Computational protocol: Association between DNA mismatch repair gene polymorphisms and platinum-based chemotherapy toxicity in non-small cell lung cancer patients

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Protocol publication

[…] All single nucleotide polymorphisms (SNPs) were selected by Haploview (Broad Institute, Cambridge, MA, USA) using pair-wise tagging with default settings (pair-wise r 2 threshold = 0.8). The following SNPs were eligible for further study: SNPs with a minor allele frequency (MAF) ≥ 5% in the Han Chinese population and SNPs in Hardy–Weinberg equilibrium (HWE) (P > 0.05).All blood samples were collected in the morning and stored at −20°C for 4 h. Genomic DNA was isolated using a Genomic DNA Purification Kit (Promega, Madison, WI, USA) and stored at −20°C before use. Genotyping was conducted using a Sequenom MassARRAY Genotyping Platform (Sequenom, San Diego, CA, USA). [...] The genotype frequencies observed among all patients were compared with their expected frequencies under Hardy–Weinberg equilibrium using a χ2 test (P > 0.05). Sex, age, smoking status, tumor histology, clinical stage, and Eastern Cooperative Oncology Group (ECOG) performance status were considered potential covariates for logistic regression. All analyses were performed using PLINK (version 1.07, http://pngu.mgh.harvard.edu/purcell/plink/) and SPSS 13.0 software (SPSS Inc, Chicago, IL, USA). Odds ratios (OR) and their 95% confidence intervals (95% CI) were used to assess the association between treatment outcomes and gene polymorphisms. P < 0.05 was considered statistically significant. […]

Pipeline specifications

Software tools Haploview, PLINK, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Carcinoma, Non-Small-Cell Lung, Gastrointestinal Diseases, Hematologic Diseases, Lung Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Platinum