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A Combined Linkage and Exome Sequencing Analysis for Electrocardiogram Parameters in the Erasmus Rucphen Family Study

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A Combined Linkage and Exome Sequencing Analysis for Electrocardiogram Parameters in the Erasmus Rucphen Family Study fgene-07-00190 November 4, 2016 Time: 17:11 # 1 ORIGINAL RESEARCH published: 08 November 2016 doi: 10.3389/fgene.2016.00190 A Combined Linkage and Exome Sequencing Analysis for Electrocardiogram Parameters in the Erasmus Rucphen Family Study Claudia T. Silva1,2,3, Irina V. Zorkoltseva4, Najaf Amin1, Ay ¸seDemirkan1,5, Elisabeth M. van Leeuwen1, Jan A. Kors6, Marten van den Berg6, Bruno H. Stricker7,8,9, André G. Uitterlinden8, Anatoly V. Kirichenko4, Jacqueline C. M. Witteman7, Rob Willemsen10, Ben A. Oostra1,11, Tatiana I. Axenovich4, Cornelia M. van Duijn1,11† and Aaron Isaacs1,11*† 1 Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands, Edited by: 2 Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia, 3 GENIUROS Group, Genetics and Gudrun A. Brockmann, Genomics Research Center CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia, Humboldt University of Berlin, 4 Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, 5 Department of Germany Human Genetics, Leiden University Medical Center, Leiden, Netherlands, 6 Department of Medical Informatics, Erasmus Reviewed by: University Medical Center, Rotterdam, Netherlands, 7 Department of Epidemiology, Erasmus University Medical Center, Catherine Stein, Rotterdam, Netherlands, 8 Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands, Case Western Reserve University, 9 Inspectorate of Health Care, The Hague, Netherlands, 10 Department of Clinical Genetics, Erasmus University Medical USA Center, Rotterdam, Netherlands, 11 Center for Medical Systems Biology, Leiden, Netherlands Anke Hinney, University of Duisburg-Essen, Germany Electrocardiogram (ECG) measurements play a key role in the diagnosis and prediction *Correspondence: of cardiac arrhythmias and sudden cardiac death. ECG parameters, such as the PR, Aaron Isaacs QRS, and QT intervals, are known to be heritable and genome-wide association studies [email protected] of these phenotypes have been successful in identifying common variants; however, †These authors have contributed equally to this work. a large proportion of the genetic variability of these traits remains to be elucidated. The aim of this study was to discover loci potentially harboring rare variants utilizing Specialty section: variance component linkage analysis in 1547 individuals from a large family-based study, This article was submitted to Applied Genetic Epidemiology, the Erasmus Rucphen Family Study (ERF). Linked regions were further explored using a section of the journal exome sequencing. Five suggestive linkage peaks were identified: two for QT interval Frontiers in Genetics (1q24, LOD D 2.63; 2q34, LOD D 2.05), one for QRS interval (1p35, LOD D 2.52) Received: 02 June 2016 and two for PR interval (9p22, LOD D 2.20; 14q11, LOD D 2.29). Fine-mapping using Accepted: 11 October 2016 Published: 08 November 2016 exome sequence data identified a C > G missense variant (c.713C > G, p.Ser238Cys) −4 Citation: in the FCRL2 gene associated with QT (rs74608430; P D 2.8 × 10 , minor allele Silva CT, Zorkoltseva IV, Amin N, frequency D 0.019). Heritability analysis demonstrated that the SNP explained 2.42% of Demirkan A, van Leeuwen EM, Kors JA, van den Berg M, the trait’s genetic variability in ERF (P D 0.02). Pathway analysis suggested that the gene Stricker BH, Uitterlinden AG, is involved in cytosolic Ca2C levels (P D 3.3 × 10−3) and AMPK stimulated fatty acid Kirichenko AV, Witteman JCM, oxidation in muscle (P D 4.1 × 10−3). Look-ups in bioinformatics resources showed Willemsen R, Oostra BA, Axenovich TI, van Duijn CM and that expression of FCRL2 is associated with ARHGAP24 and SETBP1 expression. Isaacs A (2016) A Combined Linkage This finding was not replicated in the Rotterdam study. Combining the bioinformatics and Exome Sequencing Analysis for Electrocardiogram Parameters information with the association and linkage analyses, FCRL2 emerges as a strong in the Erasmus Rucphen Family candidate gene for QT interval. Study. Front. Genet. 