Computational protocol: Evaluation of DNA Variants Associated with Androgenetic Alopecia and Their Potential to Predict Male Pattern Baldness

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Protocol publication

[…] All variant data was analyzed for concordance with Hardy-Weinberg expectations using Arlequin v.3.1 (http://cmpg.unibe.ch/software/arlequin3). Haploview version 4.2 tested linkage disequilibrium between closely positioned SNPs (www.broadinstitute.org). Chromosome positions used in the linkage disequilibrium (LD) analysis were retrieved from GRCh37.p13 genome build (coordinates listed in ). [...] The 50 SNPs were tested for association with MPB using binary logistic regression analyzed with IBM SPSS statistics v.22 (SPSS Inc., Chicago, IL, USA). The dependent variable was coded dichotomously as ‘1’ for phenotype category 1 and ‘0’ for phenotype category 2. Independent variables (SNPs) were tested using additive (SNP genotypes coded 0, 1, 2 for the number of minor alleles); dominant (SNP genotypes coded ‘0’ for no minor allele or ‘1’ for at least one minor allele) and recessive (coded ‘0’ for no minor allele or one minor allele or ‘1’ for two minor alleles) inheritance modes. X-linked SNPs coded minor allele homozygotes as ‘2’ and major allele homozygotes as ‘0’. Odds ratios, corresponding 95% confidence intervals (CI) and p-values were estimated for all minor allele classifications. All analyses considered a P-value at <0.05 as statistically significant and correction for multiple hypothesis testing was not applied in this study. Minimal OR values detectable with a power of at least 80% were calculated with Power and Sample Size Program (PS Program) v.3.1.2 (http://biostat.mc.vanderbilt.edu/wiki/Main/PowerSampleSize). […]

Pipeline specifications

Software tools Arlequin, Haploview, SPSS
Applications Miscellaneous, Population genetic analysis, GWAS
Organisms Homo sapiens