PLINK | Single SNP association

[…] matter from which trait the SNP was derived). The “traits of a region” were defined as the union of traits contributing with genome-wide significance across the SNPs of the respective region. We used PLINK and EasyStrata for the clumping and for the comparison across traits. Of note, our clumping strategy will yield a different number of independent signals compared with the two GIANT studies that […]

[…] 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 dat […]

[…] es. We removed ~45,000 SNPs on the X or Y chromosome, minor allele frequency <0.05, call rate <98%, and P < 1 × 10E−6 for deviation from Hardy–Weinberg equilibrium. The QC steps were carried out with PLINK and resulted in a total of 374 subjects with genotype data on 664,907 autosomal SNPs.We then performed genotype imputation, using the phased haplotypes from the 1000 Genomes Project dataset as t […]

[…] set into discovery (N ~ 40,000) and replication (N ~ 27,000) datasets (Fig. ). For the discovery data set, we selected the model SNPs from the genotyped SNPs, required for the subsequent GWASs using PLINK 1.9. This selection was based on the following criteria: a minor allele frequency (MAF) > 1%, a Hardy–Weinberg equilibrium (HWE) with a threshold of P-value = 1 × 10−6, and missingness < 0.0015. […]

[…] late linkage disequilibrium (LD) patterns. We used the software GTOOL-v0.7.5 (http://www.well.ox.ac.uk/%7Ecfreeman/software/gwas/gtool.html) to convert BMES IMPUTE2 data (both SNPs and Indels) to the plink format. This conversion changes A/T/G/C/I/D/R based allele coding to 1 or 2 (first and second allele). We extracted variant IDs, hg19 genomic locations and converted A/T/G/C/I/D/R (from 1/2 base […]

[…] UR and EAS samples (Supplementary Table ). In summary, ~6.1 million SNPs in 1000G and ~5.8 million SNPs in GERA after QC were used in the subsequent analyses.We used the LD-based clumping approach in PLINK to select trait-associated SNPs from GWAS summary data. The clumping approach filters out SNPs with P-values larger than a specific threshold, clusters the remaining SNPs by LD and physical dist […]