Oligogenic Disease Research Articles

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

An increasing number of disorders have been identified for which two or more distinct alleles in two or more genes are required to either cause the disease or to significantly modify its onset, severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of alleles underlying digenic and oligogenic diseases in individual whole exome or whole genome sequences. Information that links patient phenotypes to databases of gene–phenotype associations observed in clinical or non-human model organism research can provide useful information and improve variant prioritization for genetic diseases. Additional background knowledge about interactions between genes can be utilized to identify sets of variants in different genes in the same individual which may then contribute to the overall disease phenotype. We have developed OligoPVP, an algorithm that can be used to prioritize causative combinations of variants in digenic and oligogenic diseases, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods in the case of digenic diseases. Our results show that OligoPVP can efficiently prioritize sets of variants in digenic diseases using a phenotype-driven approach and identify etiologically important variants in whole genomes. OligoPVP naturally extends to oligogenic disease involving interactions between variants in two or more genes. It can be applied to the identification of multiple interacting candidate variants contributing to phenotype, where the action of modifier genes is suspected from pedigree analysis or failure of traditional causative variant identification.

A novel genetic region prioritization tool using a new statistical framework to analyse oligogenic diseases

A novel genetic region prioritization tool using a new statistical framework to analyse oligogenic diseases

P.129 - The recessive SOD1 mutation p.A90V may cause atypical motor neuron disease by oligogenic mechanisms

SOD1 mutations are the second most common cause of familial amyotrophic lateral sclerosis worldwide after the C9orf72 hexanucleotide expansion mutation. Some SOD1 mutations cause atypical phenotypes with slow progression, reduced penetrance or a purely lower motor neuron disease. Most mutations show autosomal dominant inheritance, but recessive inheritance has also been described and indeed the atypical ALS caused by homozygous p.D91A mutations is the most common form of SOD1 ALS in Finland. The phenotype caused by the SOD1 mutation p.A90V has only been reported in a few individuals thus far. A previously reported pedigree carrying the p.A90V mutation showed autosomal dominant inheritance but with reduced penetrance. We describe four Finnish patients with atypically slowly progressive ALS or lower motor neuron disease carrying the SOD1 p.A90V mutation. Three patients were found to carry a second additional mutation in SOD1 or in other known ALS genes, indicating recessive compound heterozygosity or oligogenic disease mechanisms associated with this particular SOD1 mutation, which may also explain the incomplete penetrance observed in the previously reported pedigrees. These findings provide further support for oligogenic pathomechanisms in the pathogenesis of ALS and other motor neuron disorders.

Factors affecting interactome-based prediction of human genes associated with clinical signs

BackgroundClinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome.ResultsOur analysis reveals that these approaches can locate genes associated with clinical signs with variable performance that depends on the sign and associated disease. We analyzed several clinical and biological factors that explain these variable results, including number of genes involved (mono- vs. oligogenic diseases), mode of inheritance, type of clinical sign and gene product function.ConclusionsOur results indicate that the characteristics of the clinical signs and their related diseases should be considered for interpreting the results of network-prediction methods, such as those aimed at discovering disease-related genes and variants. These results are important due the increasing use of clinical signs as an alternative to diseases for studying the molecular basis of human pathologies.

A mutation in the CACNA1C gene leads to early repolarization syndrome with incomplete penetrance: A Chinese family study.

