Computational protocol: Genetic Polymorphisms in Host Innate Immune Sensor Genes and the Risk of Nasopharyngeal Carcinoma in North Africa

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Protocol publication

[…] A total of 26 SNPs across six innate immune genes (CD209, DDX58, MBL2, TLR2, TLR3, and TLR9) were selected to the study based on data obtained from the International HapMap Project ( and the NCBI database ( for the CEU (Utah residents with Northern and Western European ancestry from the CEPH collection) and the YRI (Yoruba in Ibadan, Nigeria) populations, as no information was available for any Northern African population (; ). The selection criteria were as follows: (1) minor allele frequency ≥10%; (2) location within the coding region (nonsynonymous SNPs), the 3′ and 5′ untranslated regions (UTRs), and the promoter (up to approximately 1 kb from the transcription start site); and (3) linkage disequilibrium (LD; r2 < 0.80) between the SNPs. We explored the potential function of the associated SNPs as well as other potential causal variants in LD (r2 ≥ 0.80) with these SNPs using FuncPred ( The SNPs selected to the study are shown in . [...] The observed genotype frequencies in controls were tested for Hardy-Weinberg equilibrium using a Pearson goodness-of-fit test ( The most common genotype in the control group was assigned as the reference category and odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were estimated using multiple logistic regressions after inclusion of matching variables (center, age, and sex). All tests were considered to be statistically significant with a P < 0.05. Estimates of pair-wise LD based on the r-squared statistic were obtained using Haploview software, version 4.2. Haplotype block structure was determined using the method of with the HaploView software and the SNPtool ( impact of the alleles that were nominally associated with the risk of NPC (P < 0.10) in the present study was evaluated by counting one for a heterozygous genotype and two for a homozygous genotype. Epistasis between all studied SNPs was tested using multifactor dimensionality reduction (MDR) method for interaction (). This model-free, nonparametric data reduction method classifies multilocus genotypes into high-risk and low-risk groups. The MDR version 2.0 beta 5 with the MDRpt version 0.4.9 alpha module for permutation testing is an open-source and freely available software ( The software estimates the importance of the signals by using both cross-validation and permutation testing, which generates an empirical p-value for the result. A P < 0.05 was considered statistically significant. […]

Pipeline specifications

Software tools SNPinfo, Haploview
Databases International HapMap Project
Application GWAS
Diseases Carcinoma, Neoplasms, Epstein-Barr Virus Infections
Chemicals Tretinoin