scholarly journals P18 Investigating the role of rare genetic variants and susceptibility to juvenile idiopathic arthritis highlights the importance of monogenic disease genes

Rheumatology ◽  
2020 ◽  
Vol 59 (Supplement_2) ◽  
Author(s):  
Melissa K Tordoff ◽  
Tracy A Briggs ◽  
Samantha L Smith ◽  
Annie Yarwood ◽  
Wendy Thomson ◽  
...  
Keyword(s):  
Risk Factors ◽  
Juvenile Idiopathic Arthritis ◽  
Genetic Variants ◽  
Complex Disease ◽  
Rare Variants ◽  
Mevalonate Kinase ◽  
Common Complex Disease ◽  
Juvenile Onset ◽  
Rare Genetic Variants

Abstract Background Juvenile idiopathic arthritis (JIA) is a rheumatic disease, onset before the age of sixteen. JIA is a common complex disease, with contributions from both genetic and environmental risk factors. However, given the young age of onset for JIA, it is possible that genetic risk factors influence susceptibility to a greater extent than environmental risk factors. While several susceptibility loci have been identified for JIA, they are mainly genetic variants that are common in the population. The role of rare genetic variants has not yet been fully explored in JIA. Therefore, the aims of this research were to use rare (<5%MAF) variant based analysis to further define the genetic architecture of JIA. Methods A total of 2,162 UK JIA cases were genotyped using the Illumina HumanCoreExome array and the Understanding Society’s UK household longitudinal study provided the genotype data for 9196 controls. Single variant analysis was used to calculate the association of variants to JIA susceptibility. Gene-based aggregation analysis, specifically the SKAT-O method, were used to calculate the association of whole gene regions to JIA cases. This gene-based aggregation method increases the statistical power of associations, which is valuable when attempting to identify rare variants. Study-wide significance for this research was calculated using a Bonferroni corrected threshold (P = 3.34x10-6). Results Several strongly associated candidate gene regions were identified using SKAT-O analysis. Firstly, the region mevalonate kinase (MVK) (P = 3.95x10-10) was found to be strongly associated. MVK has been reported in mevalonate kinase deficiency, a rare juvenile disease with a phenotype akin to systemic JIA. PYCR1 (P = 1.97x10-9) was an additional region of interest. Variants in this region have been reported in geroderma osteodysplasticum; a disease that results in dysplasia of the hips, hyperextensible joints and skeletal changes. The region WISP3 (P = 8.52x10-9) was also strongly associated. Variants from this region have previously been reported in progressive pseudorheumatoid dysplasia; a disease that can be clinically misdiagnosed with JIA due to similarities in phenotypes. Furthermore, LILRA2 (P = 2.89x10-7) presented as a strong candidate region, with the gene being upregulated in synovial tissue of rheumatoid arthritis patients. Conclusion This analysis has identified promising candidate genes that influence susceptibility to JIA and highlights two key points. Firstly, gene-burden tests of rare variants have the potential to identify novel susceptibility genes for juvenile-onset disease. While MVK and WISP3 have previously been reported to be associated with JIA, these associations were modest, and the current study provides compelling evidence to support their importance. Secondly, the results highlight the importance of investigating the contribution of monogenic genes in juvenile-onset common complex disease. Disclosures M.K. Tordoff None. T.A. Briggs None. S.L. Smith None. A. Yarwood None. W. Thomson None. J. Bowes None.

scholarly journals Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson’s disease

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Muhammad Aslam ◽  
Nirosiya Kandasamy ◽  
Anwar Ullah ◽  
Nagarajan Paramasivam ◽  
Mehmet Ali Öztürk ◽  
...  
Keyword(s):  
Risk Factors ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Genetic Variants ◽  
Rare Variants ◽  
Alpha Synuclein ◽  
Younger Age ◽  
Targeted Treatments ◽  
Genes Encoding ◽  
Rare Genetic Variants