BackgroundEarly repolarization syndrome (ERS) may be a near-Mendelian or an oligogenic disease; however, no direct evidence has been provided to support this theory.Methods and resultsWe described a large Chinese family with nocturnal sudden cardiac death induced by ERS in most of the young male adults. One missense mutation (p.Q1916R) was found in the major subunit of the L-type calcium channel gene CACNA1C by the direct sequencing of candidate genes. A concomitant gain-of-function variant in the sodium channel gene SCN5A (p.R1193Q) was found to rescue the phenotype of the female CACNA1C-Q1916R mutation carriers, which led to the incomplete penetrance. The functional studies, via the exogenous expression approach, revealed that the CACNA1C-Q1916R mutation led to a decreasing L-type calcium current and the protein expression defect. The decreased calcium current produced by the mutant channel was improved by isoproterenol but exacerbated by testosterone. The effects of CACNA1C-Q1916R mutation and testosterone on cellular electrophysiology were further confirmed by the human ventricular action potential simulation.ConclusionsOur results demonstrated that the loss-of-function CACNA1C-Q1916R mutation contributed to ERS-related sudden cardiac death, and the phenotypic incomplete penetrance was modified by the SCN5A-R1193Q variant and sex. These findings suggest that phenotypes of ERS are modified by multiple genetic factors, which supports the theory that ERS may be an oligogenic disease.

Abstract P3-09-04: Beyond CHEK2 in breast cancer: Search for additional moderately penetrant risk gene variants by analyzing the oligogenic disease course in CHEK2 mutation carriers

Abstract This abstract was not presented at the symposium.

New Insights Into the Genetic Basis of Inherited Arrhythmia Syndromes.

Inherited arrhythmia syndromes encompass several different diseases, including long QT syndrome (LQTS), Brugada syndrome (BrS), catecholaminergic polymorphic ventricular tachycardia (CPVT), short QT syndrome (SQTS), idiopathic ventricular fibrillation (IVF), and progressive cardiac conduction system disease (PCCD).1 The heart is typically structurally normal with no evidence of disease macroscopically. They are an important cause for sudden cardiac death in the young, and an autopsy is typically negative.2,3 Ventricular arrhythmias are caused by mutations of ion channels and their interacting proteins, predominantly involving potassium, sodium, and calcium handling.4 Genetic studies have identified the specific genetic abnormalities that underpin these diseases, even permitting diagnosis in the deceased using postmortem genetic testing (the molecular autopsy).3 Most arrhythmia syndromes are inherited in an autosomal dominant manner, such that first-degree family members have a 50% chance of inheriting the disease. Identification of the mutation allows for predictive genetic testing in other living family members.4 Variable penetrance is common in all arrhythmia syndromes, the same mutation in the same family causing wide variation in phenotype.4 This suggests that other factors such as genetic modifiers and environmental factors may influence the phenotype. This review will highlight the latest developments in understanding the genetic basis of inherited arrhythmia syndromes and discusses the new opportunities and challenges faced with evolving genetic technologies including determining pathogenicity and the utility of large genetic databases. Finally, we will discuss newly described entities that continue the evolving theme of genetic syndromes with phenotypic overlap. Early views that a single genotype associates with a particular phenotype continue to be challenged by our greater understanding of the genotype–phenotype relationship. ### Long QT Syndrome Congenital LQTS is diagnosed in the presence of a prolonged corrected QT (QTc) interval after secondary causes (eg, QT-prolonging medications or electrolyte abnormalities) are excluded.1 The 2013 Heart Rhythm …

0219 : Genetics of ventricular fbrillation with short-coupled torsade de pointes

Origin of idiopathic ventricular fibrillation (IVF) remains unclear. The incorporation of genetic knowledge could improve the diagnosis and could create a better classification of this sub-group of patients. To this end, we collected DNA from 19 patients with VF of Purkinje origin associated with short-coupled premature ventricular beats or torsade de pointes. We aimed to determine the frequency of rare variants in 47 genes implied in ventricular arrhythmias and 20 additional genes highly expressed in Purkinje fibers. Exome sequencing was performed using Illumina technology. We selected rare non-synonymous variants with reads superior to 10, a minor allele frequency inferior to 0.1% and predicted to alter the protein sequence. Potential pathogenicity was assessed by Polyphen-2, Mutation Taster and CADD (Combined Annotation Dependent Depletion) and variants considered as benign for 2 of 3 tests were discarded. We identified 10 rare (MAF<1/10000) and 5 novel variants (absent in all available databases) in 9 genes of the 47 involved in ventricular arrhythmias like RYR2, SCN5A, CACNA1C. Only two variants in KCNH2 and GJA5 were previously reported as pathogenic. In addition, we identified 2 rare and 2 novel missense variants in the 4 of the 20 genes highly expressed in Purkinje fibers. By analyzing 67 candidate genes we identified 19 variants in 13 different genes. This suggests than the idiopathic ventricular fibrillation associated with short-coupled torsades de pointes is an oligogenic disease. We didn’t find any variants for 6 patients. We identified a high proportion of these variants affecting a calcium channel subunit, which could be meaningful since our patients are sensitive to verapamil, a calcium inhibitor. Functional studies should confirm their involvement in ventricular fibrillation with short-coupled torsade de pointes. The author hereby declares no conflict of interest

