Candidate Gene Studies Research Articles

Reevaluating the Genetic Contribution of Monogenic Dilated Cardiomyopathy.

Dilated cardiomyopathy (DCM) is genetically heterogeneous, with >100 purported disease genes tested in clinical laboratories. However, many genes were originally identified based on candidate-gene studies that did not adequately account for background population variation. Here we define the frequency of rare variation in 2538 patients with DCM across protein-coding regions of 56 commonly tested genes and compare this to both 912 confirmed healthy controls and a reference population of 60 706 individuals to identify clinically interpretable genes robustly associated with dominant monogenic DCM. We used the TruSight Cardio sequencing panel to evaluate the burden of rare variants in 56 putative DCM genes in 1040 patients with DCM and 912 healthy volunteers processed with identical sequencing and bioinformatics pipelines. We further aggregated data from 1498 patients with DCM sequenced in diagnostic laboratories and the Exome Aggregation Consortium database for replication and meta-analysis. Truncating variants in TTN and DSP were associated with DCM in all comparisons. Variants in MYH7, LMNA, BAG3, TNNT2, TNNC1, PLN, ACTC1, NEXN, TPM1, and VCL were significantly enriched in specific patient subsets, with the last 2 genes potentially contributing primarily to early-onset forms of DCM. Overall, rare variants in these 12 genes potentially explained 17% of cases in the outpatient clinic cohort representing a broad range of adult patients with DCM and 26% of cases in the diagnostic referral cohort enriched in familial and early-onset DCM. Although the absence of a significant excess in other genes cannot preclude a limited role in disease, such genes have limited diagnostic value because novel variants will be uninterpretable and their diagnostic yield is minimal. In the largest sequenced DCM cohort yet described, we observe robust disease association with 12 genes, highlighting their importance in DCM and translating into high interpretability in diagnostic testing. The other genes analyzed here will need to be rigorously evaluated in ongoing curation efforts to determine their validity as Mendelian DCM genes but have limited value in diagnostic testing in DCM at present. This data will contribute to community gene curation efforts and will reduce erroneous and inconclusive findings in diagnostic testing.

P136 EPSTEIN-BARR VIRUS TRANSCRIPTION CO-FACTORS BIND TO MANY INFLAMMATORY BOWEL DISEASE RISK LOCI

Abstract Objective IBD is a chronic inflammatory disorder of the GI tract with complex etiology that involves both genetic variants and environmental factors. Several viruses and bacteria have been suggested as potential causes of the disease. The clinical course of IBD appears to be influenced by EBV tissue infection. With a prevalence of >90% in the adult human population, EBV infection is nearly ubiquitous. We reported that the EBV transcription co-factor EBNA2 was concentrated in the risk loci of IBD relative to the remainder of the genome (Pc=1.24E-13, (RR) = 3.33, Nature Genetics 50:699, 2018). The objective of this study was to determine whether new data and studies made available since the data used for our 2018 study further supported the possibility that EBV was related to some IBD as a potential etiologic agent. Methods Genomic approaches offer previously unavailable perspectives for understanding disease mechanisms. The previous analysis was based upon the 9 viral transcription factor and co-factor (TF) datasets available in human cells in 2015.Of the 52 now available there are 29 from EBV. The number of established IBD loci qualifying for analysis has expanded from 112 in 2015 to 324 available now. We applied simulation analysis to assess statistical significance of TF associations with IBD risk loci using RELI (Regulatory Element Locus Intersection) (Nat Genet 50:699, 2018). RELI tests the probability of the observed association by the count of intersections of the same variant from two sources. We extracted 700 SNPs in European ancestry from 93 published GWAS and 350 additional candidate gene studies for IBD. All variants with linkage disequilibrium r2>0.8 of the best variant were included, while loci with r2>0.2 with a more highly significant locus were excluded. Results Among the 52 viral TF datasets, 139 of the 324 IBD loci were occupied by EBNALP (RR=2.08793, Pc=3.7321E-23), 113 by EBNA3C (RR=2.35113, Pc=2.84678E-22), 88 loci by EBNA2 (RR=3.2, Pc=7.8E-32) and 28 loci by EBNA3ABC, which used an antibody that did not distinguish between EBNA3 subtypes. Analysis of 11,535 human TF ChIP-seq datasets produced 1578 with strong associations (p<E-6) with IBD risk loci. The locus intersections of the three EBV gene products optimally clustered at 150 IBD loci (46%) with a set of 26 human TFs (p<2E-308), thereby nominating these loci as potentially having EBV-dependent mechanisms that alter genetic risk for IBD. The human TFs were enriched for (ChIP-seq) data obtained from EBV-infected B lymphocyte cell line (OR = 10.12425329, Chi-squared = 241.2925605) Moreover, the human TFs that participate in the super-enhancers that form in the latency III EBV infected and transformed B cell are also concentrated among the statistically significant associations (p<E-6) with the IBD risk loci (OR) = 2.9448, P = 10E-7). Conclusion These preliminary findings nominate EBV for a role in the pathogenesis and etiology of IBD by mechanisms operating in transformed B cells through the latency III EBV program of viral gene expression.

