Computational protocol: Genetic Variants Underlying Risk of Intracranial Aneurysms: Insights from a GWAS in Portugal

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Protocol publication

[…] Unpaired Student’s t-tests and χ2 tests were used to compare quantitative and qualitative clinical and demographic data, respectively, between IA cases and controls. The adapted Manhattan plot was created using the R freeware. χ2 tests for HWE in controls and crude allelic association of SNPs with IA risk were performed using Haploview 4.2 []. Linkage disequilibrium (LD) plots were performed using Haploview 4.2 and SNAP v2.2 []. Haplotype tagging SNPs were identified in Haploview using pairwise tagging only and an r2 threshold of 0.8.Adjusted and unadjusted association analyses between IA and each SNP were performed with logistic regression (additive genetic model) using the SNPassoc v1.4–9 package [] implemented in R. To adjust the association analyses for relevant confounding factors, hypertension and ever smoking were included as covariates in multivariate logistic regression with backward elimination of risk factors. The interaction i among these covariates in regression models was not strong (-0.5

Pipeline specifications

Software tools Haploview, SNPassoc
Application GWAS
Organisms Homo sapiens
Diseases Intracranial Aneurysm, Rupture