Variants conferring risk of atrial fibrillation on chromosome 4q25

Genome-wide association studies in atherothrombosis

Atherothrombotic diseases are complex diseases, arising from the interaction between several genetic and environmental factors. Until recently, the genetic basis of complex diseases in general, and of atherothrombosis in particular, were poorly characterized. Progress in DNA analysis techniques and the increasing level of characterization of the variability of the human genome has recently allowed to study comprehensively the association between genetic variants and diseases. To date, more than 400 genome-wide association studies have been conducted, allowing to identify more than 430 genomic regions at which common genetic variants influence the predisposition to complex diseases of great epidemiological relevance. This review article summarizes the progress achieved in the genetic basis of atherothrombotic diseases such as myocardial infarction and ischemic stroke. The advances achieved so far now await for clinical applications.

Chromosome 4q25 variants and atrial fibrillation recurrence after catheter ablation

OBJECTIVES

This study tested the hypothesis that chromosome 4q25 single-nucleotide polymorphisms (SNPs) associate with atrial fibrillation (AF) recurrence after catheter ablation.

BACKGROUND

Recent genome-wide association studies identified 2 SNPs on chromosome 4q25 associated with AF. Although the mechanisms underlying this increased risk are unknown, the closest gene, PITX2, is critical for myocardium development in the pulmonary veins.

METHODS

A total of 195 consecutive patients (mean age 56 +/- 12 years, 73% male) with drug-refractory paroxysmal (78%) or persistent (22%) AF who underwent AF catheter ablation were included. Two SNPs, rs2200733 and rs10033464, were genotyped using real-time polymerase chain reaction and fluorescence resonance energy transfer. Serial 7-day Holter electrocardiographic recordings were acquired to detect AF recurrences.

RESULTS

Early recurrence of atrial fibrillation (ERAF) (within the first 7 days) was observed in 37%, whereas late recurrence of atrial fibrillation (LRAF) (between 3 and 6 months) occurred in 21% of the patients. None of the clinical or echocardiographic baseline characteristics were associated with ERAF or LRAF. In contrast, the presence of any variant allele increased the risk for both ERAF (odds ratio [OR]: 1.994, 95% confidence interval [CI]: 1.036 to 3.837, p = 0.039) and LRAF (OR: 4.182, 95% CI: 1.318 to 12.664, p = 0.011). In patients with ERAF, 45% had LRAF, as opposed to 8% in patients without ERAF (OR: 9.274, 95% CI: 3.793 to 22.678, p < 0.001).

CONCLUSIONS

Polymorphisms on chromosome 4q25 modulate the risk for AF recurrence after catheter ablation. This finding points to a potential role for stratification of AF ablation therapy or peri-interventional management by genotype.

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations

MOTIVATION

Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease-gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease (ICD9) billing codes, which are available in most EMR systems. We have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data. As a proof of concept of this algorithm, we genotyped the first 6005 European-Americans accrued into BioVU, Vanderbilt's DNA biobank, at five single nucleotide polymorphisms (SNPs) with previously reported disease associations: atrial fibrillation, Crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. The PheWAS software generated cases and control populations across all ICD9 code groups for each of these five SNPs, and disease-SNP associations were analyzed. The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs.

RESULTS

Four of seven known SNP-disease associations using the PheWAS algorithm were replicated with P-values between 2.8 x 10(-6) and 0.011. The PheWAS algorithm also identified 19 previously unknown statistical associations between these SNPs and diseases at P < 0.01. This study indicates that PheWAS analysis is a feasible method to investigate SNP-disease associations. Further evaluation is needed to determine the validity of these associations and the appropriate statistical thresholds for clinical significance.

AVAILABILITY

The PheWAS software and code translation table are freely available at http://knowledgemap.mc.vanderbilt.edu/research.

Replication of past candidate loci for common diseases and phenotypes in 100 genome-wide association studies

Genome-wide association studies (GWASs) have created a paradigm shift in discovering genetic associations for common diseases and phenotypes, but it is unclear whether the thousands of candidate genetic association studies performed in the pre-GWAS era had found any reliable associations for common diseases and phenotypes. We aimed to systematically evaluate whether loci proposed to harbor candidate associations before the advent of GWASs are replicated in GWASs. The GWAS data published through August, 2008 and included in the NHGRI catalog were screened and variants in candidate loci were selected on the basis of statistical significance (P<0.05) to create a list of independent, non-redundant associations. Altogether, 159 articles on GWASs were evaluated, 100 of which addressed past proposed candidate loci. A total of 291 independent, nominally significant (P<0.05) candidate gene associations were assembled after keeping only the SNP with lowest P-value for each locus and each phenotype; 108 of those had P<10(-3) for association and 41 had P<10(-7). A total of 22 of these 41 candidate gene associations pertained to binary phenotypes with a median odds ratio=2.91 (IQR: 1.82-4.6) and median minor allele frequency=0.17 (IQR: 0.12-0.29) in Caucasians; for comparison, 60 new associations of binary outcomes with P<10(-7) discovered in the same GWASs had much smaller effects (median odds ratio 1.30, IQR: 1.18-1.58) and modestly larger minor allele frequencies (median 0.27, IQR: 0.15-0.43). Overall, few of the numerous genetic associations proposed in the candidate gene era have been replicated in GWASs, but those that have been conclusively replicated have large genetic effects that should not be discarded.

