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Stapp EK, Fullerton JM, Musci RJ, Zandi PP, McInnis MG, Mitchell PB, Hulvershorn LA, Ghaziuddin N, Roberts G, Ferrera AG, Nurnberger JI, Wilcox HC. Family environment and polygenic risk in the bipolar high-risk context. JCPP Adv 2023; 3:e12143. [PMID: 37378048 PMCID: PMC10292829 DOI: 10.1002/jcv2.12143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 09/27/2023] Open
Abstract
Background The interaction of polygenic risk (PRS) and environmental effects on development of bipolar disorder (BD) is understudied, as are high-risk offspring perceptions of their family environment (FE). We tested the association of offspring-perceived FE in interaction with BD-PRS on liability for BD in offspring at high or low familial risk for BD. Methods Offspring of a parent with BD (oBD; n = 266) or no psychiatric disorders (n = 174), aged 12-21 at recruitment, participated in the US and Australia. Empirically-derived profiles of FE classified offspring by their perceived levels of familial cohesion, flexibility, and conflict. Offspring BD-PRS were derived from Psychiatric Genomics Consortium BD-GWAS. Lifetime DSM-IV bipolar disorders were derived from the Schedule for Affective Disorders and Schizophrenia for School-Aged Children. We used a novel stepwise approach for latent class modeling with predictors and distal outcomes. Results Fifty-two offspring were diagnosed with BD. For those with well-functioning FE (two-thirds of the sample), higher BD-PRS tracked positively with liability for BD. However, for those with high-conflict FEs, the relationship between BD-PRS and liability to BD was negative, with highest risk for BD observed with lower BD-PRS. In exploratory analyses, European-ancestry offspring with BD had elevated history of suicidal ideation in high-conflict FE compared to well-functioning-FE, and of suicide attempt with low-BD-PRS and high-conflict FE. Conclusions The data suggest that the relationship of BD-PRS and offspring liability for BD differed between well-functioning versus high-conflict FE, potentially in line with a multifactorial liability threshold model and supporting future study of and interventions improving family dynamics.
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Affiliation(s)
- Emma K. Stapp
- Department of Mental HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
- Genetic Epidemiology BranchNational Institute of Mental HealthBethesdaMarylandUSA
| | - Janice M. Fullerton
- Neuroscience Research AustraliaRandwickNew South WalesAustralia
- School of Medical SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Rashelle J. Musci
- Department of Mental HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Peter P. Zandi
- Department of Mental HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | | | - Philip B. Mitchell
- School of PsychiatryUniversity of New South WalesSydneyNew South WalesAustralia
| | | | - Neera Ghaziuddin
- Department of PsychiatryUniversity of MichiganAnn ArborMichiganUSA
| | - Gloria Roberts
- School of PsychiatryUniversity of New South WalesSydneyNew South WalesAustralia
| | | | - John I. Nurnberger
- Department of PsychiatryIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Stark Neurosciences Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | - Holly C. Wilcox
- Department of Mental HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
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O'Sullivan JW, Raghavan S, Marquez-Luna C, Luzum JA, Damrauer SM, Ashley EA, O'Donnell CJ, Willer CJ, Natarajan P. Polygenic Risk Scores for Cardiovascular Disease: A Scientific Statement From the American Heart Association. Circulation 2022; 146:e93-e118. [PMID: 35862132 PMCID: PMC9847481 DOI: 10.1161/cir.0000000000001077] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cardiovascular disease is the leading contributor to years lost due to disability or premature death among adults. Current efforts focus on risk prediction and risk factor mitigation' which have been recognized for the past half-century. However, despite advances, risk prediction remains imprecise with persistently high rates of incident cardiovascular disease. Genetic characterization has been proposed as an approach to enable earlier and potentially tailored prevention. Rare mendelian pathogenic variants predisposing to cardiometabolic conditions have long been known to contribute to disease risk in some families. However, twin and familial aggregation studies imply that diverse cardiovascular conditions are heritable in the general population. Significant technological and methodological advances since the Human Genome Project are facilitating population-based comprehensive genetic profiling at decreasing costs. Genome-wide association studies from such endeavors continue to elucidate causal mechanisms for cardiovascular diseases. Systematic cataloging for cardiovascular risk alleles also enabled the development of polygenic risk scores. Genetic profiling is becoming widespread in large-scale research, including in health care-associated biobanks, randomized controlled trials, and direct-to-consumer profiling in tens of millions of people. Thus, individuals and their physicians are increasingly presented with polygenic risk scores for cardiovascular conditions in clinical encounters. In this scientific statement, we review the contemporary science, clinical considerations, and future challenges for polygenic risk scores for cardiovascular diseases. We selected 5 cardiometabolic diseases (coronary artery disease, hypercholesterolemia, type 2 diabetes, atrial fibrillation, and venous thromboembolic disease) and response to drug therapy and offer provisional guidance to health care professionals, researchers, policymakers, and patients.
