 22, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Jerry GuintivanoZachary A Kaminsky
Mar 12, 2013·Nucleic Acids Research·Timothy J TricheKimberly D Siegmund
Feb 6, 2014·Genome Biology·Andrew E Jaffe, Rafael A Irizarry
Oct 7, 2014·F1000Research·Jean-Philippe FortinKasper Hansen
Jan 31, 2015·Nature Methods·Wolfgang HuberMartin Morgan
Mar 29, 2016·Epigenetics : Official Journal of the DNA Methylation Society·Kelly M BakulskiM Daniele Fallin

Citations

Apr 9, 2020·Biomolecules·Elena Sánchez-LuisJavier De Las Rivas
Apr 21, 2020·Journal of the American Heart Association·Kenneth WestermanJosé M Ordovás
Apr 20, 2019·PloS One·Radhika DhingraCavin K Ward-Caviness
Jun 3, 2020·Environmental Health Perspectives·Arce Domingo-RellosoMaria Tellez-Plaza
Aug 20, 2019·Aging·Ake T LuSteve Horvath
Jun 26, 2020·Frontiers in Public Health·Katarzyna Malgorzata KwiatkowskaChiara Pirazzini
May 11, 2018·Scientific Reports·Emmanuel KarouzakisCaroline Ospelt
Aug 31, 2019·International Journal of Environmental Research and Public Health·Wei ZhaoJennifer A Smith
Aug 6, 2020·Journal for Immunotherapy of Cancer·Kirsty TaylorDaniel D De Carvalho
Sep 23, 2020·International Journal of Environmental Research and Public Health·Luke MontroseDana C Dolinoy
Mar 7, 2019·Frontiers in Pharmacology·Emma CazalyJing Tang
May 23, 2019·Frontiers in Genetics·Giuseppe PetruzzellisEvelina Miele
Jun 11, 2020·Acta Neuropathologica Communications·Harish N VasudevanDavid R Raleigh
Oct 8, 2020·Acta Neuropathologica·Sheila MansouriGelareh Zadeh
Sep 29, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Marije E WeidemaPALGA Group
Mar 13, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Bohai FengJochen Hess
Aug 21, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Thomas R PisanicIe-Ming Shih
Jan 17, 2021·International Journal of Molecular Sciences·Gilberto Ruiz-DeyaJong Y Park

Related Concepts

Computer Programs and Programming
Sequence Determinations, DNA
DNA Methylation
Cdna Microarrays
Epigenomics
Joints
Methylation
DNA Methylation
Molecular Array
Analysis

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.