Variants conferring risk of atrial fibrillation on chromosome 4q25

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.

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.

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.

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.

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.

Population-Based Genomewide Genetic Analysis of Common Clinical Chemistry Analytes

Background: Recent technologies enable genetic association studies of common clinical analytes on a genomewide basis in populations numbering thousands of individuals. The first publications using these technologies are already revealing novel biological functions for both genic and nongenic loci, and are promising to transform knowledge about the biological networks underlying disease pathophysiology. These early studies have also led to development of a set of principles for conducting a successful genomewide association study (GWAS).

Content: This review focuses on these principles with emphasis on the use of GWAS for plasma-based analytes to better understand human disease, with examples from cardiovascular biology.

Conclusions: The correlation of common genetic variation on a genomewide basis with clinical analytes, or any other outcome of interest, promises to reveal how parts of the genome work together in human physiology. Nonetheless, performing a genomewide association study demands an awareness of very specific epidemiologic and analytic principles.

Susceptibility loci for intracranial aneurysm in European and Japanese populations

Stroke is the world's third leading cause of death. One cause of stroke, intracranial aneurysm, affects approximately 2% of the population and accounts for 500,000 hemorrhagic strokes annually in mid-life (median age 50), most often resulting in death or severe neurological impairment. The pathogenesis of intracranial aneurysm is unknown, and because catastrophic hemorrhage is commonly the first sign of disease, early identification is essential. We carried out a multistage genome-wide association study (GWAS) of Finnish, Dutch and Japanese cohorts including over 2,100 intracranial aneurysm cases and 8,000 controls. Genome-wide genotyping of the European cohorts and replication studies in the Japanese cohort identified common SNPs on chromosomes 2q, 8q and 9p that show significant association with intracranial aneurysm with odds ratios 1.24-1.36. The loci on 2q and 8q are new, whereas the 9p locus was previously found to be associated with arterial diseases, including intracranial aneurysm. Associated SNPs on 8q likely act via SOX17, which is required for formation and maintenance of endothelial cells, suggesting a role in development and repair of the vasculature; CDKN2A at 9p may have a similar role. These findings have implications for the pathophysiology, diagnosis and therapy of intracranial aneurysm.

Identification and replication of three novel myopia common susceptibility gene loci on chromosome 3q26 using linkage and linkage disequilibrium mapping

Refractive error is a highly heritable quantitative trait responsible for considerable morbidity. Following an initial genome-wide linkage study using microsatellite markers, we confirmed evidence for linkage to chromosome 3q26 and then conducted fine-scale association mapping using high-resolution linkage disequilibrium unit (LDU) maps. We used a preliminary discovery marker set across the 30-Mb region with an average SNP density of 1 SNP/15 kb (Map 1). Map 1 was divided into 51 LDU windows and additional SNPs were genotyped for six regions (Map 2) that showed preliminary evidence of multi-marker association using composite likelihood. A total of 575 cases and controls selected from the tails of the trait distribution were genotyped for the discovery sample. Malecot model estimates indicate three loci with putative common functional variants centred on MFN1 (180,566 kb; 95% confidence interval 180,505–180, 655 kb), approximately 156 kb upstream from alternate-splicing SOX2OT (182,595 kb; 95% CI 182,533–182,688 kb) and PSARL (184,386 kb; 95% CI 184,356–184,411 kb), with the loci showing modest to strong evidence of association for the Map 2 discovery samples (p<10⁻⁷, p<10⁻¹⁰, and p = 0.01, respectively). Using an unselected independent sample of 1,430 individuals, results replicated for the MFN1 (p = 0.006), SOX2OT (p = 0.0002), and PSARL (p = 0.0005) gene regions. MFN1 and PSARL both interact with OPA1 to regulate mitochondrial fusion and the inhibition of mitochondrial-led apoptosis, respectively. That two mitochondrial regulatory processes in the retina are implicated in the aetiology of myopia is surprising and is likely to provide novel insight into the molecular genetic basis of common myopia.

Successful gene mapping strategies for common disease continue to require careful consideration of basic study design with the advent of genome-wide association studies. Here, we take advantage of prior information that the heritability of the quantitative trait myopia in the general population is high and shows evidence of replicated linkage to chromosome 3q26. Based on this, we conducted a fine map linkage disequilibrium association study for the region, using a high-resolution genetic map derived from population-based HapMap Phase II data. For analysis, we used efficient multi-locus tests of association using single nucleotide polymorphism markers genotyped for our sample data and placed on the genetic map measured in linkage disequilibrium units. We followed up preliminary evidence of association for the discovery samples with further genotyping in the same samples to improve the model location estimates for the common functional variants we identified. Three locations were replicated using an independent sample. Two of the identified genes are likely to play an unexpected role in myopia with both pivotal in the healthy housekeeping metabolism of retinal mitochondria. Both proteins interact with OPA1, with nonsynonymous OPA1 mutations causing the unrelated Mendelian disease Autosomal Dominant Optic Atrophy (ADOA) by triggering mitochondrial-led retinal ganglia cell apoptosis.