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3
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Bruxel EM, do Canto AM, Bruno DCF, Geraldis JC, Lopes-Cendes I. Multi-omic strategies applied to the study of pharmacoresistance in mesial temporal lobe epilepsy. Epilepsia Open 2021; 7 Suppl 1:S94-S120. [PMID: 34486831 PMCID: PMC9340306 DOI: 10.1002/epi4.12536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
Mesial temporal lobe epilepsy (MTLE) is the most common type of focal epilepsy in adults, and hippocampal sclerosis (HS) is a frequent histopathological feature in patients with MTLE. Pharmacoresistance is present in at least one-third of patients with MTLE with HS (MTLE+HS). Several hypotheses have been proposed to explain the mechanisms of pharmacoresistance in epilepsy, including the effect of genetic and molecular factors. In recent years, the increased knowledge generated by high-throughput omic technologies has significantly improved the power of molecular genetic studies to discover new mechanisms leading to disease and response to treatment. In this review, we present and discuss the contribution of different omic modalities to understand the basic mechanisms determining pharmacoresistance in patients with MTLE+HS. We provide an overview and a critical discussion of the findings, limitations, new approaches, and future directions of these studies to improve the understanding of pharmacoresistance in MTLE+HS. However, it is important to point out that, as with other complex traits, pharmacoresistance to anti-seizure medications is likely a multifactorial condition in which gene-gene and gene-environment interactions play an important role. Thus, studies using multidimensional approaches are more likely to unravel these intricate biological processes.
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Affiliation(s)
- Estela M Bruxel
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Amanda M do Canto
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Danielle C F Bruno
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Jaqueline C Geraldis
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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4
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Harrison JR, Mistry S, Muskett N, Escott-Price V. From Polygenic Scores to Precision Medicine in Alzheimer's Disease: A Systematic Review. J Alzheimers Dis 2020; 74:1271-1283. [PMID: 32250305 PMCID: PMC7242840 DOI: 10.3233/jad-191233] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Late-onset Alzheimer's disease (AD) is highly heritable. The effect of many common genetic variants, single nucleotide polymorphisms (SNPs), confer risk. Variants are clustered in areas of biology, notably immunity and inflammation, cholesterol metabolism, endocytosis, and ubiquitination. Polygenic scores (PRS), which weight the sum of an individual's risk alleles, have been used to draw inferences about the pathological processes underpinning AD. OBJECTIVE This paper aims to systematically review how AD PRS are being used to study a range of outcomes and phenotypes related to neurodegeneration. METHODS We searched the literature from July 2008-July 2018 following PRISMA guidelines. RESULTS 57 studies met criteria. The AD PRS can distinguish AD cases from controls. The ability of AD PRS to predict conversion from mild cognitive impairment (MCI) to AD was less clear. There was strong evidence of association between AD PRS and cognitive impairment. AD PRS were correlated with a number of biological phenotypes associated with AD pathology, such as neuroimaging changes and amyloid and tau measures. Pathway-specific polygenic scores were also associated with AD-related biologically relevant phenotypes. CONCLUSION PRS can predict AD effectively and are associated with cognitive impairment. There is also evidence of association between AD PRS and other phenotypes relevant to neurodegeneration. The associations between pathway specific polygenic scores and phenotypic changes may allow us to define the biology of the disease in individuals and indicate who may benefit from specific treatments. Longitudinal cohort studies are required to test the ability of PGS to delineate pathway-specific disease activity.
