eCite Digital Repository
Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
Citation
Cazaly, E and Thomson, R and Marthick, JR and Holloway, AF and Charlesworth, J and Dickinson, JL, Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses, Clinical Epigenetics, 8, (1) Article 75. ISSN 1868-7083 (2016) [Refereed Article]
![]() | PDF 1Mb |
Copyright Statement
Copyright 2016 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/
DOI: doi:10.1186/s13148-016-0241-2
Abstract
RESULTS: Stratified quantile normalisation combined with ComBat were consistently found to be the most appropriate when assessed using density, MDS and cluster plots. This was supported quantitatively by ANOVA on the first principal component where the effect of batch dropped from p < 0.01 to p = 0.97 after stratified QN and ComBat. Median absolute differences between replicated samples were the lowest after stratified QN and ComBat as were the standard error measures on known imprinted regions. Biological information was preserved after normalisation as indicated by the maintenance of a significant association between a known mQTL and methylation (p = 1.05e-05).
CONCLUSIONS: A strategy combining stratified QN with ComBat is appropriate for use in the analyses when no reference sample is available but preservation of biological variation is paramount. There is great potential for use of 450k array data to further our understanding of the methylome in a variety of similar settings. Such advances will be reliant on the determination of appropriate methodologies for processing these data such as established here.
Item Details
Item Type: | Refereed Article |
---|---|
Keywords: | 450k, Array, Familial data, Methylation, Normalisation, Pre-processing pipeline |
Research Division: | Biological Sciences |
Research Group: | Genetics |
Research Field: | Epigenetics (incl. genome methylation and epigenomics) |
Objective Division: | Expanding Knowledge |
Objective Group: | Expanding knowledge |
Objective Field: | Expanding knowledge in the biological sciences |
UTAS Author: | Cazaly, E (Ms Emma Cazaly) |
UTAS Author: | Thomson, R (Dr Russell Thomson) |
UTAS Author: | Marthick, JR (Mr James Marthick) |
UTAS Author: | Holloway, AF (Professor Adele Holloway) |
UTAS Author: | Charlesworth, J (Dr Jac Charlesworth) |
UTAS Author: | Dickinson, JL (Professor Joanne Dickinson) |
ID Code: | 110224 |
Year Published: | 2016 |
Web of Science® Times Cited: | 6 |
Deposited By: | Menzies Institute for Medical Research |
Deposited On: | 2016-07-20 |
Last Modified: | 2017-11-02 |
Downloads: | 201 View Download Statistics |
Repository Staff Only: item control page