AbstractRare variants in the beta-glucocerebrosidase gene (GBA1) are common genetic risk factors for alpha synucleinopathy, which often manifests clinically as GBA-associated Parkinson’s disease (GBA-PD). Clinically, GBA-PD closely mimics idiopathic PD, but it may present at a younger age and often aggregates in families. Most carriers of GBA variants are, however, asymptomatic. Moreover, symptomatic PD patients without GBA variant have been reported in families with seemingly GBA-PD. These observations obscure the link between GBA variants and PD pathogenesis and point towards a role for unidentified additional genetic and/or environmental risk factors or second hits in GBA-PD. In this study, we explored whether rare genetic variants may be additional risk factors for PD in two families segregating the PD-associated GBA1 variants c.115+1G>A (ClinVar ID: 93445) and p.L444P (ClinVar ID: 4288). Our analysis identified rare genetic variants of the HSP70 co-chaperone DnaJ homolog subfamily B member 6 (DNAJB6) and lysosomal protein prosaposin (PSAP) as additional factors possibly influencing PD risk in the two families. In comparison to the wild-type proteins, variant DNAJB6 and PSAP proteins show altered functions in the context of cellular alpha-synuclein homeostasis when expressed in reporter cells. Furthermore, the segregation pattern of the rare variants in the genes encoding DNAJB6 and PSAP indicated a possible association with PD in the respective families. The occurrence of second hits or additional PD cosegregating rare variants has important implications for genetic counseling in PD families with GBA1 variant carriers and for the selection of PD patients for GBA targeted treatments.

scholarly journals Identification of rare genetic variants in Juvenile Idiopathic Arthritis using whole exome sequencing

2015 ◽  
Vol 13 (S1) ◽  
Author(s):  
E Sanchez ◽  
S Grandemange ◽  
F Tran Mau-Them ◽  
P Louis-Plence ◽  
A Carbasse ◽  
...  
Keyword(s):  
Juvenile Idiopathic Arthritis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Variants ◽  
Whole Exome ◽  
Rare Genetic Variants

scholarly journals Rare variants in axonogenesis genes connect three families with sound–color synesthesia

2018 ◽  
Vol 115 (12) ◽  
pp. 3168-3173 ◽  
Author(s):  
Amanda K. Tilot ◽  
Katerina S. Kucera ◽  
Arianna Vino ◽  
Julian E. Asher ◽  
Simon Baron-Cohen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rare Variants ◽  
Autism Spectrum ◽  
Sensory Experiences ◽  
Limited Success ◽  
Whole Exome ◽  
Rare Genetic Variants ◽  
Sound Color ◽  
Stimulation Of

Synesthesia is a rare nonpathological phenomenon where stimulation of one sense automatically provokes a secondary perception in another. Hypothesized to result from differences in cortical wiring during development, synesthetes show atypical structural and functional neural connectivity, but the underlying molecular mechanisms are unknown. The trait also appears to be more common among people with autism spectrum disorder and savant abilities. Previous linkage studies searching for shared loci of large effect size across multiple families have had limited success. To address the critical lack of candidate genes, we applied whole-exome sequencing to three families with sound–color (auditory–visual) synesthesia affecting multiple relatives across three or more generations. We identified rare genetic variants that fully cosegregate with synesthesia in each family, uncovering 37 genes of interest. Consistent with reports indicating genetic heterogeneity, no variants were shared across families. Gene ontology analyses highlighted six genes—COL4A1, ITGA2, MYO10, ROBO3, SLC9A6, and SLIT2—associated with axonogenesis and expressed during early childhood when synesthetic associations are formed. These results are consistent with neuroimaging-based hypotheses about the role of hyperconnectivity in the etiology of synesthesia and offer a potential entry point into the neurobiology that organizes our sensory experiences.

scholarly journals Oxidative Stress Inside the Pathogenesis of Ascending Aorta Aneurysms: A Clearer Vision for Identifying Promising Biomarkers and Therapeutic Targets

2021 ◽  
Author(s):  
Carmela Balistreri ◽  
Calogera Pisano ◽  
Giovanni Ruvolo
Keyword(s):  
Oxidative Stress ◽  
Risk Factors ◽  
Genetic Variants ◽  
Complex Disease ◽  
Ascending Aorta ◽  
Oxygen Species ◽  
Aorta Aneurysm ◽  
Independent Risk Factors ◽  
The Impact ◽  
And Oxidative Stress

Ascending aorta aneurysm (AsAA) is a complex disease, currently defined an inflammatory disease. In the sporadic form, AsAA has, indeed, a complex physiopathology with a strong inflammatory basis, significantly modulated by genetic variants in innate/inflammatory genes, acting as independent risk factors and as largely evidenced in our recent studies performed during the last 10 years. Based on these premises, here, we want to revise the impact of reactive oxygen species (ROS) and oxidative stress on AsAA pathophysiology and consequently on the onset and progression of sporadic AsAA. This might consent to add other important pieces in the intricate puzzle of the pathophysiology of this disease with the translational aim to identify biomarkers and targets to apply in the complex management of AsAA, by facilitating the AsAA diagnosis currently based only on imaging evaluations, and the treatment exclusively founded on surgery approaches.