HapMap and mapping genes for cardiovascular disease

A key goal of biomedical science is to understand why individuals differ in their susceptibility to disease. Family history is among the established risk factors for most forms of cardiovascular disease, in part because inherited DNA sequence variants play a causal role in disease susceptibility. Consequently, the search for these variants has intensified over the past decade. One class of DNA sequence variants takes the form of single nucleotide changes(single nucleotide polymorphisms, or SNPs), usually with two variants or alleles for each SNP. SNPs are scattered throughout the 23 pairs of chromosomes of the human genome, and roughly 11 million common polymorphisms (ie,those > 1% frequency) are estimated to exist. A combination of SNP alleles along a chromosome is termed a haplotype. The International Haplotype Map Project was designed to create a public genome-wide database of common SNPs and, consequently, enable systematic studies of most common SNPs for their potential role in human disease. We review the following: (1) the concept of linkage disequilibrium orallelic association, (2) the HapMap project, and (3) several examples of the utility of HapMap data in genetic mapping for cardiovascular disease phenotypes.

The genetics of cardiovascular disease: new insights from emerging approaches

The prospect that sequencing the human genome would see rapid translation of a greater understanding of cardiovascular genetics into novel diagnostics and therapeutics has so far met with only limited success. However, diverse technological advances and exploitation of novel animal models of cardiovascular development and disease are providing ever more insight into cardiovascular diseases and development, and bring closer the prospect of 'post-genomic' diagnostics and therapies. Here we review some of these emerging approaches (genome wide association studies, deep sequencing, microRNA regulation, and zebrafish as a model of cardiovascular disease and development) and discuss their potential for finally fulfilling the promise of application to clinical cardiovascular medicine.

Common variants in KCNN3 are associated with lone atrial fibrillation

Atrial fibrillation (AF) is the most common sustained arrhythmia. A subset of patients with lone AF have no overt heart disease and an increased heritability of AF. We sought to identify common genetic variants underlying lone AF. Cases were from the German AF Network, Heart and Vascular Health Study, Atherosclerosis Risk in Communities Study, Cleveland Clinic, and Massachusetts General Hospital. Subjects were genotyped, HapMap SNPs imputed, and age- sex- and hypertension-adjusted analyses performed. A meta-analysis was conducted using 1,335 cases of lone AF and 12,844 referents. A novel locus on chromosome 1q21 was identified, and the most significant SNP, rs13376333, had an adjusted odds ratio of 1.56 (P=6.3×10⁻¹²). This association was replicated in two cohorts with lone AF for an overall odds ratio of 1.52 (P=1.83×10⁻²¹). Rs13376333 is intronic to KCNN3, a potassium channel involved in atrial repolarization. KCNN3 represents a novel potential therapeutic target in the treatment of AF.

Familiality of kidney stone disease in Iceland

OBJECTIVE

The aetiology of kidney stones is multifactorial, with environmental and genetic factors contributing to the pathogenesis. The aim of this study was to assess the role of genetic factors in kidney stone disease by examining the heritability of the trait in Icelandic patients.

MATERIAL AND METHODS

Medical records at all major hospitals and imaging centres in Iceland were searched for diagnostic codes indicative of kidney stones, yielding a cohort of 5954 incident patients with kidney stone disease. The list of patients was cross-matched with a genealogy database that covers the entire Icelandic nation. The risk ratio (RR) and kinship coefficient (KC) were calculated to determine the risk of kidney stones in relatives of stone formers and the relatedness among kidney stone patients.

RESULTS

The risk of kidney stones among family members of stone formers was significantly higher than in the general population. In 2959 patients with radiopaque stones, the RR ranged from 2.25 (p<0.001) for first degree relatives of probands (such as parents or siblings) to 1.07 (p<0.01) in fifth degree relatives. Moreover, for confirmed recurrent stone formers the RR of kidney stones in parents and offspring was in excess of 10 (p<0.001). The KC analysis shows that Icelandic patients with kidney stone disease are significantly more related to each other than is the average Icelander, even when considering only relatives separated by four meioses or more (p<0.05).

CONCLUSIONS

The results suggest that genetic factors may substantially influence the risk of kidney stone disease in Iceland.

The genetics of ischaemic stroke

In this review, we discuss the genetic factors in both the aetiology and treatment of ischaemic stroke. We discuss candidate gene association studies, family linkage studies and the more recent whole genome association studies and whole genome expression studies. We also briefly discuss genetic testing for stroke risk and genetic analysis of treatment complications.