DNAH6 and Its Interactions with PCD Genes in Heterotaxy and Primary Ciliary Dyskinesia.

Heterotaxy, a birth defect involving left-right patterning defects, and primary ciliary dyskinesia (PCD), a sinopulmonary disease with dyskinetic/immotile cilia in the airway are seemingly disparate diseases. However, they have an overlapping genetic etiology involving mutations in cilia genes, a reflection of the common requirement for motile cilia in left-right patterning and airway clearance. While PCD is a monogenic recessive disorder, heterotaxy has a more complex, largely non-monogenic etiology. In this study, we show mutations in the novel dynein gene DNAH6 can cause heterotaxy and ciliary dysfunction similar to PCD. We provide the first evidence that trans-heterozygous interactions between DNAH6 and other PCD genes potentially can cause heterotaxy. DNAH6 was initially identified as a candidate heterotaxy/PCD gene by filtering exome-sequencing data from 25 heterotaxy patients stratified by whether they have airway motile cilia defects. dnah6 morpholino knockdown in zebrafish disrupted motile cilia in Kupffer’s vesicle required for left-right patterning and caused heterotaxy with abnormal cardiac/gut looping. Similarly DNAH6 shRNA knockdown disrupted motile cilia in human and mouse respiratory epithelia. Notably a heterotaxy patient harboring heterozygous DNAH6 mutation was identified to also carry a rare heterozygous PCD-causing DNAI1 mutation, suggesting a DNAH6/DNAI1 trans-heterozygous interaction. Furthermore, sequencing of 149 additional heterotaxy patients showed 5 of 6 patients with heterozygous DNAH6 mutations also had heterozygous mutations in DNAH5 or other PCD genes. We functionally assayed for DNAH6/DNAH5 and DNAH6/DNAI1 trans-heterozygous interactions using subthreshold double-morpholino knockdown in zebrafish and showed this caused heterotaxy. Similarly, subthreshold siRNA knockdown of Dnah6 in heterozygous Dnah5 or Dnai1 mutant mouse respiratory epithelia disrupted motile cilia function. Together, these findings support an oligogenic disease model with broad relevance for further interrogating the genetic etiology of human ciliopathies.

Impaired Hepcidin Expression in Alpha-1-Antitrypsin Deficiency Causes Iron Overload and Cirrhosis

Genetic hemochromatosis is a complex oligogenic disease where relative deficiency of the iron hormone hepcidin is the underlying cause. Testing for common mutations in the hemochromatosis gene HFE is often unsufficient to explain iron overload because additional defects in other genes related to iron homeostasis or environmental factors can be present and modify disease manifestation. In clinical practice testing beyond mutations in HFE is rarely done.