scholarly journals Causal Inference in Psychopathology: A Systematic Review of Mendelian Randomisation Studies Aiming to Identify Environmental Risk Factors for Psychopathology

2016 ◽  
Vol a4 (1) ◽  
pp. 4-25 ◽  
Author(s):  
Jean-Baptiste Pingault ◽  
Charlotte A. M. Cecil ◽  
Joseph Murray ◽  
Marcus R Munafò ◽  
Essi Viding
Keyword(s):  
Risk Factors ◽  
Systematic Review ◽  
Causal Inference ◽  
Genetic Variants ◽  
Antisocial Behaviour ◽  
Smoking Initiation ◽  
Mendelian Randomisation ◽  
Future Directions ◽  
Effective Interventions

Psychopathology represents a leading cause of disability worldwide. Effective interventions need to target risk factors that are causally related to psychopathology. In order to distinguish between causal and spurious risk factors, it is critical to account for environmental and genetic confounding. Mendelian randomisation studies use genetic variants that are independent from environmental and genetic confounders in order to strengthen causal inference. We conducted a systematic review of studies (N = 19) using Mendelian randomisation to examine the causal role of putative risk factors for psychopathology-related outcomes including depression, anxiety, psychological distress, schizophrenia, substance abuse/antisocial behaviour, and smoking initiation. The most commonly examined risk factors in the reviewed Mendelian randomisation studies were smoking, alcohol use and body mass index. In most cases, risk factors were strongly associated with psychopathology-related outcomes in conventional analyses but Mendelian randomisation indicated that these associations were unlikely to be causal. However, Mendelian randomisation analyses showed that both smoking and homocysteine plasma levels may be causally linked with schizophrenia. We discuss possible reasons for these diverging results between conventional and Mendelian randomisation analyses and outline future directions for progressing research in ways that maximise the potential for identifying targets for intervention.

scholarly journals Exome Sequencing to Detect Rare Variants Associated With General Cognitive Ability: A Pilot Study

2015 ◽  
Vol 18 (2) ◽  
pp. 117-125 ◽  
Author(s):  
Michelle Luciano ◽  
Victoria Svinti ◽  
Archie Campbell ◽  
Riccardo E. Marioni ◽  
Caroline Hayward ◽  
...  
Keyword(s):  
Cognitive Ability ◽  
Exome Sequencing ◽  
Genetic Variants ◽  
Complex Traits ◽  
Rare Variants ◽  
Copy Number Variant ◽  
Apical Part ◽  
General Cognitive Ability ◽  
Sequencing Studies ◽  
Rare Genetic Variants

Variation in human cognitive ability is of consequence to a large number of health and social outcomes and is substantially heritable. Genetic linkage, genome-wide association, and copy number variant studies have investigated the contribution of genetic variation to individual differences in normal cognitive ability, but little research has considered the role of rare genetic variants. Exome sequencing studies have already met with success in discovering novel trait-gene associations for other complex traits. Here, we use exome sequencing to investigate the effects of rare variants on general cognitive ability. Unrelated Scottish individuals were selected for high scores on a general component of intelligence (g). The frequency of rare genetic variants (in n = 146) was compared with those from Scottish controls (total n = 486) who scored in the lower to middle range of the g distribution or on a proxy measure of g. Biological pathway analysis highlighted enrichment of the mitochondrial inner membrane component and apical part of cell gene ontology terms. Global burden analysis showed a greater total number of rare variants carried by high g cases versus controls, which is inconsistent with a mutation load hypothesis whereby mutations negatively affect g. The general finding of greater non-synonymous (vs. synonymous) variant effects is in line with evolutionary hypotheses for g. Given that this first sequencing study of high g was small, promising results were found, suggesting that the study of rare variants in larger samples would be worthwhile.

scholarly journals Risk Factors for Coronary Artery Diseases: A Study Among Patients With Ischemic Heart Disease in India (Kerala)

2013 ◽  
Vol 6 (2) ◽  
pp. 118-124
Author(s):  
Cyril James ◽  
Thankachan V. Attacheril ◽  
N. Balakrishnan ◽  
Diana K. Gaydarova ◽  
Nadya Y. Stancheva ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Risk Factors ◽  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Indian Population ◽  
Complex Disease ◽  
Stress Test ◽  
Common Complex Disease ◽  
Coronary Syndrome ◽  
Artery Disease

