Computational protocol: Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder

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Protocol publication

[…] Genomic DNA was extracted from peripheral blood using Omega DNA extraction Kit (Omega Bio-tek Inc., Doraville, GA). Genotypes were obtained using the Affymetrix6.0 array at CapitalBio Ltd. (Beijing) using the standard Affymetrix protocol. The Affymetrix6.0 array included 906,600 SNP probes. After mapping them to SNPs with #rs, 653,428 SNPs were left. For quality control, the individuals (1) with per-individual autosomal heterozygosity >5 s.d. away from the mean, (2) having no age or IQ information, (3) per-individual call rate <95% and (4) with relatives having genome identity PI_HAT ≥ 0.185 were removed. Then, the remaining samples were assessed for population stratification using Principal Component Analysis (PCA) implemented in EIGENSOFT4.2,. Tracy-Widom test was employed to detect significant eigenvectors (P < 0.05). Only the first eigenvector (eigenvector 1) was significant, which was used as a covariate in the subsequent statistical analysis. When controlling for the quality of SNPs, we removed SNPs if (1) per-SNP call rate <98%, (2) Hardy-Weinberg equilibrium test P < 0.001, (3) MAF < 1%. Totally, 644,166 autosomal SNPs were analyzed in 547 ADHD patients after quality control. [...] Association analysis for each quantitative trait was conducted using an additive model in linear regression in PLINK with age, IQ, sex and eigenvector 1 of PCA as covariates. Two-sided P < 5 × 10−8 was considered as genome-wide significance. We used MACH-admix 1.0 to impute non-genotyped SNPs using the ASN data (286 individuals) from the 1000 Genomes Project Integrated Phase 1 Release as the reference panel. Imputed SNPs with squared correlation between imputed and true genotypes (rsq) <0.6 or SNPs with MAF < 0.01 were removed. Association analysis after imputation was done using mach2qtl. [...] Individual ReHo map was generated in DPABI by calculating the Kendall coefficient of concordance (KCC) of the time series of a given voxel with those of its neighbors (26 voxels) in a voxel-wise way and the inclusive threshold for each voxel was set to P < 0.01. The following statistic analysis was conducted in SPM (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/). A T test was applied to identify the differences between ADHD and control, and then a full factor model was built to test the main effect of the interaction effect of genotype and diagnosis, with mean framewise displacement (FD), gender, age, cohort used as covariates. Post hoc t tests were performed to further investigate the effect of genotype in different diagnostic groups (ADHD or control). The cluster-level analysis threshold was set to P < 0.01 determined by Monte Carlo simulation correction which was also utilized for multiple comparison correction, and recalculated the kernel of smoothness. […]

Pipeline specifications

Software tools EIGENSOFT, PLINK, IMPUTE
Applications Population genetic analysis, GWAS
Organisms Homo sapiens