A Conservative Assessment of the Major Genetic Causes of Idiopathic Chronic Pancreatitis: Data from a Comprehensive Analysis of PRSS1, SPINK1, CTRC and CFTR Genes in 253 Young French Patients

Idiopathic chronic pancreatitis (ICP) has traditionally been defined as chronic pancreatitis in the absence of any obvious precipitating factors (e.g. alcohol abuse) and family history of the disease. Studies over the past 15 years have revealed that ICP has a highly complex genetic architecture involving multiple gene loci. Here, we have attempted to provide a conservative assessment of the major genetic causes of ICP in a sample of 253 young French ICP patients. For the first time, conventional types of mutation (comprising coding sequence variants and variants at intron/exon boundaries) and gross genomic rearrangements were screened for in all four major pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR. For the purposes of the study, synonymous, intronic and 5'- or 3'-untranslated region variants were excluded from the analysis except where there was persuasive evidence of functional consequences. The remaining sequence variants/genotypes were classified into causative, contributory or neutral categories by consideration of (i) their allele frequencies in patient and normal control populations, (ii) their presumed or experimentally confirmed functional effects, (iii) the relative importance of their associated genes in the pathogenesis of chronic pancreatitis and (iv) gene-gene interactions wherever applicable. Adoption of this strategy allowed us to assess the pathogenic relevance of specific variants/genotypes to their respective carriers to an unprecedented degree. The genetic cause of ICP could be assigned in 23.7% of individuals in the study group. A strong genetic susceptibility factor was also present in an additional 24.5% of cases. Taken together, up to 48.2% of the studied ICP patients were found to display evidence of a genetic basis for their pancreatitis. Whereas these particular proportions may not be extrapolable to all ICP patients, the approach employed should serve as a useful framework for acquiring a better understanding of the role of genetic factors in causing this oligogenic disease.

Acrocallosal syndrome: Identification of a novel KIF7 mutation and evidence for oligogenic inheritance

ObjectiveAcrocallosal syndrome (ACLS) is a rare genetically heterogeneous disorder characterised by a variety of developmental anomalies including agenesis or hypoplasia of the corpus callosum. ACLS and the related disorder, hydrolethalus syndrome, have recently been reported to be caused by mutations in the KIF7 gene. In the present study we report a 15 year follow up of a consanguineous family with ACLS and the results of exome sequencing. ResultsA novel in-frame deletion KIF7 mutation (p.218-221del) was detected. This is the first deletion mutation in KIF7 described in ACLS and is predicted to disrupt the KIF7 protein within the kinesin motor domain. Also present, in addition to the homozygous KIF7 mutation, were loss of function variants in known ciliopathy genes; AHI1 (p.R830W), BBS2 (p.N70S) and BBS4 (p.M472V). ConclusionKIF7 has previously been demonstrated to regulate function of primary cilia and ACLS is now categorised as a ciliopathy – a group of disorders in which oligogenic disease is frequent. The finding of known loss of function variants in ciliopathy associated genes, AHI1, BBS2 and BBS4 in addition to KIF7 mutations provides evidence for oligogenic inheritance in ACLS and suggests that this might contribute to the phenotypic variability of KIF7-related disorders.

Oligogenic basis of isolated gonadotropin-releasing hormone deficiency.

Between the genetic extremes of rare monogenic and common polygenic diseases lie diverse oligogenic disorders involving mutations in more than one locus in each affected individual. Elucidating the principles of oligogenic inheritance and mechanisms of genetic interactions could help unravel the newly appreciated role of rare sequence variants in polygenic disorders. With few exceptions, however, the precise genetic architecture of oligogenic diseases remains unknown. Isolated gonadotropin-releasing hormone (GnRH) deficiency caused by defective secretion or action of hypothalamic GnRH is a rare genetic disease that manifests as sexual immaturity and infertility. Recent reports of patients who harbor pathogenic rare variants in more than one gene have challenged the long-held view that the disorder is strictly monogenic, yet the frequency and extent of oligogenicity in isolated GnRH deficiency have not been investigated. By systematically defining genetic variants in large cohorts of well-phenotyped patients (n = 397), family members, and unaffected subjects (n = 179) for the majority of known disease genes, this study suggests a significant role of oligogenicity in this disease. Remarkably, oligogenicity in isolated GnRH deficiency was as frequent as homozygosity/compound heterozygosity at a single locus (2.5%). Among the 22% of patients with detectable rare protein-altering variants, the likelihood of oligogenicity was 11.3%. No oligogenicity was detected among controls (P < 0.05), even though deleterious variants were present. Viewing isolated GnRH deficiency as an oligogenic condition has implications for understanding the pathogenesis of its reproductive and nonreproductive phenotypes; deciphering the etiology of common GnRH-related disorders; and modeling the genetic architecture of other oligogenic and multifactorial diseases.

PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome

Usher syndrome is a genetically heterogeneous recessive disease characterized by hearing loss and retinitis pigmentosa (RP). It frequently presents with unexplained, often intrafamilial, variability of the visual phenotype. Although 9 genes have been linked with Usher syndrome, many patients do not have mutations in any of these genes, suggesting that there are still unidentified genes involved in the syndrome. Here, we have determined that mutations in PDZ domain-containing 7 (PDZD7), which encodes a homolog of proteins mutated in Usher syndrome subtype 1C (USH1C) and USH2D, contribute to Usher syndrome. Mutations in PDZD7 were identified only in patients with mutations in other known Usher genes. In a set of sisters, each with a homozygous mutation in USH2A, a frame-shift mutation in PDZD7 was present in the sister with more severe RP and earlier disease onset. Further, heterozygous PDZD7 mutations were present in patients with truncating mutations in USH2A, G protein-coupled receptor 98 (GPR98; also known as USH2C), and an unidentified locus. We validated the human genotypes using zebrafish, and our findings were consistent with digenic inheritance of PDZD7 and GPR98, and with PDZD7 as a retinal disease modifier in patients with USH2A. Pdzd7 knockdown produced an Usher-like phenotype in zebrafish, exacerbated retinal cell death in combination with ush2a or gpr98, and reduced Gpr98 localization in the region of the photoreceptor connecting cilium. Our data challenge the view of Usher syndrome as a traditional Mendelian disorder and support the reclassification of Usher syndrome as an oligogenic disease.

Genome scan of venous thrombosis in a pedigree with protein C deficiency

Kindred Vermont II has a high frequency of venous thrombosis, occurring primarily in pedigree members with type I protein C deficiency due to a 3363 inserted (Ins) C mutation in exon 6 of the protein C gene. However, only a subset of 3363 InsC carriers have suffered thrombotic episodes, suggesting that the increased risk of thrombosis results upon the co-occurrence of 3363 InsC with a second, unknown, thrombophilic mutation that segregates independently within the pedigree. To test this hypothesis and to localize the co-occurring gene, we performed a genome scan of venous thrombosis in Kindred Vermont II. Non-parametric linkage statistics identified three potential gene locations, on chromosomes 11q23 (nominal P < 0.0001), 18p11.2-q11.2 (P < 0.0007), and 10p12 (P < 0.0003), supporting the presence of at least one additional thrombophilic mutation in the pedigree. Identification of the unknown mutation(s) promises to reveal a new genetic risk factor for thrombophilia, contribute to our understanding of the blood clotting mechanism, and expand our knowledge of the diversity of oligogenic disease.

Genetic Interaction of BBS1 Mutations with Alleles at Other BBS Loci Can Result in Non-Mendelian Bardet-Biedl Syndrome

Bardet-Biedl syndrome is a genetically and clinically heterogeneous disorder caused by mutations in at least seven loci (BBS1-7), five of which are cloned (BBS1, BBS2, BBS4, BBS6, and BBS7). Genetic and mutational analyses have indicated that, in some families, a combination of three mutant alleles at two loci (triallelic inheritance) is necessary for pathogenesis. To date, four of the five known BBS loci have been implicated in this mode of oligogenic disease transmission. We present a comprehensive analysis of the spectrum, distribution, and involvement in non-Mendelian trait transmission of mutant alleles in BBS1, the most common BBS locus. Analyses of 259 independent families segregating a BBS phenotype indicate that BBS1 participates in complex inheritance and that, in different families, mutations in BBS1 can interact genetically with mutations at each of the other known BBS genes, as well as at unknown loci, to cause the phenotype. Consistent with this model, we identified homozygous M390R alleles, the most frequent BBS1 mutation, in asymptomatic individuals in two families. Moreover, our statistical analyses indicate that the prevalence of the M390R allele in the general population is consistent with an oligogenic rather than a recessive model of disease transmission. The distribution of BBS oligogenic alleles also indicates that all BBS loci might interact genetically with each other, but some genes, especially BBS2 and BBS6, are more likely to participate in triallelic inheritance, suggesting a variable ability of the BBS proteins to interact genetically with each other.

