Computational protocol: A functional polymorphism of SSBP1 gene predicts prognosis and response to chemotherapy in resected gastric cancer patients

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Protocol publication

[…] For each GC patient, including 70 additional GC patients for IHC detection, 5 mL venous blood was collected before surgery and centrifuged within 30 minute. Genomic DNA was extracted from 5 mL venous blood by using the E.Z.N.A.® blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA) in the laboratory, and then the genomic DNA was aliquoted and stored at −80°C for future analysis (1100 cases).SNPs in SSBP1 gene were selected using a set of web-based SNP selection tools (http://snpinfo.niehs.nih.gov/snpfunc.htm) according to the previous description []. Briefly, SNPs with minor allele frequency (MAF) <5% in Han Chinese population (CHB) were excluded. Potential functional SNPs were included in present study according to the following criteria: (1) SNPs in miRNA binding sites of 3′-UTR; (2) SNPs in the transcriptional factors binding site (TFBS) of the 5′-UTR (2000 bp upstream from the transcript start site); (3) SNPs in splice sites and exons. Finally, we selected 2 SNPs (rs6976500 and rs12670074) in SSBP1 gene, both in the 5′-UTR. Genotyping was carried out using Sequenom iPLEX genotyping system (Sequenom Inc., San Diego, CA) according to the manufacturer’s protocol. Laboratory technicians who performed the genotyping were blinded to patient information. Strictly quality controls were implemented in each assay during genotyping with over 99.0% concordance with the main genotyping results. The average call rate for the SNP assay was 99.5%. [...] Statistics analyses were performed using the IBM SPSS Statistics 19.0 software (IBM). Normally distributed continuous variables were expressed as the mean ± standard deviation, while abnormally distributed continuous variables were expressed as median and range. Pearson’s χ2-test was used to test the differences of categorical variables. Student’s t-test was used to analyze the difference of normally distributed continuous variables between two groups, while Mann-Whitney U-test was employed for the comparison of abnormally distributed continuous variables. For each SNP, three genetic model (dominant, additive and recessive models) were used for analysis. OS and RFS were compared with the Kaplan-Meier method and significance was determined by the log-rank test. The Cox proportional hazard regression model was applied to assess the effects of SSBP1 genotypes and patients’ characteristics on OS or RFS. A receiver operating characteristic (ROC) curve was used to determine the prediction value of a parameter. Statistics significance was set at a level of 0.05 and all P values reported in this study were two sided. […]

Pipeline specifications

Software tools SNPinfo, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Neoplasms, Stomach Neoplasms
Chemicals Nitroprusside