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Affiliation(s)
- Judith R. Harrison
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
| | - Sumit Mistry
- MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
| | - Natalie Muskett
- Cardiff University Medical School, University Hospital of Wales, Cardiff, UK
| | - Valentina Escott-Price
- Dementia Research Institute & the MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, UK
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Cowan JR, Kinnamon DD, Morales A, Salyer L, Nickerson DA, Hershberger RE. Multigenic Disease and Bilineal Inheritance in Dilated Cardiomyopathy Is Illustrated in Nonsegregating LMNA Pedigrees. Circ Genom Precis Med 2019; 11:e002038. [PMID: 30012837 DOI: 10.1161/circgen.117.002038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/24/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND We have previously described 19 pedigrees with apparent lamin (LMNA)-related dilated cardiomyopathy (DCM) manifesting in affected family members across multiple generations. In 6 of 19 families, at least 1 individual with idiopathic DCM did not carry the family's LMNA variant. We hypothesized that additional genetic cause may underlie DCM in these families. METHODS Affected family members underwent exome sequencing to identify additional genetic cause of DCM in the 6 families with nonsegregating LMNA variants. RESULTS In 5 of 6 pedigrees, we identified at least 1 additional rare variant in a known DCM gene that could plausibly contribute to disease in the LMNA variant-negative individuals. Bilineal inheritance was clear or presumed to be present in 3 of 5 families and was possible in the remaining 2. At least 1 individual with a LMNA variant also carried a variant in an additional identified DCM gene in each family. Using a multivariate linear mixed model for quantitative traits, we demonstrated that the presence of these additional variants was associated with a more severe phenotype after adjusting for sex, age, and the presence/absence of the family's nonsegregating LMNA variant. CONCLUSIONS Our data support DCM as a genetically heterogeneous disease with, at times, multigene causation. Although the frequency of DCM resulting from multigenic cause is uncertain, our data suggest it may be higher than previously anticipated.
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Affiliation(s)
- Jason R Cowan
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Daniel D Kinnamon
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Ana Morales
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Lorien Salyer
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.)
| | - Deborah A Nickerson
- Department of Internal Medicine, Ohio State University College of Medicine, Columbus. Department of Genome Sciences, University of Washington Center for Mendelian Genomics, Seattle (D.A.N.)
| | - Ray E Hershberger
- Dorothy M. Davis Heart and Lung Research Institute (J.R.C., D.D.K., A.M., L.S., R.E.H.) .,Divisions of Human Genetics (J.R.C., D.D.K., A.M., L.S., R.E.H.).,Cardiovascular Medicine (R.E.H.)
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6
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Fritsche LG, Gruber SB, Wu Z, Schmidt EM, Zawistowski M, Moser SE, Blanc VM, Brummett CM, Kheterpal S, Abecasis GR, Mukherjee B. Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. Am J Hum Genet 2018; 102:1048-1061. [PMID: 29779563 DOI: 10.1016/j.ajhg.2018.04.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
Health systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether polygenic risk scores (PRS) for common cancers are associated with multiple phenotypes in a phenome-wide association study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine. PRS for 12 cancer traits were calculated using summary statistics from the NHGRI-EBI catalog. A total of 1,711 synthetic case-control studies was used for PheWAS analyses. There were 13,490 (47.7%) patients with at least one cancer diagnosis in this study sample. PRS exhibited strong association for several cancer traits they were designed for, including female breast cancer, prostate cancer, melanoma, basal cell carcinoma, squamous cell carcinoma, and thyroid cancer. Phenome-wide significant associations were observed between PRS and many non-cancer diagnoses. To differentiate PRS associations driven by the primary trait from associations arising through shared genetic risk profiles, the idea of "exclusion PRS PheWAS" was introduced. Further analysis of temporal order of the diagnoses improved our understanding of these secondary associations. This comprehensive PheWAS used PRS instead of a single variant.
