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Series GSE39958 Query DataSets for GSE39958
Status Public on Aug 01, 2014
Title Promoter methylation data from genomic DNA in patient with rectal cancer
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary The identification of surrogate methylation markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used Infinium® Methylation Assay to detail methylation status of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers.
The chemoradiosensitivity of tumor tissue from the initial cohort of 45 patients was assessed using clinical responses of tumor regression grade (TRG). TRG was clinically categorized as complete response (CR) as TRG 1, dominant response (ER or finally as DR) as TRG 1 and 2, and efficient response (RYN or finally as ER) as TRG 1, 2, and 3 (TRG grade from Mandard et al, 1994).
Overall design Examination of genome-wide DNA methylation in 45 colon cancer tissues.
We separated patients into TRG1,2,3,4 and 5 group after chemoradiotherapy(CRT). As proposed by Mandard et al. TRG 1, complete tumor response; TRG2, residual cancer cells scattered through fibrosis; TRG 3, an increased number of residual cancer cells, with predominant fibrosis; TRG 4, residual cancer outgrowing fibrosis; and TRG 5, no regressive changes within the tumor: Responders (TRG 1 and 2) and nonresponders (TRG 3?5). Mandard et al. Cancer 1994
Group 1 and Group 2 in ER, CR and RYN was divided by TRG classification.
CR: group 1 - TRG 2,3,4 and 5; group 2 - TRG 1
ER: group 1 - TRG 3,4,5; group 2 - TRG 1 and 2
RYN: group 1 - TRG 4 and 5; group 2 - TRG 1,2 and 3
Contributor(s) Kim JC, Kim S, Kim YS
Citation(s) 25680604
Submission date Aug 08, 2012
Last update date Mar 22, 2019
Contact name Jonglyul Park
Organization name Korea Research Institute of Bioscience and Biotechnology
Department Medical genomics
Street address 52, Eoeun-dong, Yuseong-gu
City daejeon
ZIP/Postal code 305-806
Country South Korea
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (45)
GSM982259 MT.CRT 19
GSM982260 MT.CRT 20
GSM982261 MT.CRT 21
BioProject PRJNA172166

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
GSE39958_RAW.tar 183.1 Mb (http)(custom) TAR
GSE39958_signal_intensity.txt.gz 101.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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