Dataset Information

Single nucleotide polymorphisms in proximity to K-channel genes are associated with decreased longitudinal QTc variance.

ABSTRACT: Atrial fibrillation (AF) is the most common form of cardiac arrhythmia. Despite significant progress in identification of predisposing factors, the pathophysiology of AF remains to be elucidated. Previous studies have reported that single nucleotide polymorphisms (SNPs) in potassium-channel genes associate with AF and the instantaneous corrected QT interval (QTc). The purpose of this study was to examine the association between SNPs in proximity to KCNQ1, KCNH2, KCNE2, and KCNJ2 and longitudinal QTc variations in patients with AF.We conducted a retrospective cohort study of 800 electrocardiograms from 93 patients with AF. All patients were Caucasian, with an average age of 61.2 years, and 72% were male. Of all patients, 37% had persistent AF, and 63% had paroxysmal AF. Following DNA extraction from blood, SNPs at the AF-associated loci KCNQ1, KCNH2, KCNE2, and KCNJ2 were genotyped using the Sequenom MassARRAY. Using a linear regression model and adapting a resampling inference, a decrease in longitudinal QTc variance was found to associate with SNPs near KCNH2 (rs10240738) and KCNJ2 (rs8079702) when adjusted for patient age, gender, AF type, and average QTc. On average, patients with these SNPs had a shorter QTc interval. In addition, we fitted a multilevel mixed effects regression model accounting for subject level heterogeneity and found no longitudinal association between presence of SNPs near K-channel genes and changes in QTc.Polymorphisms near specific potassium-channel genes in AF patients are associated with decreased longitudinal QTc variance and a shorter average QTc. These results support the hypothesis that effects on myocardial repolarization may mediate the association of these SNPs and AF.

SUBMITTER: Mints Y

PROVIDER: S-EPMC4015345 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Single nucleotide polymorphisms in proximity to K-channel genes are associated with decreased longitudinal QTc variance.

Mints Yuliya Y Zipunnikov Vadim V Khurram Irfan I Calkins Hugh H Nazarian Saman S

Annals of noninvasive electrocardiology : the official journal of the International Society for Holter and Noninvasive Electrocardiology, Inc 20130909 1

<h4>Background</h4>Atrial fibrillation (AF) is the most common form of cardiac arrhythmia. Despite significant progress in identification of predisposing factors, the pathophysiology of AF remains to be elucidated. Previous studies have reported that single nucleotide polymorphisms (SNPs) in potassium-channel genes associate with AF and the instantaneous corrected QT interval (QTc). The purpose of this study was to examine the association between SNPs in proximity to KCNQ1, KCNH2, KCNE2, and KCN ...[more]

PMID: 24460807

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Project description:The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs) discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive.To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS), which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles) at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%). This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC) Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes.Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate genes for more detailed functional and mechanistic studies.

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Dataset Information

Single nucleotide polymorphisms in proximity to K-channel genes are associated with decreased longitudinal QTc variance.

Publications

Single nucleotide polymorphisms in proximity to K-channel genes are associated with decreased longitudinal QTc variance.

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