Computational protocol: A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients

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Protocol publication

[…] In the GWAS, Fisher’s exact test was applied to three genetic models: an allele frequency model, a dominant inheritance model, and a recessive inheritance model. SNPs were rank-ordered according to the lowest P value among the three models. Odds ratio (OR) and confidence intervals (CIs) were calculated for the allelic model using a non-risk allele or a non-risk genotype as a reference. A Manhattan plot was generated by using the minimum P value among three genetic models. For the combined analysis, the genotype count of the additional samples was added to that of the GWAS. All statistical analyses and plots were carried out using R statistical environment version 2.13.2 [], and PLINK version 1.07 [,]. Haploview software was used for haplotype analysis, to draw the Manhattan plot and linkage disequilibrium (LD) map. […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Breast Neoplasms, Neoplasms
Chemicals Calcium