Computational protocol: Are genes encoding proteoglycans really associated with the risk of anterior cruciate ligament rupture?

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Protocol publication

[…] Genotyping results were analysed using the programming environment R [] and R package, SNPassoc (version 1.9.2) []. Differences between genotype and allele frequencies were determined using Pearson’s chi-squared (χ2) and Fisher’s exact test. Post hoc analysis of the genotype frequencies considering co-dominate, dominate and recessive inheritance models was performed to identify the over represented genotype. Hardy-Weinberg equilibrium for each group was determined using SNPassoc. A Bonferroni correction was not applied to the significance level in this pilot study. This study aimed to replicate the associations found in previous studies and Bonferroni correction would mask any statistically significant effects or trends [, ]. A significance level of p<0.05 was set for all statistical analyses.Genotype data for the BGN rs1042103 and rs1126499 was used to generate allele constructs using the haplo.stats package (version 1.7.6) []. This package was further used to compare the frequency distribution of the inferred allele constructs between the control and case participants using Haplo.score []. Haplo.score is a score statistic based on the strength of the association of a haplotype (allele construct) with a given phenotype. A positive value indicates increased susceptibility to an ACLR while a negative value indicates reduced risk. Due to the previous sex–specific associations observed all analyses were stratified by sex [, ]. […]

Pipeline specifications

Software tools SNPassoc, haplo.stats
Application GWAS
Organisms Homo sapiens
Diseases Rupture, Wounds and Injuries