Computational protocol: Genetic Association Study Identifies HSPB7 as a Risk Gene for Idiopathic Dilated Cardiomyopathy

Similar protocols

Protocol publication

[…] For initial screening and replication analyses, logistic regression adjusted for gender was used. P-values, odds ratios (OR) and their 95% confidence intervals (CI) were reported. The inflation factor λ was computed in the 50K initial screening analysis for logistic regression analysis assuming a χ2 distribution with two degrees of freedom of the minus two-times logep measures (90% highest p-values). The p-values and CI from initial screening analysis were genomic-control corrected using this λ factor via standard errors (standard error[corrected] = sqrt(λ)*standard error) and beta estimates (95%CI beta[corrected] = beta±1.96*standard error[corrected]). Deviation from Hardy-Weinberg equilibrium was calculated with an exact test . Statistical and association analyses were performed using JMP 7.0.2 (SAS Institute Inc, Cary, NC, USA) and PLINK v1.07 (http://pngu.mgh.harvard.edu/~purcell/plink/) , respectively. Power analysis was carried out using Quanto 1.2.4 (http://hydra.usc.edu/gxe/). We combined the initial scan results corrected for λ with the replication studies' results using a fixed effect model. Annotation of association results on a genome level was performed with WGAViewer software (http://people.genome.duke.edu/~dg48/WGAViewer/) . LD patterns were calculated using HapMap releases #22 and #24 (http://www.hapmap.org/) . […]

Pipeline specifications

Software tools PLINK, WGAViewer
Application GWAS
Organisms Homo sapiens
Diseases Cardiomyopathy, Dilated, Cardiovascular Diseases, Heart Diseases