This article is part of the supplement: The Framingham Heart Study 100,000 single nucleotide polymorphisms resource

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Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study

Christopher Newton-Cheh1236*, Chao-Yu Guo146, Thomas J Wang136, Christopher J O'Donnell1356, Daniel Levy156 and Martin G Larson146

Author Affiliations

1 The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA

2 Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA

3 Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

4 Departments of Mathematics and Statistics, Boston University, Boston, MA, USA

5 National Heart, Lung and Blood Institute, Bethesda, MD, USA

6 On behalf of the Framingham Heart Study 100K Cardiovascular Disease Working Group

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BMC Medical Genetics 2007, 8(Suppl 1):S7  doi:10.1186/1471-2350-8-S1-S7

Published: 19 September 2007



Heritable electrocardiographic (ECG) and heart rate variability (HRV) measures, reflecting pacemaking, conduction, repolarization and autonomic function in the heart have been associated with risks for cardiac arrhythmias. Whereas several rare monogenic conditions with extreme phenotypes have been noted, few common genetic factors contributing to interindividual variability in ECG and HRV measures have been identified. We report the results of a community-based genomewide association study of six ECG and HRV intermediate traits.


Genotyping using Affymetrix 100K GeneChip was conducted on 1345 related Framingham Heart Study Original and Offspring cohort participants. We analyzed 1175 Original and Offspring participants with ECG data (mean age 52 years, 52% women) and 548 Offspring participants with HRV data (mean age 48 years, 51% women), in relation to 70,987 SNPs with minor allele frequency ≥ 0.10, call rate ≥ 80%, Hardy-Weinberg p-value ≥ 0.001. We used generalized estimating equations to test association of SNP alleles with multivariable-adjusted residuals for QT, RR, and PR intervals, the ratio of low frequency to high frequency power (LF/HFP), total power (TP) and the standard deviation of normal RR intervals (SDNN).


Associations at p < 10-3 were found for 117 (QT), 105 (RR), 111 (PR), 102 (LF/HF), 121 (TP), and 102 (SDNN) SNPs. Several common variants in NOS1AP (4 SNPs with p-values < 10-3; lowest p-value, rs6683968, p = 1 × 10-4) were associated with adjusted QT residuals, consistent with our previously reported finding for NOS1AP in an unrelated sample of FHS Offspring and other cohorts. All results are publicly available at NCBI's dbGaP at webcite.


In the community-based Framingham Heart Study none of the ECG and HRV results individually attained genomewide significance. However, the presence of bona fide QT-associated SNPs among the top 117 results for QT duration supports the importance of efforts to validate top results from the reported scans. Finding genetic variants associated with ECG and HRV quantitative traits may identify novel genes and pathways implicated in arrhythmogenesis and allow for improved recognition of individuals at high risk for arrhythmias in the general population.