Computational protocol: Polymorphic Sites at the Immunoregulatory CTLA-4 Gene Are Associated with Chronic Chagas Disease and Its Clinical Manifestations

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Protocol publication

[…] Allele and genotype frequencies were estimated by the direct counting method, and adherences of phenotypical proportions to expectations under Hardy-Weinberg equilibrium (HWE) were tested by the complete enumeration method using the GENEPOP 3.4 software []. Linkage Disequilibrium (LD) between CTLA-4 SNPs was evaluated by means of Lewontin’s standardized coefficient D’ and by a likelihood ratio test of linkage disequilibrium implemented at the ARLEQUIN software []. CTLA-4 haplotype frequencies were estimated in each population sample by a coalescence-based method implemented in the PHASE v2 software []. The frequency of each allele, genotype or haplotype was compared between patients and controls by the two-sided Fisher exact test, with the aid of the GraphPad Instat 3.05 software, which was also used to estimate the Odds Ratio (OR) and its 95% Confidence Interval (CI). The Bonferroni correction was used to adjust the significance levels for multiple testing, resulting in α = 0.0011 (i.e., 0.05/44, where 44 indicates the number of tests involving 4 alleles in 11 group comparisons), α = 0.0004 (i.e., 0.05/132, where 132 indicates the number of tests involving 12 genotypes in 11 group comparisons), and α = 0.0006 (i.e., 0.05/88, where 88 indicates the number of tests involving 8 haplotypes in 11 group comparisons). […]

Pipeline specifications

Software tools Genepop, Arlequin
Application Population genetic analysis
Organisms Homo sapiens
Diseases Chagas Disease