GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE43976 Query DataSets for GSE43976
Status Public on Mar 14, 2013
Title An evaluation of analysis pipelines for DNA methylation profiling using the Illumina Human Methylation 450k platform
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Abstract The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina Human Methylation 450k BeadChip is widely used to quantify DNA methylation, nevertheless the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate datasets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished datasets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. The blood samples included individuals with Multiple Sclerosis (MS). We evaluated the performance of different analysis pipelines and demonstrated that a) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; b) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); c) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive dataset suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450k arrays.
Overall design DNA samples from peripheral blood or CD14+ monocytes of individuals with Multiple Sclerosis (MS), were included in the study. DNA methylation levels were profiled using Illumina 450K arrays. Specifically, 50 biological sample replicates from PB and 36 biological sample replicates from monocytes were randomly assigned to 8 BeadChips with technical replicates and processed in one run (a total of 96 DNA samples). Eight samples were technically replicated in pairs, while one sample was represented in a trio of replicates. Different analysis pipelines were compared, however, the file uploaded refers to the best scored. In our publication we used this one to make all analyses and conclusions.
Contributor(s) Marabita F, Gomez-Cabrero D, Tegnér J, Jagodic M, Ekström TJ
Citation(s) 23422812, 29109506, 29921915
Submission date Feb 01, 2013
Last update date Mar 13, 2020
Contact name Francesco Marabita
Organization name Karolinska Institutet
Street address Karolinska University Hospital
City Stockholm
ZIP/Postal code 17176
Country Sweden
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (95)
GSM1075838 PB_1
GSM1075839 PB_2
GSM1075840 PB_3_r
BioProject PRJNA188414

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43976_RAW.tar 961.1 Mb (http)(custom) TAR (of IDAT)
GSE43976_matrix_norm.txt.gz 355.1 Mb (ftp)(http) TXT
GSE43976_matrix_raw.txt.gz 216.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap