Computational protocol: Genome-Wide Association Mapping in Dogs Enables Identification of the Homeobox Gene, NKX2-8, as a Genetic Component of Neural Tube Defects in Humans

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Protocol publication

[…] DNA samples were genotyped using the Illumina 170K CanineHD BeadChip (Illumina, San Diego, CA). Quality control checks on the canine dataset were performed for individuals and SNPs using GenABEL in the R statistical package . SNPs were excluded if they had a minor allele frequency (MAF)<5%, a genotype call rate <95%, or if they deviated from the Hardy-Weinberg Equilibrium (HWE). A total of 114,775 SNPs passed the quality control check and were available for analysis. The retained SNPs were then used for case-control chi-square statistical analysis by PLINK , and Manhattan and quantile-quantile (QQ) plots were generated using GenABEL . We assessed the effect of population stratification by examining the QQ plots for deviation of the p-values from the null hypothesis. We considered a significant genome-wide association if the SNPs p-value was below the 5% Bonferroni-corrected threshold (p≤0.05; −log 10≥1.3). To derive the genome-wide significance thresholds we repeated the GWAS with 100K Max (T) permutations. […]

Pipeline specifications

Software tools GenABEL, PLINK
Application GWAS
Organisms Canis lupus familiaris, Homo sapiens
Diseases Abnormalities, Drug-Induced, Brain Diseases, Nervous System Malformations, Neural Tube Defects, Spinal Dysraphism