Transcriptomics

Dataset Information

5

SNP data from genomic DNA in patient with rectal cancer


ABSTRACT: The identification of surrogate single nucleotide polymorphism (SNP) 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 Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers. The chemoradiosensitivity of tumor tissue from the initial cohort of 43 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). 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 TRG responses.

ORGANISM(S): Homo sapiens  

SUBMITTER: Tae-Wook Kang   Yong S Kim  Jin C Kim  Seun-Young Kim 

PROVIDER: E-GEOD-35282 | ArrayExpress | 2012-12-31

SECONDARY ACCESSION(S): GSE35282PRJNA151577

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-35282.idf.txt Idf
E-GEOD-35282.processed.1.zip Processed
E-GEOD-35282.processed.2.zip Processed
E-GEOD-35282.processed.3.zip Processed
E-GEOD-35282.processed.4.zip Processed
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