Genotyping and Quality Control of GENRES, PEAR, GERA Samples

The DNA samples of 228 GENRES study subjects were successfully genotyped (success rates >99%) at the Institute for Molecular Medicine Technology Centre, University of Helsinki using the Illumina HumanOmniExpress‐12 BeadChip (Illumina, Inc, San Diego, CA). The genotypes (NCBI build 37, hg19) were called and quality controlled using GenomeStudio v. 2011.1 software (Illumina, Inc) and in‐house‐developed database tools. Further quality steps, including identity‐by‐state clustering and gender check, were performed using Plink software and PLINK v1.07 toolset.^{20 (link)} Of the total of 709 357 genotyped autosomal SNPs, 707 658 passed these quality‐control steps. After this, SNPs with Hardy‐Weinberg equilibrium P value <1×10⁻⁵ (393 SNPs) and minor allele frequency <0.01 (75 421 SNPs) were excluded, which resulted in 631 844 autosomal SNPs that were used for analysis.
DNA samples from PEAR were genotyped using Illumina Human Omni1‐Quad BeadChip (Illumina) as previously described.^{11 (link)} DNA samples from GERA I and II study participants were genotyped using the Affymetrix GeneChip Human Mapping 6.0 Array Sets.^{10 (link)–11 (link)} SOPHIA samples were genotyped using the Illumina Human1M‐Duo array (Illumina) and imputed using MACH software and the HapMap CEU haplotypes (release 22) as reference.

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Hiltunen T.P., Donner K.M., Sarin A., Saarela J., Ripatti S., Chapman A.B., Gums J.G., Gong Y., Cooper‐DeHoff R.M., Frau F., Glorioso V., Zaninello R., Salvi E., Glorioso N., Boerwinkle E., Turner S.T., Johnson J.A, & Kontula K.K. (2015). Pharmacogenomics of Hypertension: A Genome‐Wide, Placebo‐Controlled Cross‐Over Study, Using Four Classes of Antihypertensive Drugs. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 4(1), e001521.

Publication 2015

HumanOmniExpress‐12 BeadChip GenomeStudio v. 2011.1 software Illumina Human Omni1‐Quad BeadChip Illumina Human1M‐Duo array

Genechip Haplotypes Hapmap Human Mach Pear Snps

Corresponding Organization :

Other organizations : Helsinki University Hospital, University of Helsinki, Institute for Molecular Medicine Finland, Wellcome Sanger Institute, Emory University, Mayo Clinic in Arizona, University of Florida, Fondazione Filarete, University of Milan, University of Sassari, The University of Texas Health Science Center at Houston, Mayo Clinic, WinnMed

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Variable analysis

independent variables

DNA samples from GENRES study subjects
DNA samples from PEAR study
DNA samples from GERA I and II studies
DNA samples from SOPHIA study

dependent variables

Genotypes (NCBI build 37, hg19) called and quality controlled using GenomeStudio v. 2011.1 software (Illumina, Inc) and in‐house‐developed database tools
Identity‐by‐state clustering and gender check performed using Plink software and PLINK v1.07 toolset

control variables

Quality‐control steps, including Hardy‐Weinberg equilibrium P value <1×10^−5 and minor allele frequency <0.01, performed to filter out SNPs

controls

Positive control: Not explicitly mentioned.
Negative control: Not explicitly mentioned.

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