Molecular genetics of atrial fibrillation

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. There is genetic predisposition for the development of AF. Recently, by linkage analysis, several loci have been mapped for monogenetic AF, including 11p15.5, 21q22, 17q, 7q35-36, 5p13, 6q14-16, and 10q22. Some of these loci encode for subunits of potassium channels (KCNQ1, KCNE2, KCNJ2, and KCNH2 genes), and the remaining are yet unidentified. All of the known mutations are associated with a gain of function of repolarization potassium currents, resulting in a shortening of action potential duration and atrial refractory period, which facilitate multiple re-entrant circuits in AF. In addition to familial AF, common AF often occurs in association with acquired diseases such as hypertension, valvular heart disease, and heart failure. By genetic association study, some genetic variants or polymorphisms related to the mechanism of AF have been found to be associated with common AF, including genes encoding for subunits of potassium or sodium channels, sarcolipin gene, renin-angiotensin system gene, connexin-40 gene, endothelial nitric oxide synthase gene, and interleukin-10 gene. These observations suggest that genes related to ionic channels, calcium handling protein, fibrosis, conduction and inflammation play important roles in the pathogenesis of common AF. The complete elucidation of genetic loci for common AF is still in its infancy. However, the availability of genomewide scans with hundreds or thousands of polymorphisms has made it possible. However, challenges and pitfalls exist in association studies, and consideration of particular features of study design is necessary before making definite conclusions from these studies.

Clinical use of and future perspectives on antiarrhythmic drugs

Cardiac arrhythmias are associated with significant morbidity and mortality. Antiarrhythmic drug therapy was traditionally the mainstay of arrhythmia treatment; however, the limited efficacy and proarrhythmic potential of conventional antiarrhythmic drugs has generated interest in new approaches to the treatment of arrhythmias. Over the last decade, there has been improved characterization of the molecular pathways that culminate in arrhythmias. By analyzing mechanisms that increase susceptibility to arrhythmias in individuals with genetic syndromes, it might be possible to not only improve current therapies but also to develop novel approaches to treat and prevent common arrhythmias.

Genomics: risk and outcomes in cardiac surgery

Coronary artery bypass graft surgery is associated with several frequent postoperative adverse events. Outcome prediction is valued by patients and practitioners, because it provides some measure of balancing risks and benefits and provides expensive or higher-risk therapies to individuals at highest risk. Surgeons and anesthesiologists traditionally have relied on demographic, preoperative, and intraoperative risk factors to predict outcomes after cardiac surgery. Yet, such predictions often have poor positive and negative predictive value for the individual patient. Perioperative genetics attempts to determine the impact of an individual's genetic variation on the risk of developing adverse postoperative outcomes. In this article, the authors discuss emerging evidence that a patient's genetic makeup predisposes him or her to adverse outcomes following cardiac surgery and provide examples from perioperative bleeding, myocardial injury/infarction, and atrial fibrillation.

Isolated populations and complex disease gene identification

Isolated populations can be useful for the identification of genes underlying common complex diseases.

The utility of genetically isolated populations (population isolates) in the mapping and identification of genes is not only limited to the study of rare diseases; isolated populations also provide a useful resource for studies aimed at improved understanding of the biology underlying common diseases and their component traits. Well characterized human populations provide excellent study samples for many different genetic investigations, ranging from genome-wide association studies to the characterization of interactions between genes and the environment.

Atrial fibrillation: evidence for genetically determined disease

PURPOSE OF REVIEW

Atrial fibrillation is traditionally regarded as a sporadic, nongenetic disorder. Nevertheless, recent growing evidence points to an important heritable basis for atrial fibrillation, with significant genetic determinants. This paper reviews recent progress in understanding the role of genetic contributors to the pathogenesis of atrial fibrillation and its familial susceptibility.

RECENT FINDINGS

Population-based studies have demonstrated a significant heritable component in atrial fibrillation, with specific contributors including single-gene mutations and single-nucleotide polymorphisms. Variants in both ion-channel and nonion-channel genes have been identified as potential atrial fibrillation-risk determinants. In addition, studies have pointed to interesting combined roles of genetic and environmental factors in atrial fibrillation pathogenesis, providing insights into gene-environment interactions. Clinical studies suggest that individual genetic profiles may determine the therapeutic response of atrial fibrillation.

SUMMARY

Rapidly evolving work indicates that there are important genetic determinants of atrial fibrillation, and suggests that understanding these determinants will help us both to appreciate better the underlying pathophysiology and to provide new approaches in diagnosis, prevention and treatment of this common cardiac condition.

Role of potassium currents in cardiac arrhythmias

Abnormal excitability of myocardial cells may give rise to ectopic beats and initiate re-entry around an anatomical or functional obstacle. As K(+) currents control the repolarization process of the cardiac action potential (AP), the K(+) channel function determines membrane potential and refractoriness of the myocardium. Both gain and loss of the K(+) channel function can lead to arrhythmia. The former because abbreviation of the active potential duration (APD) shortens refractoriness and wave length, and thereby facilitates re-entry and the latter because excessive prolongation of APD may lead to torsades de pointes (TdP) arrhythmia and sudden cardiac death. The pro-arrhythmic consequences of malfunctioning K(+) channels in ventricular and atrial tissue are discussed in the light of three pathophysiologically relevant aspects: genetic background, drug action, and disease-induced remodelling. In the ventricles, loss-of-function mutations in the genes encoding for K(+) channels and many drugs (mainly hERG channel blockers) are related to hereditary and acquired long-QT syndrome, respectively, that put individuals at high risk for developing TdP arrhythmias and life-threatening ventricular fibrillation. Similarly, down-regulation of K(+) channels in heart failure also increases the risk for sudden cardiac death. Mutations and polymorphisms in genes encoding for atrial K(+) channels can be associated with gain-of-function and shortened, or with loss-of-function and prolonged APs. The block of atrial K(+) channels becomes a particular therapeutic challenge when trying to ameliorate atrial fibrillation (AF). This arrhythmia has a strong tendency to cause electrical remodelling, which affects many K(+) channels. Atrial-selective drugs for the treatment of AF without affecting the ventricles could target structures such as I(Kur) or constitutively active I(K,ACh) channels.