Genetics of Circadian and Sleep Measures in Adults: Implications for Sleep Medicine

In this review, we comprehensively discuss recent reports of heritability and genetic associations using candidate gene and genome-wide association (GWA) approaches in circadian and sleep phenotypes in adults, including chronotype (morningness-eveningness), sleep duration and daytime sleepiness, circadian rhythm sleep-wake disorders, and insomnia. Recent findings derive from GWA studies with objective measures and candidate gene studies examining the role of genetic ancestry and health disparities for sleep and circadian measures. The discovery of key, novel genetic markers using various methods has critical implications for future research in terms of identification, treatment, and countermeasures in the field of sleep medicine.

Genetics of Degenerative Cervical Myelopathy: A Systematic Review and Meta-Analysis of Candidate Gene Studies.

Degenerative cervical myelopathy (DCM) is estimated to be the most common cause of adult spinal cord impairment. Evidence that is suggestive of a genetic basis to DCM has been increasing over the last decade. A systematic search was conducted in MEDLINE, EMBASE, Cochrane, and HuGENet databases from their origin up to 14th December 2019 to evaluate the role of single genes in DCM in its onset, clinical phenotype, and response to surgical intervention. The initial search yielded 914 articles, with 39 articles being identified as eligible after screening. We distinguish between those contributing to spinal column deterioration and those contributing to spinal cord deterioration in assessing the evidence of genetic contributions to DCM. Evidence regarding a total of 28 candidate genes was identified. Of these, 22 were found to have an effect on the radiological onset of spinal column disease, while 12 genes had an effect on clinical onset of spinal cord disease. Polymorphisms of eight genes were found to have an effect on the radiological severity of DCM, while three genes had an effect on clinical severity. Polymorphisms of six genes were found to have an effect on clinical response to surgery in spinal cord disease. There are clear genetic effects on the development of spinal pathology, the central nervous system (CNS) response to bony pathology, the severity of both bony and cord pathology, and the subsequent response to surgical intervention. Work to disentangle the mechanisms by which the genes that are reviewed here exert their effects, as well as improved quality of evidence across diverse populations is required for further investigating the genetic contribution to DCM.

Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer

Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.

Do Genomic Factors Play a Role in Diabetic Retinopathy?

Although there is strong clinical evidence that the control of blood glucose, blood pressure, and lipid level can prevent and slow down the progression of diabetic retinopathy (DR) as shown by landmark clinical trials, it has been shown that these factors only account for 10% of the risk for developing this disease. This suggests that other factors, such as genetics, may play a role in the development and progression of DR. Clinical evidence shows that some diabetics, despite the long duration of their diabetes (25 years or more) do not show any sign of DR or show minimal non-proliferative diabetic retinopathy (NPDR). Similarly, not all diabetics develop proliferative diabetic retinopathy (PDR). So far, linkage analysis, candidate gene studies, and genome-wide association studies (GWAS) have not produced any statistically significant results. We recently initiated a genomics study, the Diabetic Retinopathy Genetics (DRGen) Study, to examine the contribution of rare and common variants in the development of different phenotypes of DR, as well as their responsiveness to anti-VEGF treatment in diabetic macular edema (DME). Our preliminary findings reveal a novel set of genetic variants involved in the angiogenesis and inflammatory pathways that contribute to DR progression or protection. Further investigation of variants can help to develop novel biomarkers and lead to new therapeutic targets in DR.

Commentary: lessons from molecular genetic studies on reporting false-positive results.

