Genome-Wide Genotyping and Imputation

Genomic DNA was extracted from the peripheral blood collected at week 0 (Macherey-Nagel kit, NucleoSpin Blood XL, Düren, Germany; or with standard method).
Two hundred and eighty-two PHSS patients were genotyped using the Illumina Human1M-Duo array (Illumina Inc, San Diego, California, USA) within HYPERGENES project [19 (link)] and 119 using the Illumina HumanOmniExpress array within InterOmics project (http://www.interomics.eu/).
Two hundred and fifteen HCTZ-Milan samples were genotyped using the Illumina Human1M-Duo array within HYPERGENES project [19 (link)].
The imputation was performed using Minimac [20 (link)] and 1000 Genomes haplotypes as reference (release March 2012). Imputed single-nucleotide polymorphisms (SNPs) with low imputation quality (Rsq < 0.8) were not used in the association analysis. Genotyping and imputation details are in Methods S5 (Supplemental Digital Content, http://links.lww.com/HJH/A467).

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Chittani M., Zaninello R., Lanzani C., Frau F., Ortu M.F., Salvi E., Fresu G., Citterio L., Braga D., Piras D.A., Carpini S.D., Velayutham D., Simonini M., Argiolas G., Pozzoli S., Troffa C., Glorioso V., Kontula K.K., Hiltunen T.P., Donner K.M., Turner S.T., Boerwinkle E., Chapman A.B., Padmanabhan S., Dominiczak A.F., Melander O., Johnson J.A., Cooper-Dehoff R.M., Gong Y., Rivera N.V., Condorelli G., Trimarco B., Manunta P., Cusi D., Glorioso N, & Barlassina C. (2015). TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives. Journal of hypertension, 33(6), 1301-1309.

Publication 2015

Illumina Human1M-Duo array

Blood Genomes Haplotypes Hctz Patients Phss Single nucleotide polymorphisms

Corresponding Organization : University of Sassari

Other organizations : Vita-Salute San Raffaele University, Helsinki University Hospital, University of Helsinki, Institute for Molecular Medicine Finland, Mayo Clinic, The University of Texas Health Science Center at Houston, Emory University, University of Glasgow, Lund University, Karolinska University Hospital, Karolinska Institutet, Humanitas University, National Research Council, University of Naples Federico II

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Variable analysis

independent variables

Genotyping array (Illumina Human1M-Duo, Illumina HumanOmniExpress)

dependent variables

Genotypes of single-nucleotide polymorphisms (SNPs)

control variables

Peripheral blood samples
Genomic DNA extraction method (Macherey-Nagel kit, NucleoSpin Blood XL, or standard method)
Imputation quality (Rsq >= 0.8)

controls

Positive control: Illumina Human1M-Duo array used within HYPERGENES project
Positive control: Illumina HumanOmniExpress array used within InterOmics project
Negative control: Imputed SNPs with low imputation quality (Rsq < 0.8) not used in the association analysis

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