Association and linkage for age at onset of a common oligogenic disease using genetic variance component models.

The aims of our analysis were: (1) to investigate association of single nucleotide polymorphisms (SNPs) and other covariates with age at onset in the simulated Genetic Analysis Workshop (GAW) 12 general population data, and (2) to use the polygenic random effects estimated during model fitting (sigma squared A random effects) as input to a Haseman-Elston linkage analysis. The association analyses used genetic variance component models in a generalized linear mixed models framework and were fitted using Gibbs sampling. This method successfully detected the only three sequenced genes that were also major genes. The single-point linkage analysis used all markers provided. Regions of linkage were found close to all four of the sites of major genes that explained a non-trivial component of the variance of age at onset. In all four cases the linkage peak fell within 5 cM of the true location. In three cases the peak significance was p < 0.01.

A single nucleotide polymorphism in exon 1 of cytotoxic T-lymphocyte-associated-4 (CTLA-4) is not associated with rheumatoid arthritis.

Rheumatoid arthritis (RA) is an oligogenic disease for which only one susceptibility locus has been identified to date. Genes involved in T-cell regulation are potential candidates. Association to cytotoxic T-lymphocyte-associated-4 (CTLA-4) protein, a negative regulator of T-cell activation, has previously been described in a subset of German RA patients carrying the HLA DRB1*0401 subtype. Linkage and association with another oligogenic autoimmune disease, insulin-dependent diabetes mellitus, has also been described in a Spanish population. To investigate the association of CTLA-4 with RA in Spanish and UK subjects. Caucasoid UK RA patients (n=192), UK controls (n=96), Spanish RA patients (n=136) and Spanish controls (n=144) were typed for an A/G bi-allelic polymorphism in exon 1 of CTLA-4 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) (enzyme). No significant differences in the frequency of the G allele or the GG genotype were found in either the UK or Spanish RA patients compared with controls. No significant evidence was found of an association between RA and CTLA-4.

Multipoint Oligogenic Analysis of Age-at-Onset Data with Applications to Alzheimer Disease Pedigrees

It is usually difficult to localize genes that cause diseases with late ages at onset. These diseases frequently exhibit complex modes of inheritance, and only recent generations are available to be genotyped and phenotyped. In this situation, multipoint analysis using traditional exact linkage analysis methods, with many markers and full pedigree information, is a computationally intractable problem. Fortunately, Monte Carlo Markov chain sampling provides a tool to address this issue. By treating age at onset as a right-censored quantitative trait, we expand the methods used by Heath (1997) and illustrate them using an Alzheimer disease (AD) data set. This approach estimates the number, sizes, allele frequencies, and positions of quantitative trait loci (QTLs). In this simultaneous multipoint linkage and segregation analysis method, the QTLs are assumed to be diallelic and to interact additively. In the AD data set, we were able to localize correctly, quickly, and accurately two known genes, despite the existence of substantial genetic heterogeneity, thus demonstrating the great promise of these methods for the dissection of late-onset oligogenic diseases.

Complex Segregation Analyses: Uses and Limitations

Complex segregation analysis (CSA) is a general method for evaluating the transmission of a trait within pedigrees. It proceeds by testing models of varying degrees of generality, both to determine whether a Mendelian locus is likely to exert a large effect on the phenotype of interest and to estimate the magnitude of genetic sources of variation in the trait. This information is valuable both as a prelude to linkage analysis, which generally assumes Mendelian transmission, and in providing a model on which to base parametric linkage methods.