Computational protocol: Complex genetic control of lung tumorigenesis in resistant mice strains

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Protocol publication

[…] Nlung and Vlung values were square‐root transformed to improve the normality of distribution. Sex differences in transformed Nlung and Vlung were tested by ANOVA.To identify QTLs, transformed values of Nlung and Vlung were analyzed together with SNP genotype data by parametric simple interval mapping using R/qtl, adjusting by sex. The resulting logarithm of the odds (LOD) scores were considered significant if greater than the 95% LOD threshold (α = 0.05), calculated by 10 000 permutations. The percent phenotypic variance explained by a given QTL was calculated from the LOD score using the following formula: R2=1−10(−2LOD/n), where n is the sample size. Similarly, the total variance using an additive model was calculated by the same formula using the total LOD score obtained by the “fitqtl” command in the R/qtl.Associations between Kras mutations (a categorical phenotype: present or absent) and SNP genotypes were tested by single‐point analysis using the “assoc” command of the PLINK program, which runs a χ2 allelic test. For statistical significance, 10 000 permutations were carried out to obtain, at individual SNP, both the nominal P‐value estimate and the corrected P‐value for multiple testing. […]

Pipeline specifications

Software tools R/qtl, PLINK
Applications WGS analysis, GWAS
Diseases Adenoma, Lung Neoplasms, Neoplasms
Chemicals Urethane