PMC:3480676 / 2806-5475 JSONTXT

{"project":"2_test","denotations":[{"id":"23105937-19396169-44845696","span":{"begin":186,"end":187},"obj":"19396169"},{"id":"23105937-19396169-44845697","span":{"begin":1026,"end":1027},"obj":"19396169"},{"id":"23105937-17701901-44845698","span":{"begin":2079,"end":2080},"obj":"17701901"},{"id":"23105937-17786212-44845699","span":{"begin":2532,"end":2533},"obj":"17786212"}],"text":"Methods\n\nSubjects\nIn the discovery stage, the association results for pulse rate were obtained from the KARE study. The information for subjects of the KARE GWAS is described elsewhere [5]. Subjects for the replication stage were recruited from the Health Examinee cohorts, called HEXA-shared cohorts. The standardized examinations that were applied in this survey included 4,302 participants aged 40 to 70 years. The characteristics of the cohorts are described in Table 1.\n\nThe measurement of pulse rate\nPulse rate is the frequency of the heart beat (BPM). Pulse rate of KARE was measured 3 times while the participant was lying down, and the average value was used for the analysis (before the first measurement, participants rested for 5 min, and 3 measurements were taken at least 30 s apart). In HEXA-shared cohorts, the first measurement of the participants, who rested for 5 min, was used.\n\nGenotyping and quality control\nThe methods for genotyping and quality control for the KARE GWAS have been described elsewhere [5]. For the HEXA GWAS, genomic DNA was extracted from 4,302 participants from an urban cohort and genotyped with Affymetrix Genome-Wide Human SNP array 6.0 (Affymetrix, Inc., Santa Clara, CA, USA). From 4,302 genotyped samples, we excluded samples with a low call rate (≥ 95%, n = 443), high heterozygosity (n = 25), outliers (n = 26), and gender inconsistencies (n = 8), and those obtained from individuals who had developed any kind of cancer (n = 61) were excluded from subsequent analyses, along with related or identical individuals whose computed average pairwise identity-by-state value was higher than that estimated from cryptic first-degree relatives of samples (n = 33). SNP markers with a high missing genotype rate (\u003e 5%), minor allele frequency (MAF) (\u003c 0.01), and significant deviation from Hardy-Weinberg equilibrium (p \u003c 1 × 10-6) were excluded, leaving a total of 627,659 markers to be examined in 3,703 individuals.\n\nStatistical analysis\nAssociation analyses were performed using PLINK (http://pngu.mgh.harvared.edu/~purcell/plink/) [6], SAS version 9.2 (SAS institute Inc., Cary, NC, USA), and R statistics package (version 2.7.1) (http://r-project.org/). The SNP association for pulse rate was tested by linear regression analysis with an additive model, adjusting for age, sex, and recruitment area. The KARE GWAS and replication GWAS were combined by an inverse-variance meta-analysis method, assuming fixed effects, with Cochran's Q test used to assess between-study heterogeneity [7]. Meta-analysis calculations were performed using METAL (http://www.sph.umich.edu/csg/abecasis/Metal) in the R program (version 2.7.1)."}