Computational protocol: Six Novel Susceptibility Loci for Early-Onset Androgenetic Alopecia and Their Unexpected Association with Common Diseases

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Protocol publication

[…] The genotyping platforms, imputation methods and genome wide association methods used in participant studies are provided in . Extensive quality control thresholds were applied to include common SNPs (minor allele frequency ≥1%) with a high call rate (≥95%) for genotyped SNPs, and imputed SNPs with high quality metrics (variance ratio ≥0.3 for MACH and proper info statistic ≥0.4 for IMPUTE) , . In addition, SNPs demonstrating deviation from Hardy Weinberg Equilibrium (p>10−6) were excluded. The test statistics for each cohort at each SNP were corrected for their respective genomic inflation factors to avoid inflation of results due to population stratification. [...] We carried out a meta-analysis under both fixed- and random-effects models using the inverse-variance method to combine results from each study using an additive genetic model, while correcting for the genomic inflation factor for each study and the overall meta-analysis. To implement this strategy GWAMA software was used for SNPs on autosomes . Based on the data available, association results using pre-imputation SNPs from Bonn, CoLaus, TwinsUK cohort, Nigmegen Biomedical Study, 23andMe and Australian population based twin study were used for meta-analysis on X chromosome through YAMAS program (http://yamas.meb.uni-bonn.de/index.html). Proxy association was applied to gain a higher power. We also tested for evidence of heterogeneity of effects between SNPs and AGA across studies using the Cochran's Q statistics and I2 measurement. SNPs with low heterogeneity (Q p value>0·10 and I2<50%) and present in at least three individual studies are reported. In order to test for an inflation of test statistics and the presence of a signal arising from the data for the variants influencing AGA, we constructed quantile-quantile (QQ) plots . Genome-wide significance was set at a p value of 5×10−8 .Genome-wide suggestive SNPs (5×10−8

Pipeline specifications

Software tools IMPUTE, GWAMA
Application GWAS
Organisms Homo sapiens
Diseases Parkinson Disease