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, 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