Computational protocol: WEE1 kinase polymorphism as a predictive biomarker for efficacy of platinum-gemcitabine doublet chemotherapy in advanced non-small cell lung cancer patients

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Protocol publication

[…] The four tag SNPs (rs3829254, rs3910384, rs4370932 and rs1049403) representing 50 SNPs of WEE1 were selected from the CHB data of the phase 2 HapMap SNP database (http://www.hapmap.org/) using a minor allele frequency (MAF) cutoff of 0.05 and a correlation coefficient (r2) threshold of 0.8. Genomic DNA was extracted from patients’ peripheral blood samples using the QIAamp DNA Maxi Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions. The SNPs were genotyped using the iSelect HD Bead-Chip (Illumina, San Diego, CA, USA) with the following quality-control criteria: genotyping call rate >0.95; MAF >0.05; and GenCall score >0.2. The concordance among replicates was >99.9% and the GeneMap software was used to analyze the data and prepare reports.Linkage disequilibrium was analyzed in Haploview Software (Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA). Three putative functional SNPs, i.e. rs6486433, rs3763869 and rs3763868 in the WEE1 promoter region which are closely linked with rs3910384 were selected using MAF >0.2 and D’ >0.8 cutoff. The function of SNPs was predicted with FuncPred tools (National Institute of Environmental Health Sciences, USA). Individual haplotype frequencies for the selected SNPs were evaluated using the Hyploview or PHASE 2.0 Program (version 2.0.2) based on the Bayesian algorithm. […]

Pipeline specifications

Software tools Gencall, Haploview, SNPinfo
Databases GeneMap
Application GWAS
Organisms Homo sapiens
Diseases Carcinoma, Non-Small-Cell Lung
Chemicals Platinum