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Series GSE66505 Query DataSets for GSE66505
Status Public on Nov 01, 2015
Title DNA Methylation Sequencing of Prostate Tumors Reveals Possible Molecular Mechanisms for Cancer Aggressiveness
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary A major challenge in the clinical management of prostate cancer is the inability to definitively diagnose indolent versus aggressive cases. Contributing to this challenge is a lack of basic science understanding of the molecular basis behind aggressiveness subtypes in prostate cancer. DNA methylation is the epigenetic addition of a methyl group to the DNA base cytosine and has been found to regulate cell proliferation and environmental adaptation. We hypothesized that DNA methylation changes are a mechanism by which an aggressive cancer attains phenotypes that distinguish it from indolent cases via disruption of regulatory networks. This hypothesis was tested by comparing DNA methylation between benign prostate and both low grade (Gleason score 6) and high grade (Gleason score 8 to 10) groups. Methylome-wide next generation sequencing was performed on formalin-fixed paraffin embedded (FFPE) samples from radical prostatectomy cases using MBD-isolated genome sequencing (MiGS). This technique uses a DNA methylation binding protein (MBD) to purify fragments from a genomic library with a high level of CpG DNA methylation. These fragments were then sequenced via next generation sequencing, the reads were aligned to a reference genome, and then the reads were counted within non-overlapping 50bp windows genome wide. Statistical analysis was then performed on these windowed counts to produce differentially methylated regions (DMRs).
 
Overall design MBD-isolated Genome Sequencing (MiGS) for groups of benign prostate (from cystoprostatectomy), low grade prostate cancer (from radical prostatectomy with Gleason Score 6), and high grade prostate cancer (from radical prostatectomy with Gleason Scores 8 to 10) in both European Americans and African Americans
 
Contributor(s) Bhasin JM, Matkin L, Taylor MG, Lee BH, Magi-Galluzi C, Klein EA, Hu B, Xu Y, Ting AH
Citation(s) 26628371, 26673711
NIH grant(s)
Grant ID Grant title Affiliation Name
F31 CA195887 The function of differential DNA methylation in aggressive prostate cancer CLEVELAND CLINIC LERNER COLLEGE OF MEDICINE - CWRU Bhasin
R01 CA154356 Characterizing the DNA methylomes of indolent and aggressive prostate cancers CLEVELAND CLINIC LERNER COLLEGE OF MEDICINE - CWRU Ting
Submission date Mar 04, 2015
Last update date Oct 18, 2019
Contact name Angela H Ting
E-mail(s) ahting@mdanderson.org
Organization name The University of Texas MD Anderson Cancer Center
Department Epigenetics and Molecular Carcinogenesis
Lab Ting
Street address 1881 East Road
City Houston
State/province Tx
ZIP/Postal code 77054-1901
Country USA
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (22)
GSM1624174 BE1
GSM1624175 BE2
GSM1624176 BE3
Relations
BioProject PRJNA277194
SRA SRP055821

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE66505_Bhasin2015_ProcessedMigsCounts.txt.gz 451.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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