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Series GSE52635 Query DataSets for GSE52635
Status Public on Jan 01, 2016
Title A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic and analytical pipelines for an efficient systems level analysis and interpretation. In the present study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the -established in transcriptomic microarrays- logarithmic ratio of the Methylated versus the Unmethylated signal intensities, quoted as M-value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures based on coefficient variation measurements of DNA methylation between control and case samples alleviate the impact of technical variation. The results presented here are juxtaposed to those derived by applying classical pre-processing and statistical selection methodologies. Overall, in comparison to traditional approaches, the introduced framework's superior performance in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies.
 
Overall design Bisulphite converted DNA from the samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip
 
Contributor(s) Kyrtopoulos SA, Georgiadis P, Chatzionnou A, Sifakis E, Valavanis I
Citation(s) 27600245
Submission date Nov 21, 2013
Last update date Oct 02, 2019
Contact name panagiotis georgiadis
E-mail(s) panosg@eie.gr
Phone 302107273743
Organization name NHRF
Department IBMCB
Lab Chemical Carcinogenesis
Street address 48 vas costantinou
City athens
State/province Greece
ZIP/Postal code 11635
Country Greece
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (114)
GSM1273078 normal (E_BC_CO_001_5935534021.RO5C01)
GSM1273079 normal (E_BC_CO_003_5935534021.RO2C02)
GSM1273080 normal (E_BC_CO_005_5935534021.RO4C02)
Relations
BioProject PRJNA229508

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
GSE52635_RAW.tar 183.1 Mb (http)(custom) TAR
GSE52635_Signal_Intensities.txt.gz 342.2 Mb (ftp)(http) TXT
Processed data included within Sample table
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