Genome-wide association study of PR interval

The electrocardiographic PR interval reflects atrial and atrioventricular nodal conduction, disturbances of which increase risk of atrial fibrillation (AF). To identify underlying common genetic variation, we meta-analyzed genome-wide association results for PR interval from seven community-based studies of European-ancestry individuals in the CHARGE consortium: AGES, ARIC, CHS, FHS, KORA, Rotterdam Study, and SardiNIA (N=28,517). Statistically significant loci (P<5×10^-8) were tested for association with AF (N=5,741 cases). We identified nine loci associated with PR interval. At chromosome 3p22.2, we observed two independent associations in voltage gated sodium channel genes SCN10A and SCN5A, while six loci were near cardiac developmental genes CAV1/CAV2, NKX2-5 (CSX1), SOX5, WNT11, MEIS1, and TBX5/TBX3. Another signal was at ARHGAP24, a locus without known relevance to the heart. Five of the nine loci, SCN5A, SCN10A, NKX2-5, CAV1/CAV2, and SOX5, were also associated with AF (P<0.0056). Common genetic variation, particularly in ion channel and developmental genes, contributes significantly to atrial and atrioventricular conduction and to AF risk.

[Genetics of atrial fibrillation]

Atrial fibrillation is the most common cardiac arrhythmia. The identification of familial forms of atrial fibrillation as well as epidemiological studies have confirmed the presence of a genetic background. Familial forms are rare diseases, and the common form is a multifactorial and probably multigenic disease largely modulated by environmental factors. New research developments, based on GWAS studies of well define large cohorts, should, in the near future, help to better characterize the different genetic profiles of this disease, the first step for the identification of new therapeutic targets.

Genetics and the general physician: insights, applications and future challenges

Scientific and technological advances in our understanding of the nature and consequences of human genetic variation are now allowing genetic determinants of susceptibility to common multifactorial diseases to be defined, as well as our individual response to therapy. I review how genome-wide association studies are robustly identifying new disease susceptibility loci, providing insights into disease pathogenesis and potential targets for drug therapy. Some of the remarkable advances being made using current genetic approaches in Crohn's disease, coronary artery disease and atrial fibrillation are described, together with examples from malaria, HIV/AIDS, asthma, prostate cancer and venous thrombosis which illustrate important principles underpinning this field of research. The limitations of current approaches are also noted, highlighting how much of the genetic risk remains unexplained and resolving specific functional variants difficult. There is a need to more clearly understand the significance of rare variants and structural genomic variation in common disease, as well as epigenetic mechanisms. Specific examples from pharmacogenomics are described including warfarin dosage and prediction of abacavir hypersensitivity that illustrate how in some cases such knowledge is already impacting on clinical practice, while in others prospective evaluation of clinical utility and cost-effectiveness is required to define opportunities for personalized medicine. There is also a need for a broader debate about the ethical implications of current advances in genetics for medicine and society.

Structures and Assumptions: Strategies to Harness Gene × Gene and Gene × Environment Interactions in GWAS

Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many phenotypes. There is a strong assumption that interactions between SNPs or genes and interactions between genes and environmental factors substantially contribute to the genetic risk of a disease. Identification of such interactions could potentially lead to increased understanding about disease mechanisms; drug × gene interactions could have profound applications for personalized medicine; strong interaction effects could be beneficial for risk prediction models. In this paper we provide an overview of different approaches to model interactions, emphasizing approaches that make specific use of the structure of genetic data, and those that make specific modeling assumptions that may (or may not) be reasonable to make. We conclude that to identify interactions it is often necessary to do some selection of SNPs, for example, based on prior hypothesis or marginal significance, but that to identify SNPs that are marginally associated with a disease it may also be useful to consider larger numbers of interactions.

A genome-wide association study primer for clinicians

Genome-wide association studies (GWAS) use high-throughput genotyping technology to relate hundreds of thousands of genetic markers (genotypes) to clinical conditions and measurable traits (phenotypes). This review is intended to serve as an introduction to GWAS for clinicians, to allow them to better appreciate the value and limitations of GWAS for genotype-disease association studies. The input of clinicians is vital for GWAS, since disease heterogeneity is frequently a confounding factor that can only really be solved by clinicians. For diseases that are difficult to diagnose, clinicians should ensure that the cases do indeed have the disease; for common diseases, clinicians should ensure that the controls are truly disease-free.

Genetics of familial atrial fibrillation

Atrial fibrillation (AF) remains one of the most common and challenging arrhythmias encountered in clinical practice. While familial forms had remained mostly unknown, in this last decade, the identification of genetic defects, which mainly affect ionic currents, has been the key in our understanding of the pathophysiology of the inherited form of the arrhythmia. Despite the limited prevalence of the familial disease, elucidation of the molecular mechanisms that cause familial AF will likely facilitate understanding of the more common acquired forms of the disease. Therefore, as data keep unravelling, clinicians can expect that soon better therapeutic and preventive options for this arrhythmia will emerge from the discoveries in basic science.

Genetic variation in the rhythmonome: ethnic variation and haplotype structure in candidate genes for arrhythmias

AIMS

The 'rhythmonome' is the term we have adopted to describe the set of genes that determine the normal coordinated electrical activity in the heart. Elements of this set include pore-forming ion channels, function-modifying proteins and intracellular calcium control elements. Rare mutations in many of these genes are known to cause unusual congenital monogenic arrhythmia syndromes, and single common variants have been reported to modify arrhythmia phenotypes. Here, we report an evaluation of the variation and haplotype structure in six key components of the rhythmonome.

MATERIALS & METHODS

SNPs were typed using DNA extracted from Coriell cell lines to survey allele frequencies and haplotype structure in six genes (ANK2, SCN5A, KCNE1 and 2 gene cluster, KCNQ1, KCNH2 and RYR2) across four human populations (African-American, European American, Han Chinese and Mexican American).

