Computational protocol: Assessing the Causality between Blood Pressure and Retinal Vascular Caliber through Mendelian Randomisation

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Protocol publication

[…] Participants were genotyped by using Human610-Quad BeadChip (Illumina, Inc. San Diego, CA), which included ~600,000 single nucleotide polymorphisms (SNPs). Stringent quality control filters were used to remove poorly performing samples and SNP markers. SNPs with a call-rate of <95%, MAF of <0.1%, or showing deviation from Equilibrium (P < 10−6) were removed. Routine quality control criteria on a per-sample basis were carried out, and poorly performing samples were removed from further analysis. The remaining samples were then subjected to biological relationship verification by using the principle of variability in allele sharing according to the degree of relationship. Identity-by-state information was derived using the PLINK software. Pairs of individuals who showed evidence of cryptic relatedness were identified, and samples with the lower call rate were removed before performing principal component analysis (PCA). PCA was undertaken using smartPCA program (EIGENSTRAT software v4.2) accounting for spurious associations resulting from ancestral differences of individual SNPs. Genotype data, which had undergone strict quality checks, were merged together and only SNPs shared by all three ethnic groups were used for analysis. This method and PCA figures have been described and shown in the published data in the same cohort. […]

Pipeline specifications

Software tools PLINK, EIGENSOFT
Applications Population genetic analysis, GWAS
Organisms Homo sapiens
Diseases Hypotension, Retinal Diseases