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Series GSE48684 Query DataSets for GSE48684
Status Public on Sep 08, 2014
Title Global DNA methylation alterations reveal multiple pathways in the initiation and progression of colorectal cancer
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Genetic and epigenetic alterations are a fundamental aspect of colorectal cancer formation. There is considerable heterogeneity between colorectal cancers regarding the mutations and methylated genes they carry, and this heterogeneity may arise early in the polyp-cancer sequence. However, our understanding of the epigenetic alterations and gene mutations in colon adenomas and their relation to colorectal cancer is incomplete. Thus, we have assessed the methylome in normal colon mucosa, tubular adenomas, and colorectal adenocarcinomas and have determined the relationship of these findings between adenomas and cancer in the colon. Genome-wide alterations in DNA methylation were found in the normal colon mucosa adjacent to colorectal cancer, tubular adenomas, and colorectal cancer. Three subgroups of CRCs and two subgroups of adenomas were identified on the basis of their DNA methylation patterns. The adenomas separated into a high-frequency methylation class (Adenoma-H) and a low-frequency methylation class. The adenoma-H polyps have a methylated DNA signature similar to non-CIMP CRCs, whereas those of the Adenoma-L class have a similar methylation pattern to normal colon mucosa. The CpGs that account for these signatures are located in intragenic/intergenic regions, which suggests that these two groups of adenomas arise from different stem cell populations.
Overall design We conducted genome-wide array-based studies and comprehensive data analyses of aberrantly methylated loci in 41 normal colon samples, 42 colon adenomas, and 64 colorectal cancers.

Supplementary file 'GSE48684_Matrix_signal_intensities_1.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1183439-GSM1183561.
Supplementary file 'GSE48684_Matrix_signal_intensities_2.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1235135-GSM1235158.
Contributor(s) Luo Y, Grady W
Citation(s) 24793120
Submission date Jul 10, 2013
Last update date Mar 22, 2019
Contact name Yanxin Luo
Phone 206-667-1823
Organization name Fred Hutchinson Cancer Research Center
Department Clinical Research Division
Lab D4-255
Street address 1100 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (147)
GSM1183439 Genomic DNA from normal individual 1
GSM1183440 Genomic DNA from normal individual 2
GSM1183441 Genomic DNA from normal individual 3
BioProject PRJNA211221

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
GSE48684_Matrix_signal_intensities_1.txt.gz 299.8 Mb (ftp)(http) TXT
GSE48684_Matrix_signal_intensities_2.txt.gz 109.0 Mb (ftp)(http) TXT
GSE48684_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table

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