Poor replication of published research results is the subject of debate. A common problem is the failure to adequately account for multiple testing issues. In this regard, the evolution of mapping studies to identify genetic risk factors for common diseases has been instructive. Large genome-wide association studies (GWAS) reliably detect the genetic factors with small effects that contribute to risk for many common diseases. GWAS superseded candidate gene studies from the previous decade and looking back, almost no genetic risk factors reported from earlier candidate gene studies replicate in the GWAS results. Candidate gene studies often used small samples and failed to appreciate and adequately account for the multiple testing issues. The failure to replicate results from most candidate gene studies highlights the importance of study power and appropriate statistical analysis to prevent publication of false-positive results.

The emergent phenomenon of aspirin resistance: insights from genetic association studies.

Despite the clinical benefits of aspirin, the interindividual variation in response to this antiplatelet drug is considerable. The manifestation of aspirin resistance (AR) is frequently observed, although this complex process remains poorly understood. While AR etiology is likely to be multifactorial, genetic factors appear to be preponderant. According to several genetic association studies, both genome-wide and candidate gene studies, numerous SNPs in cyclooxygenase, thromboxane and platelet receptors-related genes have been identified as capable of negatively affecting aspirin action. Thus, it is essential to understand the clinical relevance of AR-related SNPs as potential predictive and prognostic biomarkers as they may be essential to defining the AR phenotype.

Association between the MUC1 rs4072037 Polymorphism and Risk of Gastric Cancer and Clinical Outcomes.

PurposeMucin 1 (MUC1) was identified as a gastric cancer (GC) susceptibility gene by genome-wide association studies in Asians and candidate gene studies in Europeans. This study aimed to investigate the association between the MUC1 rs4072037 polymorphism and GC in terms of the Lauren classification and long-term clinical outcomes.Materials and MethodsA total of 803 patients with GC and 816 unrelated healthy controls were enrolled in the study. The association between the MUC1 rs4072037 variant and GC histological types and clinical outcomes, including tumor recurrence and prognosis was investigated.ResultsThe major A allele of rs4072037 was associated with increased GC risk (P<0.05). In subtype analysis, the association was most significant for diffuse-type GC (P<0.05) and in a dominant model (P<0.05), whereas there was no association with intestinal-type GC (P>0.05). Cox proportional hazards analysis revealed the heterozygote AG rs4072037 allele as an independent risk factor influencing tumor recurrence and disease-related death in diffuse-type GC (P<0.05). but not in intestinal-type GC (P>0.05).ConclusionsThe exonic single nucleotide polymorphism rs4072037 in MUC1 was associated with diffuse-type GC and was an independent risk factor influencing tumor recurrence and disease-related death in diffuse-type GC.

Genetics in Atopic Dermatitis: Historical Perspective and Future Prospects.

Atopic dermatitis (AD) is a common, complex trait, arising from the interplay of multiple genetic and environmental factors. This review provides an overview of developments in the field of AD genetics. AD shows high heritability; strategies to investigate genetic risk include linkage, candidate gene studies, genome-wide association and animal modelling. Loss-of-function mutations in FLG, encoding the skin barrier protein filaggrin, remain the strongest genetic risk factor identified for AD, but variants influencing skin and systemic immune function are also important. AD is at the forefront of genetic research, from large-scale population studies to in vitro models and detailed molecular analyses. An understanding of genetic risk factors has considerably improved knowledge of mechanisms leading to atopic skin inflammation. Together this work has identified avenues for therapeutic intervention, but further research is needed to fully realise the opportunities of personalised medicine for this complex disease, to optimise patient benefit.

Diabetes and Genetics: A Relationship Between Genetic Risk Alleles, Clinical Phenotypes and Therapeutic Approaches.

Unveiling human genome through successful completion of Human Genome Project and International HapMap Projects with the advent of state of art technologies has shed light on diseases associated genetic determinants. Identification of mutational landscapes such as copy number variation, single nucleotide polymorphisms or variants in different genes and loci have revealed not only genetic risk factors responsible for diseases but also region(s) playing protective roles. Diabetes is a global health concern with two major types - type 1 diabetes (T1D) and type 2 diabetes (T2D). Great progress in understanding the underlying genetic predisposition to T1D and T2D have been made by candidate gene studies, genetic linkage studies, genome wide association studies with substantial number of samples. Genetic information has importance in predicting clinical outcomes. In this review, we focus on recent advancement regarding candidate gene(s) associated with these two traits along with their clinical parameters as well as therapeutic approaches perceived. Understanding genetic architecture of these disease traits relating clinical phenotypes would certainly facilitate population stratification in diagnosing and treating T1D/T2D considering the doses and toxicity of specific drugs.

