Computational protocol: Functional polymorphisms of ATP citrate lyase gene predicts clinical outcome of patients with advanced colorectal cancer

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Protocol publication

[…] Functional SNPs in ACLY gene was selected using a set of web-based SNP selection tools (http://snpinfo.niehs.nih.gov/snpfunc.htm) as described previously []. The 5′ and 3′ flanking regions were arbitrarily set at 2,000 bp for all genes. Only validated SNPs were selected, and SNPs with minor allele frequency (MAF) <5% in Chinese population were excluded. In the case of multiple potentially functional SNPs within the same haplotype block (defined by the linkage coefficient r2 > 0.8), only one SNP was included. Functional SNPs included missense SNPs in exons, SNPs in miRNA-binding sites of 3′UTR, SNPs in transcription factor binding site of 5′ flanking region, as well as SNPs in splice sites.Through the selection process, two SNPs in ACLY gene were selected for further genotyping, including one missense SNP (rs2304497) and one SNP in transcription factor binding site (rs9912300). Genotyping was performed using genomic DNA on Sequenom iPLEX genotyping system (Sequenom, San Diego, CA, USA). The laboratory personnel conducting genotyping were blinded to patient information. Strict quality control measures were implemented during genotyping with more than 99.0% concordance with the main genotyping results. [...] The clinical outcomes of CRC patients include two major endpoints, which are overall survival (OS) and recurrence-free survival (RFS). Overall survival time was defined as the time from initial surgery to death from any cause. Recurrence-free survival time was defined as the time from initial surgery to local recurrence, distant recurrent metastasis. All statistical analyses were performed using the SPSS Statistics 19.0 software (IBM, Armonk, NY, USA). The dominant genetic model was applied to assess the association of single SNPs with clinical outcome of CRC patients. Hazard ratios (HRs) and 95% confidence interval (95% CI) were estimated from a multivariate Cox proportional hazards model, adjusting for gender, age, hospital site, tumor position, TNM stage, tumor differentiation, and treatment after surgery where appropriate. The cumulative effect of unfavorable genotypes on OS or RFS was estimated in Cox model. Haplotypes were determined using the HaploView software package (version 4.2). Kaplan-Meier curve and log-rank test were used to assess the differences of overall survival. All P values in this study were two-sided. P ≤ 0.05 was considered the threshold of statistical significance. […]

Pipeline specifications

Software tools SNPinfo, SPSS, Haploview
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Neoplasms, Colorectal Neoplasms
Chemicals Adenosine Triphosphate