RESULTS

A total of 307 SNPs were analyzed across the six genes, revealing significant allele-frequency differences between populations and clear differences in haplotype structure.

CONCLUSIONS

The pattern of variation we report is an important step towards incorporating common variation across the rhythmonome in studies of arrhythmia susceptibility.

Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery

BACKGROUND

Atrial fibrillation (AF) is the most common adverse event following coronary artery bypass graft surgery. A recent study identified chromosome 4q25 variants associated with AF in ambulatory populations. However, their role in postoperative AF is unknown. We hypothesized that genetic variants in the 4q25 chromosomal region are independently associated with postoperative AF after coronary artery bypass graft surgery.

METHODS AND RESULTS

Two prospectively collected cohorts of patients undergoing coronary artery bypass graft surgery, with or without concurrent valve surgery, at 3 US centers. From a discovery cohort of 959 patients, clinical and genomic multivariate predictors of postoperative AF were identified by genotyping 45 single-nucleotide polymorphisms (SNPs) encompassing the 4q25 locus. Three SNPs were then assessed in a separately collected validation cohort of 494 patients. After adjustment for clinical predictors of postoperative AF and multiple comparisons, rs2200733, rs13143308, and 5 other linked SNPs independently predicted postoperative AF in the discovery cohort. Additive odds ratios for the 7 associated 4q25 SNPs ranged between 1.57 and 2.17 (P=8.0x10(-4) to 3.4x10(-6)). Association with postoperative AF were measured and replicated for rs2200733 and rs13143308 in the validation cohort.

CONCLUSIONS

In 2 independently collected cardiac surgery cohorts, noncoding SNPs within the chromosome 4q25 region are independently associated with postoperative AF after coronary artery bypass graft surgery after adjusting for clinical covariates and multiple comparisons.

Atrial fibrillation: a developmental point of view

The myocardial sleeves of the systemic venous tributaries and the pulmonary veins are known to be common anatomic substrates for atrial fibrillation. Rapidly evolving evidence has shown that a substantial part of the paroxysmal variant of this abnormal rhythm has a familial heritage, and the number of genes found to be involved is increasing. One of the mechanisms underlying the condition is ectopic pacemaking activity. Knowledge of the normal embryological development of the atrial myocardium, in particular the myocardial sleeves clothing the systemic venous tributaries and the pulmonary veins at their junctions with the atrial chambers, may contribute to the understanding of the origins of such ectopic pacing. In this respect, it is now well established that the myocardial sleeves of the systemic venous tributaries have a distinct origin and program of gene expression when compared with the pulmonary venous myocardium. The myocardium clothing the pulmonary veins, however, is particularly susceptible to changes in the levels of gene expression, with the changes then favoring the presence of genes responsible for pacemaking. Only recently has interest developed in the genetic and heritable bases of atrial fibrillation, and much is still to be learned. Better understanding of both the developmental and genetic factors, nonetheless, will surely be helpful in the diagnosis, prevention, and treatment of this troublesome arrhythmia. With this in mind, therefore, we have reviewed the current knowledge concerning the initial development of the pulmonary venous myocardium, emphasizing its crucial differences from the systemic venous myocardium.

A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke

We expanded our genome-wide association study on atrial fibrillation (AF) in Iceland, which previously identified risk variants on 4q25, and tested the most significant associations in samples from Iceland, Norway and the United States. A variant in the ZFHX3 gene on chromosome 16q22, rs7193343-T, associated significantly with AF (odds ratio OR = 1.21, P = 1.4 x 10(-10)). This variant also associated with ischemic stroke (OR = 1.11, P = 0.00054) and cardioembolic stroke (OR = 1.22, P = 0.00021) in a combined analysis of five stroke samples.

Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry

We conducted meta-analyses of genome-wide association studies (GWAS) for atrial fibrillation (AF) in participants from five community-based cohorts. Meta-analyses of 896 prevalent (15,768 referents) and 2,517 incident (21,337 referents) AF cases identified a novel locus for AF (ZFHX3, rs2106261, risk ratio [RR]=1.19; P=2.3×10⁻⁷), an association that was replicated in the German AF Network (odds ratio=1.44; P=1.6×10⁻¹¹). Combining the discovery and replication results, rs2106261 was significantly associated with AF (RR=1.25; P=1.8×10⁻¹⁵).

Validating, augmenting and refining genome-wide association signals

Studies using genome-wide platforms have yielded an unprecedented number of promising signals of association between genomic variants and human traits. This Review addresses the steps required to validate, augment and refine such signals to identify underlying causal variants for well-defined phenotypes. These steps include: large-scale exact replication across both similar and diverse populations; fine mapping and resequencing; determination of the most informative markers and multiple independent informative loci; incorporation of functional information; and improved phenotype mapping of the implicated genetic effects. Even in cases for which replication proves that an effect exists, confident localization of the causal variant often remains elusive.

Clair D, Andreassen OA, Reich D, Kong A, Stefansson K. The impact of divergence time on the nature of population structure: an example from Iceland

The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.

