201
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Russell LE, Schwarz UI. Variant discovery using next-generation sequencing and its future role in pharmacogenetics. Pharmacogenomics 2020; 21:471-486. [DOI: 10.2217/pgs-2019-0190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) has enabled the discovery of a multitude of novel and mostly rare variants in pharmacogenes that may alter a patient’s therapeutic response to drugs. In addition to single nucleotide variants, structural variation affecting the number of copies of whole genes or parts of genes can be detected. While current guidelines concerning clinical implementation mostly act upon well-documented, common single nucleotide variants to guide dosing or drug selection, in silico and large-scale functional assessment of rare variant effects on protein function are at the forefront of pharmacogenetic research to facilitate their clinical integration. Here, we discuss the role of NGS in variant discovery, paving the way for more comprehensive genotype-guided pharmacotherapy that can translate to improved clinical care.
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Affiliation(s)
- Laura E Russell
- Department of Physiology & Pharmacology, Western University, Medical Sciences Building, London, ON, N6A 5C1, Canada
| | - Ute I Schwarz
- Department of Physiology & Pharmacology, Western University, Medical Sciences Building, London, ON, N6A 5C1, Canada
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre – University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada
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202
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Abstract
Biofilm bacteria co‐evolve and reach a symbiosis with the host on the gingival surface. The disruption of the homeostatic relationship between plaque bacteria and the host can initiate and promote periodontal disease progression. Recent advances in sequencing technologies allow researchers to profile disease‐associated microbial communities and quantify microbial metabolic activities and host transcriptional responses. In addition to confirming the findings from previous studies, new putative pathogens and novel genes that have not previously been associated with periodontitis, emerge. For example, multiple studies have reported that Synergistetes bacteria are associated with periodontitis. Genes involved in epithelial barrier defense were downregulated in periodontitis, while excessive expression of interleukin‐17 was associated with a hyperinflammatory response in periodontitis and with a unique microbial community. Bioinformatics‐enabled gene ontology pathway analyses provide a panoramic view of the bacterial and host activities as they shift from periodontal health to disease. Additionally, host innate factors, such as genetic variants identified by either a candidate‐gene approach or genome‐wide association analyses, have an impact on subgingival bacterial colonization. Transgenic mice carrying candidate genetic variants, or with the deletion of candidate genes mimicking the deleterious loss‐of‐function variant effect, provide experimental evidence validating the biologic relevance of the novel markers associated with the microbial phenotype identified through a statistical approach. Further refinement in bioinformatics, data management approaches, or statistical tools, are required to gain insight into host‐microbe interactions by harmonizing the multidimensional “big” data at the genomic, transcriptional, and proteomic levels.
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Affiliation(s)
- Shaoping Zhang
- Periodontics Department, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
| | - Ning Yu
- Applied Oral Science Department, The Forsyth Institute, Cambridge, Massachusetts, USA
| | - Roger M Arce
- Department of Periodontics, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
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203
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Bandres-Ciga S, Diez-Fairen M, Kim JJ, Singleton AB. Genetics of Parkinson's disease: An introspection of its journey towards precision medicine. Neurobiol Dis 2020; 137:104782. [PMID: 31991247 PMCID: PMC7064061 DOI: 10.1016/j.nbd.2020.104782] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/15/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022] Open
Abstract
A substantial proportion of risk for Parkinson's disease (PD) is driven by genetics. Progress in understanding the genetic basis of PD has been significant. So far, highly-penetrant rare genetic alterations in SNCA, LRRK2, VPS35, PRKN, PINK1, DJ-1 and GBA have been linked with typical familial PD and common genetic variability at 90 loci have been linked to risk for PD. In this review, we outline the journey thus far of PD genetics, highlighting how significant advances have improved our knowledge of the genetic basis of PD risk, onset and progression. Despite remarkable progress, our field has yet to unravel how genetic risk variants disrupt biological pathways and molecular networks underlying the pathobiology of the disease. We highlight that currently identified genetic risk factors only represent a fraction of the likely genetic risk for PD. Identifying the remaining genetic risk will require us to diversify our efforts, performing genetic studies across different ancestral groups. This work will inform us on the varied genetic basis of disease across populations and also aid in fine mapping discovered loci. If we are able to take this course, we foresee that genetic discoveries in PD will directly influence our ability to predict disease and aid in defining etiological subtypes, critical steps for the implementation of precision medicine for PD.
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Affiliation(s)
- Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada 18016, Spain.
| | - Monica Diez-Fairen
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of Neurology, University Hospital Mútua Terrassa, Terrassa 08221, Barcelona, Spain
| | - Jonggeol Jeff Kim
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA.
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204
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Abstract
Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.
