SNP data from genomic DNA in patient with rectal cancer. Homo sapiens

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. Overall design: 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.

本数据集旨在筛选可预测直肠癌患者术前放化疗（Chemoradiotherapy, CRT）响应的替代单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记。全基因组关联研究在理论上可识别放化疗后肿瘤退缩相关的生物标记物。我们采用Affymetrix SNP芯片6.0对术前放化疗响应存在差异的患者队列进行遗传多态性分析，并完成SNP生物标志物的筛选。
总体实验设计：针对初始队列的43例患者，通过肿瘤退缩分级（Tumor Regression Grade, TRG）的临床响应评估其肿瘤组织的放化疗敏感性。TRG的临床分类参考Mandard等人1994年的研究标准：完全缓解（Complete Response, CR）对应TRG 1；优势缓解（Dominant Response, ER，最终记为DR）对应TRG 1与2；有效缓解（Efficient Response, RYN，最终记为ER）对应TRG 1、2与3。采集所有患者的外周血基因组DNA，与Affymetrix SNP芯片6.0进行杂交。基于BRLMM-P算法，使用Affymetrix基因分型控制台软件（版本2.1）确定样本基因型。我们采用方差分析（ANOVA）检验筛选与定量TRG响应相关的SNP位点。