The Icelandic population is a structured population, in that geographic regions of Iceland exhibit differences in allele frequencies of genetic markers. Although these differences are relatively small, previous work has shown that they can bias association statistics in disease studies if cases and controls are sampled in different proportions across the geographic regions. In this study, we show that by using dense genotype data it is possible to distinguish the regional geographic ancestry of individuals from Iceland. We further show that the allele frequency differences between regions of Iceland are due to genetic drift since the settling of Iceland, not to differences in contributions from ancestral populations. A consequence of this is that the allele frequency differences follow a null distribution, devoid of unusually large differences caused by the action of natural selection, so that ensuing false positive associations in disease studies will be minimal. This is in stark contrast to populations (such as European Americans) in which subpopulation differences are due to more ancient divergence, allowing the action of natural selection to produce unusually large allele frequency differences that can lead to false positive associations. Our results highlight an important distinction between population differences attributable to recent genetic drift and those arising from more ancient divergence.

Molecular genetics of atrial fibrillation

Atrial fibrillation (AF) is the most common persistent cardiac dysrhythmia and the number one cause of arrhythmia-related hospitalizations. In addition, AF is a major contributor to stroke. With life expectancies increasing, the growing global disability from AF has crippling implications for society. Several family studies have shown a strong polygenetic predisposition for AF but, so far, most of the linkage analysis and candidate gene studies have discovered only monogenic, rare, deleterious mutations. Recent breakthroughs in high-throughput genotyping technology have allowed improved scanning of the genome with greater statistical power to detect susceptibility alleles for AF. Using this technology, a region on 4q25 has now been identified and validated in thousands of cases as a common susceptibility factor for AF with an odds ratio of over 3.0 for homozygotes. The Paired-like homeodomain transcription factor 2 (PITX2) gene, which is involved in embryonic cardiac development, has now been identified as the causal variant for the 4q25 susceptibility locus. Additional susceptibility variants are anticipated that will have direct ramifications for prognosis and treatment of this highly pervasive and clinically significant disorder.

Novel KCNA5 loss-of-function mutations responsible for atrial fibrillation

Accumulating evidence reveals that genetic variants play pivotal roles in familial atrial fibrillation (AF). However, the molecular defects in most patients with AF remain to be identified. Here, we report on three novel KCNA5 mutations that were identified in 4 of 120 unrelated AF families. Among them, T527M was found in two AF families, and A576V and E610K in two other AF families, respectively. The mutations T527M and A576V were also detected in 2 and 1 of 256 patients with idiopathic AF, respectively. The same mutations were not observed in 200 secondary AF patients and 500 controls. Functional analyses revealed consistent loss-of-function effects of mutant KCNA5 proteins on the ultrarapidly activating delayed rectifier potassium currents. These findings expand the spectrum of mutations in KCNA5 linked to AF and provide new insight into the molecular mechanism involved in AF.

Familial aggregation of atrial fibrillation: a study in Danish twins

BACKGROUND

Heritability may play a role in nonfamilial atrial fibrillation (AF). We hypothesized that a monozygotic (MZ) twin whose co-twin was diagnosed with AF would have an increased risk of the disease compared with a dizygotic (DZ) twin in the same situation.

METHODS AND RESULTS

A sample of 1137 same-sex twin pairs (356 MZ and 781 DZ pairs) in which one or both members were diagnosed with AF were identified in The Danish Twin Registry. Concordance rates were twice as high for MZ pairs than for DZ pairs regardless of sex (22.0% versus 11.6%, P<0.0001). In a Cox regression of event-free survival times, we compared the time span between occurrences of disease in MZ and DZ twins. The unaffected twin was included when his or her twin-sibling (the index twin) was diagnosed with AF. After adjustment for age at entry, MZ twins had a significantly shorter event-free survival time (hazard ratio, 2.0; 95% CI, 1.3 to 3.0), thereby indicating a genetic component. Using biometric models, we estimated the heritability of AF to be 62% (55% to 68%), due to additive genetics. There were no significant differences across sexes.

CONCLUSIONS

All the analyses of twin similarities in the present study indicate that genetic factors play a substantial role in the risk of AF for both sexes. The recurrence risk for co-twins (12% to 22%) is clinically relevant and suggests that co-twins of AF-affected twins belong to a high-risk group for AF.

Mutation in the S3 segment of KCNQ1 results in familial lone atrial fibrillation

BACKGROUND

Mutations in several ion channel genes have been reported to cause rare cases of familial atrial fibrillation (AF).

OBJECTIVE

The purpose of this study was to determine the genetic basis for AF in a family with autosomal dominant AF.

METHODS

Family members were evaluated by 12-lead ECG, echocardiogram, signal-averaged P-wave analysis, and laboratory studies. Fourteen family members in AF-324 were studied. Six individuals had AF, with a mean age at onset of 32 years (range 16-59 years).

RESULTS

Compared with unaffected family members, those with AF had a longer mean QRS duration (100 vs 86 ms, P = .015) but no difference in the corrected QT interval (423 +/- 15 ms vs 421 +/- 21 ms). The known loci for AF and other cardiovascular diseases were evaluated. Evidence of linkage was obtained with marker D11S4088 located within KCNQ1, and a highly conserved serine in the third transmembrane region was found to be mutated to a proline (S209P). Compared to the wild-type channel, the S209P mutant activates more rapidly, deactivates more slowly, and has a hyperpolarizing shift in the voltage activation curve. A fraction of the mutant channels are constitutively open at all voltages, resulting in a net increase in I(Ks) current.