7:190. doi: 10.3389/fgene.2016.00190 Keywords: genetics, epidemiology, electrocardiography, linkage, exome Frontiers in Genetics | www.frontiersin.org 1 November 2016 | Volume 7 | Article 190 fgene-07-00190 November 4, 2016 Time: 17:11 # 2 Silva et al. Electrocardiogram Linkage Analysis INTRODUCTION region, where they were examined in person (Aulchenko et al., 2004). Interviews at the time of blood sampling were performed The electrocardiogram (ECG) is an important tool for by medical practitioners and included questions on a broad diagnosing, monitoring and evaluating risk in patients with range of topics, including current medication use and medical cardiovascular disease (CVD; Lin et al., 2013; Pelto et al., 2013). history (Sayed-Tabatabaei et al., 2005). Height and weight were ECG measurements, such as PR interval, QRS complex duration, measured with the participant in light underclothing and body and QT interval, are used for the diagnosis and prediction of mass index (kg/m2) was computed. Blood pressure (BP) was cardiac arrhythmias and sudden cardiac death (SCD; Kolder measured twice on the right arm in a sitting position after at et al., 2012). Myocardial depolarization and repolarization least five minutes rest, using an automated device (OMRON time are measured by the QT interval: the time between the 711, Omron Healthcare, Bannockburn, IL, USA). The average onset of the QRS complex and the end of the T wave. QT of the two measures was used for analysis. Hypertension was shortening or prolongation has been associated with an increased defined through the use of antihypertensive medication and/or risk for arrhythmias and SCD (Newton-Cheh and Shah, through the assessment of BP measurements according to the 2007). PR interval and QRS duration are measures of cardiac World Health Organization(1999) guidelines (individuals with conduction time; QRS duration reflects conduction through BP ≥ 140/90 mmHg should be regarded as hypertensive). The the ventricular myocardium, while PR interval measures atrial Medical Ethics Committee of the Erasmus University Medical and atrioventricular conduction from the sinoatrial node to the Center approved the ERF study protocol and all participants, or ventricular myocardium, primarily through the atrioventricular their legal representatives, provided written informed consent. node (Cheng et al., 2015; Mozos and Caraba, 2015). There are significant genetic contributions to ECG ECG Measurement and Interpretation measurements; genome-wide association studies (GWAS) Examinations included 10 s 12-lead ECG measurements, identified at least 71 common variants associated with their recorded with an ACTA-ECG (Esaote, Florence, Italy) with a variability (Arking et al., 2006, 2014; Newton-Cheh et al., 2007, sampling frequency of 500 Hz. Digital measurements of the ECG 2009; Pfeufer et al., 2009, 2010; Holm et al., 2010; Sotoodehnia parameters were made using the Modular ECG Analysis System et al., 2010). A number of these associations were established (MEANS; van Bemmel et al., 1990). Briefly, MEANS operates on in loci containing genes that encode proteins with previously multiple simultaneously recorded leads, which are transformed known roles in heart development and function, such as cardiac to a detection function that brings out the QRS complex and transcription factors; sodium, calcium, and potassium ion the other parts of the signal. MEANS determines common channels; genes with a role in myocardial electrophysiology; onsets and offsets for all 12 leads together on one representative and others involved in the conduction of electrical impulses averaged beat, with the use of template matching techniques. (Kolder et al., 2012). These include ARHGAP24, SETBP1, LRIG1, The measurement and diagnostic performance of MEANS have CREBBP, MEIS1, TBX20, and TBX5. Some ion channel encoding been extensively evaluated, both by the developers and by others genes, such as SCN5A, HERG, KCNE1, and KCNE2, have been (Willems et al., 1987, 1991; van Bemmel et al., 1990; de Bruyne associated with long QT syndrome (LQTS; Tristani-Firouzi et al., et al., 1997; Eijgelsheim et al., 2009). The MEANS criteria for MI 2001), atrial fibrillation (AF) and Brugada Syndrome (Hedley are mainly based on pathological Q waves, QR ratio, and R-wave et al., 2011). Collectively, however, these loci explain only modest progression (Leening et al., 2010). A cardiologist, specialized in proportions of phenotypic variability; GWAS SNPs specific for ECG methodology, ascertained the final diagnosis of MI. QT each trait account for limited trait heritability (17% for QRS, 4% interval was corrected for heart rate using Bazett’s formula in all for QT, and 2% for PR) (Silva et al., 2015). analyses (Funck-Brentano and Jaillon, 1993). Genome-wide association studies generally interrogate only common variants, typically of small effect. Families, in addition to being robust against population stratification, may be enriched Genotyping and Statistical Analyses of for less frequent variants, which can potentially be identified by the Linkage Study linkage and fine mapping. The aim of this study, therefore, was Illumina’s HumanHap6k Genotyping BeadChip (6K Illumina to discover less frequent variants using linkage analysis in a large Linkage IV Panels R ) was used for genotyping for the linkage family-based study, the Erasmus Rucphen Family Study (ERF).
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