Computational protocol: Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva

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Protocol publication

[…] Prior to the GWA analysis, the following linear model was fitted in R Studio v3.2.3: anti-Lu. longipalpis SGH IgG level ~ mean + origin + sex + age + repellent collar.For the analysis of antibody response (quantitative data), an ordinary least squares regression was used. Then, residuals of the fitted models were used as pseudo-phenotypes to test the association between genotypes and phenotypes in a mixed linear model controlled for polygenic effects and sample structure (EMMAX) [] in SNP & Variation Suite (SVS) v.8 (Golden Helix, Inc., Bozeman, MT, USA, www.goldenhelix.com). Genotypes were filtered in order to remove SNPs with a call rate below 95%, a minor allele frequency (MAF) below 5% and a p-value in an exact test for Hardy-Weinberg equilibrium (HWE) less than 10−5. Samples with a call rate less than 90% were also removed. Markers were prioritized for investigation based on a significance level of p <1 × 10−5 []. Gene coordinates in the CanFam v3.1 assembly were obtained from Ensembl Genes 84 using the BioMart tool (available at: http://www.ensembl.org/biomart/martview/). Genes mapping to a maximum distance of 1 Mb from associated markers were considered positional candidates. The inflation factor and variance explained by the markers were obtained in SVS. […]

Pipeline specifications

Software tools EMMAX, SVS, BioMart
Applications Genome annotation, GWAS
Organisms Canis lupus familiaris, Drosophila melanogaster