CONCLUSION

We identified a family with lone AF due to a mutation in the highly conserved S3 domain of KCNQ1, a region of the channel not previously implicated in the pathogenesis of AF.

Genetics of atrial fibrillation

Recent studies of AF have identified mutations in a series of ion channels; however, these mutations appear to be relatively rare causes of AF. A genome-wide association study has identified novel variants on chromosome 4 associated with AF, although the mechanism of action for these variants remains unknown. Ultimately, a greater understanding of the genetics of AF should yield insights into novel pathways, therapeutic targets, and diagnostic testing for this common arrhythmia.

Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis

Evidence from human genetic studies of several disorders suggests that interactions between alleles at multiple genes play an important role in influencing phenotypic expression. Analytical methods for identifying Mendelian disease genes are not appropriate when applied to common multigenic diseases, because such methods investigate association with the phenotype only one genetic locus at a time. New strategies are needed that can capture the spectrum of genetic effects, from Mendelian to multifactorial epistasis. Random Forests (RF) and Relief-F are two powerful machine-learning methods that have been studied as filters for genetic case-control data due to their ability to account for the context of alleles at multiple genes when scoring the relevance of individual genetic variants to the phenotype. However, when variants interact strongly, the independence assumption of RF in the tree node-splitting criterion leads to diminished importance scores for relevant variants. Relief-F, on the other hand, was designed to detect strong interactions but is sensitive to large backgrounds of variants that are irrelevant to classification of the phenotype, which is an acute problem in genome-wide association studies. To overcome the weaknesses of these data mining approaches, we develop Evaporative Cooling (EC) feature selection, a flexible machine learning method that can integrate multiple importance scores while removing irrelevant genetic variants. To characterize detailed interactions, we construct a genetic-association interaction network (GAIN), whose edges quantify the synergy between variants with respect to the phenotype. We use simulation analysis to show that EC is able to identify a wide range of interaction effects in genetic association data. We apply the EC filter to a smallpox vaccine cohort study of single nucleotide polymorphisms (SNPs) and infer a GAIN for a collection of SNPs associated with adverse events. Our results suggest an important role for hubs in SNP disease susceptibility networks. The software is available at http://sites.google.com/site/McKinneyLab/software.

Susceptibility to many diseases and disorders is caused by breakdown at multiple points in the genetic network. Each of these points of breakdown by itself may have a very modest effect on disease risk but the points may have a much stronger effect through statistical interactions with each other. Genome-wide association studies provide the opportunity to identify alleles at multiple loci that interact to influence phenotypic variation in common diseases and disorders. However, if each SNP is tested for association as though it were independent of the rest of the genome, then the full advantage of the variation from markers across the genome will be unfulfilled. In this study, we illustrate the utility of a new approach to high-dimensional genetic association analysis that treats the collection of SNPs as interacting on a system level. This approach uses a machine-learning filter followed by an information theoretic and graph theoretic approach to infer a phenotype-specific network of interacting SNPs.

Mutations in sodium channel β1- and β2-subunits associated with atrial fibrillation

BACKGROUND

We and others have reported mutations in the cardiac predominant sodium channel gene SCN5A in patients with atrial fibrillation (AF). We also have reported that SCN1B is associated with Brugada syndrome and isolated cardiac conduction disease. We tested the hypothesis that mutations in the 4 sodium channel beta-subunit genes SCN1B-SCN4B contribute to AF susceptibility.

METHODS AND RESULTS

Screening for mutations in the 4 beta-subunit genes was performed in 480 patients with AF (118 patients with lone AF and 362 patients with AF and cardiovascular disease) and 548 control subjects (188 ethnically defined anonymized subjects and 360 subjects without AF). The effects of mutant beta-subunits on SCN5A mediated currents were studied using electrophysiological studies. We identified 2 nonsynonymous variants in SCN1B (resulting in R85H, D153N) and 2 in SCN2B (R28Q, R28W) in patients with AF. These occur at residues highly conserved across mammals and were absent in control subjects. In 3 of 4 mutation carriers, the ECGs showed saddleback-type ST-segment elevation in the right precordial leads. Transcripts encoding both SCN1B and SCN2B were detected in human atrium and ventricle. In heterologous expression studies using Chinese hamster ovary cells, the mutant beta1- or beta2-subunits reduced SCN5A-mediated current and altered channel gating compared with coexpression of wild-type subunits.

CONCLUSIONS

Loss of function mutations in sodium channel beta-subunits were identified in patients with AF and were associated with a distinctive ECG phenotype. These findings further support the hypothesis that decreased sodium current enhances AF susceptibility.