Genetic basis of otosclerosis

Introduction. Otosclerosis is a disorder of the bone labyrinth and stapes resulting in conductive hearing loss. The genetic basis of otosclerosis still remains unknown. We aimed at reporting a comprehensive review of up-to-date knowledge on genetic basis of otosclerosis. Methods. Narrative literature review was undertaken to summarize the data about genetics of otosclerosis. Results. Genetics of otosclerosis has not been studied extensively and the literature on this topic is scarce. However, knowledge of genetic basis of otosclerosis is recently increasing. We have presented an overview of the knowledge of association of genetic markers with otosclerosis, gained from linkage analyses, candidate-gene studies, and modern high-throughput genomic studies. Conclusion. Due to its complex pathophysiology, otosclerosis is not a disease whose genetic base will be easily understood. Multiple omics analysis and bioinformatics will lead to elucidation of genetic basis of otosclerosis.

The Role of Epigenetic Dysregulation in Suicidal Behaviors.

Suicidal behaviors have been associated with both heritable genetic variables and environmental risk factors. Epigenetic processes, such as DNA methylation, have important roles in mediating the effects of the environment on behavior. Dysregulation of these processes has been observed in many psychiatric disorders, and evidence suggests that they may also be involved in suicidal behaviors. Herein, we have summarized candidate gene and epigenome-wide studies which have investigated DNA methylation in relation to suicidal behaviors, as well as discussed some of the limitations of the field to date.

Clinical features of chronic bronchitis and genetic risk factors for the development of chronic obstructive pulmonary disease in adolescent smokers

The aim is to study the clinical features of the course of CB in adolescent smokers and to study the genetic risk factors for the development of COPD. Materials and methods: There were examined 40 adolescent smokers with CB, 30 never-smokers adolescents with CB and 37 healthy adolescents smokers (control group). The study included the collection of anamnesis, objective examination. calculation of the smoking index and the «pack/year», molecular genetic investigations. Results: It was proved that smoking leads to the development of chronic bronchitis as early as adolescence and affects its course, increasing the frequency and duration of exacerbations. We identified an association of the 2G/2G genotype of MMP1 gene with the development of chronic bronchitis in adolescent smokers. The TT genotype of CYP1A1 gene may be considered as a possible sustainability factor for the development of chronic bronchitis in adolescent smokers. Conclusions: The study of candidate genes for COPD in childhood and adolescence will facilitate the early detection of high-risk groups in the formation of this pathology, which will allow doctors to take the necessary preventive measures.

Genetic disorder-related candidate gene studies in Hanwoo

Genetic disorder-related candidate gene studies in Hanwoo

Genetic variations associated with spleen-yang deficiency pattern of non-alcoholic fatty liver disease: A candidate gene study

IntroductionIn traditional Chinese medicine (TCM) clinical practice, Spleen-Yang deficiency pattern (SYDP) is the basic and core pattern present in non-alcoholic fatty liver disease (NAFLD). The aim of this study was to investigate the role of the susceptibile gene polymorphisms for NAFLD in SYDP in a Chinese Han population. MethodsA total of 12 single nucleotide polymorphisms (SNPs) were genotyped in 341 healthy subjects for control group and 341 subjects for NAFLD group (including 163 subjects for SYDP group and 178 subjects for non-SYDP group). Hardy-Weinberg equilibrium, allele and genotype frequency distribution, genotype association analysis, linkage disequilibrium (LD) and haplotype analysis were calculated. ResultsBetween the SYDP group and the control group: rs1260326, rs780094 and rs780093 in glucokinase regulator (GCKR) demonstrated significant differences in allele and genotype frequency distribution. Genotype association analysis showed the three SNPs all increased SYDP risk after adjustment for confounding factors. There was no significant deviation of the three SNPs between the non-SYDP group and the control group. The three SNPs were identified as a strong LD block and the haplotype TTT increased SYDP risk. In SYDP group, the allele C of the three SNPs showed a decreasing trend with an increase in the degree of SYDP. Additionally, the SYDP subjects with the mutant type CT/TT of rs1260326 and rs780094 had higher SYDP scores. ConclusionsThe rs1260326, rs780094 and rs780093 in GCKR were significantly associated with SYDP in NAFLD, as well as the degree of SYDP. GCKR polymorphisms might be a potential genetic biomarker of SYDP, as well as NAFLD.

A candidate gene analysis and GWAS for genes associated with maternal nondisjunction of chromosome 21.

