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450k Analysis Pipeline

Project Leader: Dr Tiffany Morris

This project involves the development of computational tools for analysis of DNA methylation data from the Illumina 450k array.

Illumina Infinium 450k Array Analysis

This project focuses on the analysis of Illumina's Infinium HumanMethylation450 BeadChip. This platform was designed with two different probe types. Technical differences have been shown to exist between the two probe types and normalisation methods that adjust for this Type 2 bias have been developed (Dedeurwaerder et al., 2011, Makismovic et al., 2012, Teschendorff et al., 2013). In addition, careful study design is important to avoid issues with batch effects. 

Our group has assembled ChAMP -Chip Analysis Methylation Pipeline (Morris et al., 2014) that incorporates available tools for data upload, quality control and normalisation. In addition, it offers novel methods including: SVD (Single Value Decomposition) for visualising the largest components of biological/technical variation to enable the identification of batch effects (Teschendorff et al, 2011); Probe Lasso DMR Hunter which is based on a feature-oriented dynamic window ("lasso") that aims to capture neighbouring significant probes and bundle them into DMRs (Butcher unpublished); and also a CNA analysis module which takes raw intensity data, normalises and corrects for batch effects related to BeadChip, smooths and segments the data and returns a data frame of segments which can be filtered to find significant gains and losses (Feber et. al, 2014). 

Illumina Infinium 450k Analysis Workshop London

To aid in the discussion of analysis issues and ideas related to the Illumina 450k array we have hosted two workshops in London. In 2012, the workshop was held at UCL and the focus was on normalising for Type 2 bias, (Morris et al., 2012). In 2013, we hosted a second workshop held at QMUL. In this workshop the topics had gone past normalisation and focused on established pipelines and options for downstream analysis (Lowe et al., 2013). The most recent workshop in 2014 was again held at UCL and focussed on cell composition correction. For workshop information see http://webspace.qmul.ac.uk/rlowe/450kworkshop

References

1. Sarah Dedeurwaerder, Matthieu Defrance, Emilie Calonne, Helene Denis, Christos Sotiriou, and Francois Fuks: Evaluation of the Infinium Methylation 450K technology Epigenomics 2011, 3:771-784.

2. Jovana Makismovic, Lavinia Gordon, and Alicia Oshlack: Subset quantile within-array normalization for Illumina Infinium HumanMethylation450 BeadChips, in review.

3. Teschendorff, A. E. et. a. (2013). A beta-mixture quantile normalization method for correcting probe design bias in illumina infinium 450 k dna methylation data. Bioinformatics, 29(2), 189–96.

4. Teschendorff A E et al.: Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics 2011;27:1496-1505

5. Morris T, Butcher L, Feber A, Teschendorff A, Chakravarthy, AR, Wojdacz TK and Beck S (2014). ChAMP - Chip Analysis Methylation Pipeline. Bioinformatics 2014.

6. Feber A. et. al. (2014). CNA profiling using high density DNA methylation arrays, Genome Biology 2014.

7. Morris T and Lowe R: Report on the Infinium 450k methylation array analysis workshop: April 20, 2012 UCL, London, UK. Epigenetics 2012 Aug;7(8).

8. Lowe R and Morris T: Report on the 2nd Annual Infinium HumanMethylation450 Array Workshop 15 April 2013 QMUL London UK. Epigenetics 2013 Aug 15; 8(10).