Prevention of atrial fibrillation: report from a national heart, lung, and blood institute workshop

The National Heart, Lung, and Blood Institute convened an expert panel April 28 to 29, 2008, to identify gaps and recommend research strategies to prevent atrial fibrillation (AF). The panel reviewed the existing basic scientific, epidemiological, and clinical literature about AF and identified opportunities to advance AF prevention research. After discussion, the panel proposed the following recommendations: (1) enhance understanding of the epidemiology of AF in the population by systematically and longitudinally investigating symptomatic and asymptomatic AF in cohort studies; (2) improve detection of AF by evaluating the ability of existing and emerging methods and technologies to detect AF; (3) improve noninvasive modalities for identifying key components of cardiovascular remodeling that promote AF, including genetic, fibrotic, autonomic, structural, and electrical remodeling markers; (4) develop additional animal models reflective of the pathophysiology of human AF; (5) conduct secondary analyses of already-completed clinical trials to enhance knowledge of potentially effective methods to prevent AF and routinely include AF as an outcome in ongoing and future cardiovascular studies; and (6) conduct clinical studies focused on secondary prevention of AF recurrence, which would inform future primary prevention investigations.

Joint analysis of tightly linked SNPs in screening step of genome-wide association studies leads to increased power

Recent developments in genome-wide association studies (GWAS) have lead to the localization of disease genes for many complex diseases. The scrutiny of the respective publications reveals, first, that statistical analysis is restricted typically to single-marker analysis in the first step, and that, second, the presence of multiple, independently associated SNPs within the same linkage disequilibrium (LD) region is a common phenomenon. Motivated by this observation, we show through a power simulation study that a simultaneous analysis of tightly linked SNPs in the initial GWAS analysis step would lead to increased power, when compared with that in single-marker analysis. This is true for all the three approaches we considered (implementations in BEAGLE, FAMHAP and UNPHASED). The best performance was obtained using a two-marker haplotype analysis. In conclusion, we would expect additional gene findings for re-analyzing successful GWAS with a multi-marker approach.

Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae

BACKGROUND

Cardiac conduction, as assessed by electrocardiographic PR interval and QRS duration, is an important electrophysiological trait and a determinant of arrhythmia risk.

OBJECTIVE

We sought to identify common genetic determinants of these measures.

METHODS

We examined 1604 individuals from the island of Kosrae, Federated States of Micronesia, an isolated founder population. We adjusted for covariates and estimated the heritability of quantitative electrocardiographic QRS duration and PR interval and, secondarily, its subcomponents, P-wave duration and PR segment. Finally, we performed a genome-wide association study (GWAS) in a subset of 1262 individuals genotyped using the Affymetrix GeneChip Human Mapping 500K microarray.

RESULTS

The heritability of PR interval was 34% (standard error [SE] 5%, P = 4 x 10(-18)); of PR segment, 31% (SE 6%, P = 3.2 x 10(-13)); and of P-wave duration, 17% (SE 5%, P = 5.8 x 10(-6)), but the heritablility of QRS duration was only 3% (SE 4%, P = .20). Hence, GWAS was performed only for the PR interval and its subcomponents. A total of 338,049 single nucleotide polymorphisms (SNPs) passed quality filters. For the PR interval, the most significantly associated SNPs were located in and downstream of the alpha-subunit of the cardiac voltage-gated sodium channel gene SCN5A, with a 4.8 ms (SE 1.0) or 0.23 standard deviation increase in adjusted PR interval for each minor allele copy of rs7638909 (P = 1.6 x 10(-6), minor allele frequency 0.40). These SNPs were also associated with P-wave duration (P = 1.5 x 10(-4)) and PR segment (P = .01) but not with QRS duration (P > or =.22).

CONCLUSIONS

The PR interval and its subcomponents showed substantial heritability in a South Pacific islander population and were associated with common genetic variation in SCN5A.

Sudden cardiac death: The larger problem... The larger genome

This perspective considers progress in understanding how genetic influences modulate susceptibility to lethal ventricular arrhythmias in cardiac patients and the population at large, as opposed to those with rare inherited arrhythmic conditions, such as the Long-QT and Brugada syndromes. It addresses largely unresolved issues, such as how important these effects may be and what we know of underlying mediators and pathways. Attention is given to newly revealed mechanisms of genomic function and the problem of identifying new susceptibility genes and targets useful in developing improved strategies for sudden death prevention.

Common polymorphic transcript variation in human disease

Most human genes are thought to express different transcript isoforms in different cell types; however, the full extent and functional consequences of polymorphic transcript variation (PTV), which differ between individuals within the same cell type, are unknown. Here we show that PTV is widespread in B-cells from two human populations. Tens of thousands of exons were found to be polymorphically expressed in a heritable fashion, and over 1000 of these showed strong correlations with single nucleotide polymorphism (SNP) genotypes in cis. The SNPs associated with PTV display signs of having been subject to recent positive selection in humans, and they are also highly enriched for SNPs implicated by recent genome-wide association studies of four autoimmune diseases. From this disease-association overlap, we infer that PTV is the likely mechanism by which eight common polymorphisms contribute to disease risk. A catalog of PTV will be a valuable resource for interpreting results from future disease-association studies and understanding the spectrum of phenotypic differences among humans.

Prediction of cardiovascular disease outcomes and established cardiovascular risk factors by genome-wide association markers

BACKGROUND

Genome-wide association (GWA) platforms have yielded a rapidly increasing number of new genetic markers. The ability of these markers to improve prediction of clinically important outcomes is debated.