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Affiliation(s)
- Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, 7491 Trondheim, Sør-Trøndelag, Norway
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Stephanie E Moser
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Victoria M Blanc
- Central Biorepository, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chad M Brummett
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sachin Kheterpal
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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Roessler E, Hu P, Muenke M. Holoprosencephaly in the genomics era. Am J Med Genet C Semin Med Genet 2018; 178:165-174. [PMID: 29770992 DOI: 10.1002/ajmg.c.31615] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 01/08/2023]
Abstract
Holoprosencephaly (HPE) is the direct consequence of specific genetic and/or environmental insults interrupting the midline specification of the nascent forebrain. Such disturbances can lead to a broad range of phenotypic consequences for the brain and face in humans. This malformation sequence is remarkably common in utero (1 in 250 human fetuses), but 97% typically do not survive to birth. The precise molecular pathogenesis of HPE in these early human embryos remains largely unknown. Here, we outline our current understanding of the principal driving factors leading to HPE pathologies and elaborate our multifactorial integrated genomics approach. Overall, our understanding of the pathogenesis continues to become simpler, rather than more complicated. Genomic technologies now provide unprecedented insight into disease-associated variation, including the overall extent of genetic interactions (coding and noncoding) predicted to explain divergent phenotypes.
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Affiliation(s)
- Erich Roessler
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ping Hu
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maximilian Muenke
- Medical Genetics Branch, National Human, Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Giusti B, Sticchi E, De Cario R, Magi A, Nistri S, Pepe G. Genetic Bases of Bicuspid Aortic Valve: The Contribution of Traditional and High-Throughput Sequencing Approaches on Research and Diagnosis. Front Physiol 2017; 8:612. [PMID: 28883797 PMCID: PMC5573733 DOI: 10.3389/fphys.2017.00612] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/09/2017] [Indexed: 12/20/2022] Open
Abstract
Bicuspid aortic valve (BAV) is a common (0.5-2.0% of general population) congenital heart defect with increased prevalence of aortic dilatation and dissection. BAV has an autosomal dominant inheritance with reduced penetrance and variable expressivity. BAV has been described as an isolated trait or associated with syndromic conditions [e.g., Marfan Marfan syndrome or Loeys-Dietz syndrome (MFS, LDS)]. Identification of a syndromic condition in a BAV patient is clinically relevant to personalize aortic surgery indication. A 4-fold increase in BAV prevalence in a large cohort of unrelated MFS patients with respect to general population was reported, as well as in LDS patients (8-fold). It is also known that BAV is more frequent in patients with thoracic aortic aneurysm (TAA) related to mutations in ACTA2, FBN1, and TGFBR2 genes. Moreover, in 8 patients with BAV and thoracic aortic dilation, not fulfilling the clinical criteria for MFS, FBN1 mutations in 2/8 patients were identified suggesting that FBN1 or other genes involved in syndromic conditions correlated to aortopathy could be involved in BAV. Beyond loci associated to syndromic disorders, studies in humans and animal models evidenced/suggested the role of further genes in non-syndromic BAV. The transcriptional regulator NOTCH1 has been associated with the development and acceleration of calcium deposition. Genome wide marker-based linkage analysis demonstrated a linkage of BAV to loci on chromosomes 18, 5, and 13q. Recently, a role for GATA4/5 in aortic valve morphogenesis and endocardial cell differentiation has been reported. BAV has also been associated with a reduced UFD1L gene expression or involvement of a locus containing AXIN1/PDIA2. Much remains to be understood about the genetics of BAV. In the last years, high-throughput sequencing technologies, allowing the analysis of large number of genes or entire exomes or genomes, progressively became available. The latter issue together with the development of "BigData" analysis methods improving their interpretation and integration with clinical data represents a promising opportunity to increase the disease knowledge and diagnosis in monogenic and multifactorial complex traits. This review summarized the main knowledge on the BAV genetic bases, the role of genetic diagnosis in BAV patient managements and the crucial challenges for the comprehension of genetics of BAV in research and diagnosis.
