Computational protocol: The Association between Individual SNPs or Haplotypes of Matrix Metalloproteinase 1 and Gastric Cancer Susceptibility, Progression and Prognosis

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Protocol publication

[…] Haploview 4.2 software was used to evaluate LD and construct haplotypes as described previously . LD between the seven SNPs used in haplotype analysis was measured by a pairwise D′ statistic. The structure of the LD block was examined using the method of Gabriel et al. , using the 80% confidence bounds of D′ to define sites of historical recombination between SNPs. Haplotypes were constructed from genotype data in the full-size case-control panel within blocks using an accelerated expectation-maximization algorithm method with Haploview 4.2 software , . Furthermore, we made SNP genotype combinations to find their association with gastric cancer risk . [...] A two-sided chi-square (χ2) test was used to estimate population distribution characteristics, compare differences in allelic and genotypic frequencies between cases and controls and estimate associations between individual SNPs and clinicopathological parameters. To assess significance, a permutation procedure (1,000 tests) was used to correct the P value of single-locus association results . A permutation test is a type of statistical significance test in which the distribution of the test statistic under the null hypothesis is obtained by calculating all possible values of the test statistic under rearrangements of the labels on the observed data points. Moreover, the Bonferroni correction was used for multiple testing correction . Logistic regression was used to analyze the association between genotype frequencies and gastric cancer risk, adjusted for sex and age. Survival analyses were done with the log-rank test and Cox proportional hazards model. The Haploview 4.2 software package was used to: estimate pair-wise LD, detect departure from the Hardy–Weinberg equilibrium, construct haplotypes, calculate haplotype frequencies and estimate associations between haplotypes and gastric cancer risk. We also used Haplo.states software to assess associations between haplotypes and clinicopathologic features , . The THEsias software based on Cox proportional hazards survival regression in haplotype-based association analysis using the Stochastic-EM algorithm was used to produce survival analysis of haplotypes . Because of multiple hypothesis testing, the P value for significance was adjusted conservatively by Bonferroni correction to <0.007 (0.05/7) […]

Pipeline specifications

Software tools Haploview, THESIAS
Application GWAS
Organisms Homo sapiens
Diseases Neoplasms, Stomach Neoplasms