Human nondisjunction errors in oocytes are the leading cause of pregnancy loss, and for pregnancies that continue to term, the leading cause of intellectual disabilities and birth defects. For the first time, we have conducted a candidate gene and genome-wide association study to identify genes associated with maternal nondisjunction of chromosome 21 as a first step to understand predisposing factors. A total of 2,186 study participants were genotyped on the HumanOmniExpressExome-8v1-2 array. These participants included 749 live birth offspring with standard trisomy 21 and 1,437 parents. Genotypes from the parents and child were then used to identify mothers with nondisjunction errors derived in the oocyte and to establish the type of error (meiosis I or meiosis II). We performed a unique set of subgroup comparisons designed to leverage our previous work suggesting that the etiologies of meiosis I and meiosis II nondisjunction differ for trisomy 21. For the candidate gene analysis, we selected genes associated with chromosome dynamics early in meiosis and genes associated with human global recombination counts. Several candidate genes showed strong associations with maternal nondisjunction of chromosome 21, demonstrating that genetic variants associated with normal variation in meiotic processes can be risk factors for nondisjunction. The genome-wide analysis also suggested several new potentially associated loci, although follow-up studies using independent samples are required.

BIN1 rs744373 variant shows different association with Alzheimer\u2019s disease in Caucasian and Asian populations

BackgroundThe association between BIN1 rs744373 variant and Alzheimer’s disease (AD) had been identified by genome-wide association studies (GWASs) as well as candidate gene studies in Caucasian populations. But in East Asian populations, both positive and negative results had been identified by association studies. Considering the smaller sample sizes of the studies in East Asian, we believe that the results did not have enough statistical power.ResultsWe conducted a meta-analysis with 71,168 samples (22,395 AD cases and 48,773 controls, from 37 studies of 19 articles). Based on the additive model, we observed significant genetic heterogeneities in pooled populations as well as Caucasians and East Asians. We identified a significant association between rs744373 polymorphism with AD in pooled populations (P = 5 × 10− 07, odds ratio (OR) = 1.12, and 95% confidence interval (CI) 1.07–1.17) and in Caucasian populations (P = 3.38 × 10− 08, OR = 1.16, 95% CI 1.10–1.22). But in the East Asian populations, the association was not identified (P = 0.393, OR = 1.057, and 95% CI 0.95–1.15). Besides, the regression analysis suggested no significant publication bias. The results for sensitivity analysis as well as meta-analysis under the dominant model and recessive model remained consistent, which demonstrated the reliability of our finding.ConclusionsThe large-scale meta-analysis highlighted the significant association between rs744373 polymorphism and AD risk in Caucasian populations but not in the East Asian populations.

The Search for the Genes of Vasovagal Syncope.

Only humans faint, and not all do so. Syncope tends to recur, and the predisposition to syncope can persist over many decades. Observations such as these have suggested that there may be a genetic predisposition to vasovagal syncope. It seems to have a high prevalence in some families; having a parent who faints increases the likelihood of an offspring fainting, and this is increased even further if both biological parents faint. Numerous studies have correlated a number of genotypes with positive tilt tests. However, the control subjects are usually those who faint, but have negative tilt tests, making the conclusions about association with the clinical phenotype less certain. Twin studies, highly focused genome-wide association studies, and gene duplicate studies all suggest there are sites in the genome that associate with vasovagal syncope, although the specific genes, pathways, and proteins are unknown. A recent large, candidate gene study of kindreds with high, multigenerational prevalence of the vasovagal syncope identified 3 genes that associate with vasovagal syncope. Our understanding of the genetic correlates of vasovagal syncope is in its infancy, with much to be understood.

Candidate genes-association study to identify loci related to oleic acid in Brassica napus using SNP markers and their heterologous expression in yeast

Brassica napus (rapeseed) serves as a main source of edible oil, and the oil's quality is mainly determined by the relative proportions of fatty acids. A high oleic acid concentration in B. napus oil increases its shelf life and oxidative stability. Therefore, attaining a high oleic acid concentration is necessary to enhance the nutritional quality of rapeseed oil. Here, an association study of candidate genes was conducted using a population of 324 genetically diverse rapeseed accessions, and several loci related to oleic acid content were identified. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae to assess their functions, and the promising candidate loci were validated using single nucleotide polymorphic markers in an independent inbred population. The results increased our understanding of fatty acid metabolism in B. napus. Moreover, these findings may assist in marker-based breeding efforts to improve the fatty acid composition and quality of B. napus oil.