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Affiliation(s)
- Betti Giusti
- Department of Experimental and Clinical Medicine, Section of Critical Medical Care and Medical Specialities, University of FlorenceFlorence, Italy.,Marfan Syndrome and Related Disorders Regional (Tuscany) Referral Center, Careggi HospitalFlorence, Italy.,Advanced Molecular Genetics Laboratory, Atherothrombotic Diseases Center, Careggi HospitalFlorence, Italy.,Center of Excellence for the Study at Molecular and Clinical Level of Chronic, Degenerative and Neoplastic Diseases to Develop Novel Therapies (DENOTHE), University of FlorenceFlorence, Italy
| | - Elena Sticchi
- Department of Experimental and Clinical Medicine, Section of Critical Medical Care and Medical Specialities, University of FlorenceFlorence, Italy.,Marfan Syndrome and Related Disorders Regional (Tuscany) Referral Center, Careggi HospitalFlorence, Italy.,Advanced Molecular Genetics Laboratory, Atherothrombotic Diseases Center, Careggi HospitalFlorence, Italy.,Center of Excellence for the Study at Molecular and Clinical Level of Chronic, Degenerative and Neoplastic Diseases to Develop Novel Therapies (DENOTHE), University of FlorenceFlorence, Italy
| | - Rosina De Cario
- Department of Experimental and Clinical Medicine, Section of Critical Medical Care and Medical Specialities, University of FlorenceFlorence, Italy.,Marfan Syndrome and Related Disorders Regional (Tuscany) Referral Center, Careggi HospitalFlorence, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, Section of Critical Medical Care and Medical Specialities, University of FlorenceFlorence, Italy.,Advanced Molecular Genetics Laboratory, Atherothrombotic Diseases Center, Careggi HospitalFlorence, Italy
| | - Stefano Nistri
- Center of Excellence for the Study at Molecular and Clinical Level of Chronic, Degenerative and Neoplastic Diseases to Develop Novel Therapies (DENOTHE), University of FlorenceFlorence, Italy.,Cardiology Service, Centro Medico Strumentale Riabilitativo (CMSR) Veneto MedicaAltavilla Vicentina, Italy
| | - Guglielmina Pepe
- Department of Experimental and Clinical Medicine, Section of Critical Medical Care and Medical Specialities, University of FlorenceFlorence, Italy.,Marfan Syndrome and Related Disorders Regional (Tuscany) Referral Center, Careggi HospitalFlorence, Italy.,Center of Excellence for the Study at Molecular and Clinical Level of Chronic, Degenerative and Neoplastic Diseases to Develop Novel Therapies (DENOTHE), University of FlorenceFlorence, Italy
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Shah SAV, Kondkar AA, Ashavaid TF. An in-house multilocus SNP genotyping assay for evaluation of complex genetic diseases. Scand J Clin Lab Invest 2016; 76:590-595. [PMID: 27562454 DOI: 10.1080/00365513.2016.1218535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND With an increase in the discovery of newer genetic loci/polymorphisms in complex multifactorial diseases, there is also an increased need for methods that can simultaneously genotype multiple loci in a cost-effective manner. Using coronary artery disease (CAD) as a model, the study aimed to develop an in-house multilocus assay for simultaneous detection of 17 genetic