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Series GSE26853 Query DataSets for GSE26853
Status Public on Dec 31, 2011
Title SNP data from blood DNAs of patients with gastric cancer
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Summary The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to chemotherapy could enable the efficient selection of patients for various regimens. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of influencing drug responses. We used Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to various regimens and profiled SNP biomarkers for various regimens.
 
Overall design The chemosensitivity of tumor tissue from the initial cohort of 93 patients was assessed using the histoculture drug response assay (HDRA) and the following six established drugs. Then the inhibition rate (IR) cut-off value for a positive response was previously determined as 30%. Blood DNAs were prepared from each patients and hybridized to Affymetrix’s SNP Array 6.0. Genotypes were determined using the Affymetrix Genotyping Console software (version 2.1) based on the BRLMM-P algorithm. We used an ANOVA test to identify SNPs associated with quantitative HDRA drug sensitivity.
Nine different drug regimens were used. For each of the nine regimens, we provided raw drug sensitivity (HDRA) data and binary data (i.e. >= 30 or < 30) at 30% cutoff.
Publication focuses on six drug regimens: CDP, DTAX, FU, OXA, TAX, and TSI.
Publication discusses 93 of the 95 samples contained in this Series.
 
Contributor(s) Kim J, Kim S, Kim Y
Citation(s) 22199298
Submission date Jan 25, 2011
Last update date Nov 27, 2018
Contact name Tae-Wook Kang
E-mail(s) twkang76@gmail.com
Organization name KRIBB
Street address 111 Gwahangno, Yuseong-gu
City daejeon
ZIP/Postal code 305-334
Country South Korea
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (95)
GSM661056 Blood genomic DNA in patient with gastric cancer HRGC-4
GSM661057 Blood genomic DNA in patient with gastric cancer HRGC-5
GSM661058 Blood genomic DNA in patient with gastric cancer HRGC-6
Relations
BioProject PRJNA135977

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
GSE26853_RAW.tar 4.0 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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