METHODS AND RESULTS

A systematic review was performed of GWA-derived markers associated with cardiovascular outcomes or other phenotypes that represent common established risk factors for cardiovascular outcomes. Sources of information included the National Human Genome Research Institute catalog of published GWA studies, and perusal of the eligible GWA articles, meta-analyses on the respective associations, and articles on the incremental predictive performance of common variants in the GWA era. A total of 95 eligible associations were retrieved from the National Human Genome Research Institute catalogue of published GWA studies as of September 2008. Of those 36 have statistical support of P<10(-7). In depth evaluation of the respective articles shows 28 independent associations with such statistical support, pertaining to coronary artery disease, myocardial infarction, atrial fibrillation/flutter, prolongation of QT interval, as well as type 2 diabetes, body mass index, high-density lipoprotein levels, low-density lipoprotein levels, and nicotine dependence. Between-study heterogeneity is not taken into account usually, but it seems common and it would pose a challenge to generalizability across different populations for these markers. Still limited data are available in non-white populations. Effect sizes are small and may be even smaller in subsequent replications and meta-analysis. Population attributable fractions are substantial, given the large frequency of the risk alleles. However, individualized risk measures are typically very small (proportion of variance explained <1% per marker). When used in conjunction with traditional predictors, improvement in overall prediction (eg, area under the curve) or risk reclassification is limited, and subject to methodological caveats.

CONCLUSIONS

Despite very promising signals in terms of statistical significance, evidence for improvement in cardiovascular prediction by currently available markers derived from GWA studies is sparse. Clinical use of such markers currently would be premature.

Large scale replication and meta-analysis of variants on chromosome 4q25 associated with atrial fibrillation

AIMS

A recent genome-wide association study identified a haplotype block on chromosome 4q25 associated with atrial fibrillation (AF). We sought to replicate this association in four independent cohorts.

METHODS AND RESULTS

The Framingham Heart Study and Rotterdam Study are community-based longitudinal studies. The Vanderbilt AF Registry and German AF Network (AFNet) are case-control studies. Participants with AF (n = 3508) were more likely to be male and were older than referent participants (n = 12 173; Framingham 82 +/- 10 vs. 71 +/- 13 years; Rotterdam 73 +/- 8 vs. 69 +/- 9 years; Vanderbilt 54 +/- 14 vs. 57 +/- 14 years; AFNet 62 +/- 12 vs. 49 +/- 14 years). Single nucleotide polymorphism (SNP) rs2200733 was associated with AF in all four cohorts, with odds ratios (ORs) ranging from 1.37 in Rotterdam [95% confidence interval (CI) 1.18-1.59; P = 3.1 x 10(-5)] to 2.52 in AFNet (95% CI 2.22-2.8; P = 1.8 x 10(-49)). There also was a significant association between AF and rs10033464 in Framingham (OR 1.34; 95% CI 1.03-1.75; P = 0.031) and AFNet (OR 1.30; 95% CI 1.13-1.51; P = 0.0002), but not Vanderbilt (OR 1.16; 95% CI 0.86-1.56; P = 0.33). A meta-analysis of the current and prior AF studies revealed an OR of 1.90 (95% CI 1.60-2.26; P = 3.3 x 10(-13)) for rs2200733 and of 1.36 (95% CI 1.26-1.47; P = 6.7 x 10(-15)) for rs10033464.

CONCLUSION

The non-coding SNPs rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent. These results confirm the significant relations between AF and intergenic variants on chromosome 4.

DNA variations in human and medical genetics: 25 years of my experience

DNA variations have contributed enormously to the fields of medical and forensic science, especially through their use in studies on genes responsible or susceptible to various diseases and those on screening of chromosomal abnormalities in tumors. The types of genetic variations used in these studies have changed in the past 25 years and can be classified into five major classes: RFLP (restriction fragment length polymorphism), VNTR (variable number of tandem repeat), STR (short tandem repeat or microsatellite), SNP (single-nucleotide polymorphism) and CNV (copy-number variation). Genetic linkage analysis using these tools helped to map and discover genes responsible for hundreds of hereditary diseases. Furthermore, construction of the international SNP database and recent development of high-throughput SNP typing platforms enabled us to perform genome-wide association studies, which have identified genes (or genetic variations) susceptible to common diseases or those associated with drug responses. Genome-wide sequencing of individual DNAs is gaining immense scope. Here, I summarize the history of polymorphic DNA markers and their contribution to the genetic analysis of both rare hereditary diseases and common diseases, as well as recent advances in pharmacogenetics, including our contribution to these areas.

Design of tag SNP whole genome genotyping arrays

Whole genome association studies have recently been enabled by combining tag SNP information derived from the International HapMap project with novel whole genome genotyping array technologies. In particular, Infinium whole genome genotyping (WGG) technology now has the power to genotype over 1 million SNPs on a single array. Additionally, this assay provides access to virtually any SNP in the genome enabling selection of optimized SNP content . In this chapter, we provide an overview of the tag SNP-based selection strategy for Infinium whole-genome genotyping BeadChips, including the Human 1 M BeadChip. These advances in both SNP content and technology have enabled both large-scale whole-genome disease association (WGAS) and copy number variation (CNV) studies with the ultimate goal of identifying common genetic variants, disease-associated loci, proteins, and biomarkers.