variants in 11 genes implicated in CAD. METHODS A multiplex polymerase chain reaction (PCR)-based reverse line blot hybridization (MPCR-RLBH) approach was used, where each DNA sample was amplified using two separate MPCRs, and the alleles were genotyped using covalently immobilized, amino-linked sequence-specific oligonucleotide probes using an enhanced chemiluminescence system. The assay performance was tested on 75 healthy controls and 75 angiographically proven CAD cases. Validation was done by automated Sanger sequencing. RESULTS The assay could successfully discriminate both the alleles at CETP (I405V), LPL (D9N), NOS3 (T-786G and E298D), LIPC (C-514T), FGB (G-455A), ITGB3 (L33P), AGT (M235T), and MTR (A2756G) loci. Certain mutations included in this assay such as ins242G, ins397G, E387K, L393K in the LDLR; N291S in the LPL; D442G in the CETP; and T833C in the CBS genes were found to be absent. The genotype results obtained using this assay showed 100% concordance with sequencing. CONCLUSION The study demonstrated development and validation of a multiplex SNP genotyping assay that can be used to assess genetic risk factors in CAD. The assay provides a cost-effective alternative to expensive high throughput genotyping systems in common molecular research laboratories.
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Affiliation(s)
- Swarup A V Shah
- a Research Laboratories , P. D. Hinduja National Hospital and Medical Research Centre , Mumbai , India
| | - Altaf A Kondkar
- a Research Laboratories , P. D. Hinduja National Hospital and Medical Research Centre , Mumbai , India
| | - Tester F Ashavaid
- a Research Laboratories , P. D. Hinduja National Hospital and Medical Research Centre , Mumbai , India.,b Department of Biochemistry , P. D. Hinduja National Hospital and Medical Research Centre , Mumbai , India
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Abstract
Early presumptions opined that autism spectrum disorder (ASD) was related to the rearing of these children by emotionally-distant mothers. Advances in the 1960s and 1970s clearly demonstrated the biologic basis of autism with a high heritability. Recent advances have demonstrated that specific etiologic factors in autism spectrum disorders can be identified in 30%–40% of cases. Based on early reports newer, emerging genomic technologies are likely to increase this diagnostic yield to over 50%. To date these investigations have focused on etiologic factors that are largely mono-factorial. The currently undiagnosed causes of ASDs will likely be found to have causes that are more complex. Epigenetic, multiple interacting loci, and four dimensional causes (with timing as a variable) are likely to be associated with the currently unidentifiable cases. Today, the “Why” is more important than ever. Understanding the causes of ASDs help inform families of important issues such as recurrence risk, prognosis, natural history, and predicting associated co-morbid medical conditions. In the current era of emerging efforts in “personalized medicine”, identifying an etiology will be critical in identifying endo-phenotypic groups and individual variations that will allow for tailored treatment for persons with ASD.
