Computational protocol: BRCA1 missense polymorphisms are associated with poor prognosis of pancreatic cancer patients in a Chinese population

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Protocol publication

[…] We utilized Ensembl genome browser (http://asia.ensembl.org/index.html) to retrieve all the missense variants on BRCA1 and BRCA2, with global minor allele frequency (MAF) greater than 0.01 (using 1000 genome phase 3 data). Among which, we focused on the common variants in CHB (Han Chinese in Beijing, China) population with MAF in CHB greater than 0.05 (a total of seven variants met the standard, four on BRCA1 and three on BRCA2. .). Then we took advantage of SIFT and PolyPhen to predict variant effects on protein function, and meanwhile measured linkage disequilibrium (LD) relations between each pair of variants using 1000 genome phase 3 data (Figure ). Synthesizing the above results, we selected 3 tagSNPs (rs1799966 on BRCA1; rs766173 and rs144848 on BRCA2) with most likely functional as candidate for genotyping. [...] The overall survival time was defined as the time from pancreatic cancer diagnosis to either death or the last known date alive. Cox proportional hazards regression under a log-additive genetic model with adjustment for gender, age, smoking and drinking status and stage of disease was used to measure the effects of candidate SNPs on survival. Haploview software was used to determine pair-wise LD relations. Kaplan–Meier survival estimates were plotted and P values were assessed using the log-rank test for trend. Survival analyses were performed with R (3.3.0) using “coxph” function in “Survival package”. For all analyses, statistical significance was set at P < 0.05 and all tests were two sided. […]

Pipeline specifications

Software tools PolyPhen, Haploview
Applications GWAS, Genome data visualization
Organisms Homo sapiens
Diseases Neoplasms, Pancreatic Neoplasms