Summary Coronary artery disease (CAD) is a condition that develops due to accumulation of atherosclerotic plaque in the epicardial coronary arteries, leading to myocardial ischemia. It is the leading cause of death worldwide and is a common complex disease. A study was carried out in a group of 496 patients with acute coronary syndrome or with angiographic or stress test evidence for coronary artery disease, admitted to the Department of Cardiology at Lourdes Heart Institute and Neuro Centre during the period June-August 2012. The risk factors studied were hypertension, diabetes mellitus, dyslipidemia, body mass index, smoking and family history of CAD. The results demonstrated that in both males and females of the Indian population studies, diabetes and dyslipidemia were major risk factors for CAD, while hypertension was not a major risk factor. Therefore, early detection and treatment of diabetes mellitus and dyslipidemia play a vital role in prevention of CAD in Indian population.

scholarly journals The Spectrum of Genetic Variants Associated with the Development of Monogenic Obesity in Qatar

Obesity Facts ◽  
2022 ◽  
Author(s):  
Nadien AbouHashem ◽  
Roan E. Zaied ◽  
Kholoud Al-Shafai ◽  
Mariam Nofal ◽  
Najeeb Syed ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Rare Variants ◽  
Normal Weight ◽  
Routine Testing ◽  
Monogenic Obesity ◽  
Syndromic Obesity ◽  
The Impact

Introduction: Monogenic obesity (MO) is a rare genetic disease characterized by severe early-onset obesity in affected individuals. Previous genetic studies revealed 8 definitive genes for monogenic non-syndromic obesity; many were discovered in consanguineous populations. Here, we examined MO in the Qatari population, whose population is largely consanguineous (54%) and characterized by extensive obesity (45%). Methods: Whole genome sequences of Qatar Biobank samples from 250 subjects with obesity and 250 subjects with normal weight, obtained in association with the Qatar Genome Programme, were searched for genetic variants in the genes known to be associated with MO (i.e., LEP, LEPR, POMC, PCSK1, MC3R, MC4R, MRAP2 and ADCY3). The impact of the variants identified was investigated utilizing in silico tools for prediction in combination with protein visualization by PyMOL. Results: We identified potential MO variants in more than 5% of the cases in our cohort. We revealed 11 rare variants in 6 of the genes targeted, including two disease-causing variants in MC4R and MRAP2, all of which were heterozygous. Moreover, enrichment of a heterozygous ADCY3 variant (c.1658C>T; p.A553V) appeared to cause severe obesity in an autosomal dominant manner. Conclusion: These findings highlight the importance of implementing routine testing for genetic variants that predispose for MO in Qatar. Clearly, additional studies of this nature on populations not yet examined are required. At the same time, functional investigations, both in vitro and in vivo, are necessary in order to better understand the role of the variants identified in the pathogenesis of obesity.

Investigating the role of rare genetic variants of GP6 gene in platelet function

The Lancet ◽  
2014 ◽  
Vol 383 ◽  
pp. S74
Author(s):  
Claudia-Gabriela Mitrofan ◽  
Sjoert Hansen ◽  
Peter Smethurst ◽  
Willem Ouwehand
Keyword(s):  
Platelet Function ◽  
Genetic Variants ◽  
Rare Genetic Variants

scholarly journals Rare variants association testing for a binary outcome when pooling individual level data from heterogeneous studies

2020 ◽  
Author(s):  
Tamar Sofer ◽  
Na Guo
Keyword(s):  
Genetic Variants ◽  
Error Control ◽  
Rare Variants ◽  
Score Test ◽  
Saddlepoint Approximation ◽  
Rare Allele ◽  
Association Testing ◽  
Type 1 Error ◽  
Rare Genetic Variants

AbstractWhole genome and exome sequencing studies are used to test the association of rare genetic variants with health traits. Many existing WGS efforts now aggregate data from heterogeneous groups, e.g. combining sets of individuals of European and African ancestries. We here investigate the statistical implications on rare variant association testing with a binary trait when combining together heterogeneous studies, defined as studies with potentially different disease proportion and different frequency of variant carriers. We study and compare in simulations the type 1 error control and power of the naïve Score test, the saddlepoint approximation to the score test (SPA test), and the BinomiRare test in a range of settings, focusing on low numbers of variant carriers. We show that type 1 error control and power patterns depend on both the number of carriers of the rare allele and on disease prevalence in each of the studies. We develop recommendations for association analysis of rare genetic variants. (1) The Score test is preferred when the case proportion in the sample is 50%. (2) Do not down-sample controls to balance case-control ratio, because it reduces power. Rather, use a test that controls the type 1 error. (3) Conduct stratified analysis in parallel with combined analysis. Aggregated testing may have lower power when the variant effect size differs between strata.

Sign in / Sign up

Export Citation Format

Share Document