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Bury JJ, Highley JR, Cooper-Knock J, Goodall EF, Higginbottom A, McDermott CJ, Ince PG, Shaw PJ, Kirby J. Oligogenic inheritance of optineurin (OPTN) and C9ORF72 mutations in ALS highlights localisation of OPTN in the TDP-43-negative inclusions of C9ORF72-ALS. Neuropathology 2015; 36:125-34. [PMID: 26303227 DOI: 10.1111/neup.12240] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by motor neurone loss resulting in muscle weakness, spasticity and ultimately death. 5-10% are caused by inherited mutations, most commonly C9ORF72, SOD1, TARDBP and FUS. Rarer genetic causes of ALS include mutation of optineurin (mt OPTN). Furthermore, optineurin protein has been localized to the ubiquitylated aggregates in several neurodegenerative diseases, including ALS. This study: (i) investigated the frequency of mt OPTN in ALS patients in England; (ii) characterized the clinical and neuropathological features of ALS associated with a mt OPTN; and (iii) investigated optineurin neuropathology in C9ORF72-related ALS (C9ORF72-ALS). We identified a heterozygous p.E322K missense mutation in exon 10 of OPTN in one familial ALS patient who additionally had a C9ORF72 mutation. This patient had bulbar, limb and respiratory disease without cognitive problems. Neuropathology revealed motor neurone loss, trans-activation response DNA protein 43 (TDP-43)-positive neuronal and glial cytoplasmic inclusions together with TDP-43-negative neuronal cytoplasmic inclusions in extra motor regions that are characteristic of C9ORF72-ALS. We have demonstrated that both TDP-43-positive and negative inclusion types had positive staining for optineurin by immunohistochemistry. We went on to show that optineurin was present in TDP-43-negative cytoplasmic extra motor inclusions in C9ORF72-ALS cases that do not carry mt OPTN. We conclude that: (i) OPTN mutations are associated with ALS; (ii) optineurin protein is present in a subset of the extramotor inclusions of C9ORF72-ALS; (iii) It is not uncommon for multiple ALS-causing mutations to occur in the same patient; and (iv) studies of optineurin are likely to provide useful dataregarding the pathophysiology of ALS and neurodegeneration.
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Affiliation(s)
- Joanna J Bury
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - J Robin Highley
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Emily F Goodall
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Christopher J McDermott
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Paul G Ince
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
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Fitzgerald-Butt SM, Klima J, Kelleher K, Chisolm D, McBride KL. Genetic knowledge and attitudes of parents of children with congenital heart defects. Am J Med Genet A 2014; 164A:3069-75. [PMID: 25256359 DOI: 10.1002/ajmg.a.36763] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 08/10/2014] [Indexed: 12/21/2022]
Abstract
Clinical genetic testing for specific isolated congenital heart defects (CHD) is becoming standard of care in pediatric cardiology practice. Both genetic knowledge and attitudes toward genetic testing are associated with an increased utilization of genetic testing, but these factors have not been evaluated in parents of children with CHD. We mailed a survey to measure the demographics, genetic knowledge, and attitudes towards genetic testing of parents of children with CHD who previously consented to participate in a separate research study of the genetic etiology of left ventricular outflow tract malformations (LVOT). Of the 378 eligible families, 190 (50%) returned surveys with both parents completing surveys in 97 (51%) families, resulting in 287 participants. Genetic knowledge was assessed on an adapted measure on which the mean percent correct was 73.8%. Educational attainment and household income were directly and significantly associated with genetic knowledge (P < 0.001). Attitudes about the health effects of genetic testing were favorable with at least 57% agreeing that genetic testing would be used for managing health care and finding cures for disease. Conversely, a minority of participants found it likely that genetic testing would be used for insurance (up to 39.9%), employment (15.8%), or racial/social discrimination (up to 11.2%). Parents of younger children were less likely to endorse employment or racial/social discrimination. Genetic knowledge was not correlated with specific attitudes. Among parents of children with CHD, genetic knowledge was directly associated with household income and education, but additional research is necessary to determine what factors influence attitudes towards genetic testing.
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Affiliation(s)
- Sara M Fitzgerald-Butt
- Center for Cardiovascular and Pulmonary Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio
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Gambhir L, Höller T, Müller M, Schott G, Vogt H, Detlefsen B, Ebert AK, Fisch M, Beaudoin S, Stein R, Boyadjiev SA, Gearhart JP, Rösch W, Utsch B, Boemers TM, Reutter H, Ludwig M. Epidemiological survey of 214 families with bladder exstrophy-epispadias complex. J Urol 2008; 179:1539-43. [PMID: 18295266 PMCID: PMC2674109 DOI: 10.1016/j.juro.2007.11.092] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Indexed: 11/29/2022]
Abstract
PURPOSE We sought to identify causative nongenetic and genetic risk factors for the bladder exstrophy-epispadias complex. MATERIALS AND METHODS A total of 237 families with the bladder exstrophy-epispadias complex were invited to participate in the study, and information was obtained from 214 families, mainly from European countries. RESULTS Two families showed familial occurrence. Male predominance was found among all subgroups comprising epispadias, classic bladder exstrophy and cloacal exstrophy, with male-to-female ratios of 1.4:1, 2.8:1 and 2.0:1, respectively (p = 0.001). No association with parental age, maternal reproductive history or periconceptional maternal exposure to alcohol, drugs, chemical noxae, radiation or infections was found. However, periconceptional maternal exposure to smoking was significantly more common in patients with cloacal exstrophy than in the combined group of patients with epispadias/classic bladder exstrophy (p = 0.009). Only 16.8% of mothers followed the current recommendations of periconceptional folic acid supplementation, and 17.6% had started supplementation before 10 weeks of gestation. Interestingly, in the latter group mothers of patients with cloacal exstrophy were more compliant with folic acid supplementation than were mothers of the combined group of patients with epispadias/classic bladder exstrophy (p = 0.037). Furthermore, mothers of children with cloacal exstrophy knew significantly more often prenatally that their child would have a congenital malformation than did mothers of children with epispadias/classic bladder exstrophy (p <0.0001). CONCLUSIONS Our study corroborates the hypothesis that epispadias, classic bladder exstrophy and cloacal exstrophy are causally related, representing a spectrum of the same developmental defect, with a small risk of recurrence within families. Embryonic exposure to maternal smoking appears to enforce the severity, whereas periconceptional folic acid supplementation does not seem to alleviate it. There is a disproportional prenatal ultrasound detection rate between severe and mild phenotypes, possibly due to the neglect of imaging of full bladders with a focus on neural tube defects.
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Affiliation(s)
- L Gambhir
- Dept. of Clinical Biochemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - T Höller
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - M Müller
- Dept. of Pediatrics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - G Schott
- Dept. of Urology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - H Vogt
- Dept. of Pediatric Surgery and Pediatric Urology, Childrens Hospital, Cologne, Germany
| | - B Detlefsen
- Dept. of Pediatric Surgery and Pediatric Urology, Childrens Hospital, Cologne, Germany
| | - AK Ebert
- Dept. of Pediatric Urology, St. Hedwig Hospital Barmherzige Brüder, Regensburg, Germany
| | - M Fisch
- Dept. of Urology, Asklepios Hospital Harburg, Hamburg, Germany
| | - S Beaudoin
- Dept. de Chirurgie Pédiatrique, Hôpital Saint-Vincent de Paul, Paris, France
| | - R Stein
- Dept. of Urology, Johannes Gutenberg-University, Mainz, Germany
| | - SA Boyadjiev
- Section of Genetics, Dept. of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - JP Gearhart
- Dept. of Urology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - W Rösch
- Dept. of Pediatric Urology, St. Hedwig Hospital Barmherzige Brüder, Regensburg, Germany
| | - B Utsch
- Dept. of Pediatrics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - TM Boemers
- Dept. of Pediatric Surgery and Pediatric Urology, Childrens Hospital, Cologne, Germany
| | - H Reutter
- Dept. of Human Genetics, University of Bonn, Bonn, Germany
- Dept. of Pediatrics, University of Bonn, Bonn, Germany
| | - M Ludwig
- Dept. of Clinical Biochemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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Farrell SA. Multifactorial inheritance in man. Can Fam Physician 1988; 34:867-871. [PMID: 21253092 PMCID: PMC2218978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The interaction of genetic and non-genetic factors, termed `multifactorial inheritance', contributes to a large proportion of medical disorders. Spina bifida and type-II diabetes mellitus are two common conditions considered to be multifactorial. Using clinical examples, the author of this paper explores the basis of this mode of inheritance and its relevance to patient care.
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