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Affiliation(s)
- Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Desislava Petkova
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL
- Department of Ecology & Evolution, University of Chicago, Chicago, IL
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205
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Gil-Varea E, Spataro N, Villar LM, Tejeda-Velarde A, Midaglia L, Matesanz F, Malhotra S, Eixarch H, Patsopoulos N, Fernández Ó, Oliver-Martos B, Saiz A, Llufriu S, Ramió-Torrentà L, Quintana E, Izquierdo G, Alcina A, Bosch E, Navarro A, Montalban X, Comabella M. Targeted resequencing reveals rare variants enrichment in multiple sclerosis susceptibility genes. Hum Mutat 2020; 41:1308-1320. [PMID: 32196808 DOI: 10.1002/humu.24016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 12/25/2022]
Abstract
Although genome-wide association studies have identified a number of common variants associated with multiple sclerosis (MS) susceptibility, little is known about the relevance of rare variants. Here, we aimed to explore the role of rare variants in 14 MS risk genes (FCRL1, RGS1, TIMMDC1, HHEX, CXCR5, LTBR, TSFM, GALC, TRAF3, STAT3, TNFSF14, IFI30, CD40, and CYP24A1) by targeted resequencing in an Iberian population of 524 MS cases and 546 healthy controls. Four rare variants-enriched regions within CYP24A1, FCRL1, RGS1, and TRAF3 were identified as significantly associated with MS. Functional studies revealed significantly decreased regulator of G protein signaling 1 (RGS1) gene expression levels in peripheral blood mononuclear cells from MS patients with RGS1 rare variants compared to noncarriers, whereas no significant differences in gene expression were observed for CYP24A1, FCRL1, and TRAF3 between rare variants carriers and noncarriers. Immunophenotyping showed significant decrease in RGS1 expression in peripheral blood B lymphocytes from MS patients with RGS1 rare variants relative to noncarriers. Lastly, peripheral blood mononuclear cell from MS patients carrying RGS1 rare variants showed significantly lower induction of RGS1 gene expression by interferon-β compared to MS patients lacking RGS1 variants. The presence of rare variants in RGS1 reinforce the ideas of high genetic heterogeneity and a role of rare variants in MS pathogenesis.
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Affiliation(s)
- Elia Gil-Varea
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Luisa María Villar
- Departments of Immunology and Neurology, Multiple Sclerosis Unit, Hospital Ramon y Cajal, (IRYCIS), Madrid, Spain
| | - Amalia Tejeda-Velarde
- Departments of Immunology and Neurology, Multiple Sclerosis Unit, Hospital Ramon y Cajal, (IRYCIS), Madrid, Spain
| | - Luciana Midaglia
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Herena Eixarch
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nikolaos Patsopoulos
- Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Óscar Fernández
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Begoña Oliver-Martos
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Albert Saiz
- Servicio de Neurología, Hospital Clinic and Institut d'Investigació Biomèdica Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Llufriu
- Servicio de Neurología, Hospital Clinic and Institut d'Investigació Biomèdica Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, Faculty of Medicine, Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdIBGi), University of Girona, Girona, Spain
| | - Ester Quintana
- Department of Medical Sciences, Faculty of Medicine, Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdIBGi), University of Girona, Girona, Spain
| | - Guillermo Izquierdo
- Departamento de Neurología, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Elena Bosch
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Arcadi Navarro
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain.,Centre de Regulació Genòmica (CRG), Barcelona, España.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Cataluña, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Center d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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206
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Meng J, Zhu W, Li C, Jon K. A novel association test for rare variants based on algebraic statistics. J Theor Biol 2020; 493:110228. [PMID: 32135159 DOI: 10.1016/j.jtbi.2020.110228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/22/2020] [Accepted: 02/29/2020] [Indexed: 01/26/2023]
Abstract
With the rapid growth of next-generation sequencing technology, more and more rare variants are available in the human genome. In recent years, the point of study has already changed direction to rare variants in genome-wide association studies (GWAS). Although a variety of approaches have been proposed to test associations between rare variants and phenotypes of interest, it is far from the end of this problem, and it is worth exploring new statistical methods based on special features of rare variants. As we all know, the most direct way is to evaluate the association in a two-way contingency table if the phenotype is a discrete variable. The numbers of observations are very close or equal to 0s for most of cells in the contingency table due to the extremely low mutation rates of rare variants. In this paper, we propose a novel association test for rare variants based on a generalization of Fisher's exact test, and the p-value of this exact test can be computed under the multivariate hypergeometric distribution in the framework of algebraic statistics. Simulation results show that our proposed method outperforms the existing methods, despite there is heterogeneity among causal variants. We also successfully apply our method into the genetic association study of coronary artery disease and hypertension from the Wellcome Trust Case Control Consortium.
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Affiliation(s)
- Jingbo Meng
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China
| | - Wensheng Zhu
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China.
| | - Canhui Li
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China
| | - Kyongson Jon
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China; Faculty of Mathematics, Kim Il Sung University, Pyongyang, 999093, Democratic People's Republic of Korea
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207
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Sinclair-Waters M, Ødegård J, Korsvoll SA, Moen T, Lien S, Primmer CR, Barson NJ. Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. Genet Sel Evol 2020; 52:9. [PMID: 32050893 PMCID: PMC7017552 DOI: 10.1186/s12711-020-0529-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest. RESULTS Here, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes (P-values: 8.7 × 10-133-9.8 × 10-8), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans. DISCUSSION These results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Jørgen Ødegård
- AquaGen, Trondheim, Norway.,Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Nicola J Barson
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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208
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A polygenic predictor of treatment-resistant depression using whole exome sequencing and genome-wide genotyping. Transl Psychiatry 2020; 10:50. [PMID: 32066715 PMCID: PMC7026437 DOI: 10.1038/s41398-020-0738-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/02/2020] [Accepted: 01/10/2020] [Indexed: 12/18/2022] Open
Abstract
Treatment-resistant depression (TRD) occurs in ~30% of patients with major depressive disorder (MDD) but the genetics of TRD was previously poorly investigated. Whole exome sequencing and genome-wide genotyping were available in 1209 MDD patients after quality control. Antidepressant response was compared to non-response to one treatment and non-response to two or more treatments (TRD). Differences in the risk of carrying damaging variants were tested. A score expressing the burden of variants in genes and pathways was calculated weighting each variant for its functional (Eigen) score and frequency. Gene-based and pathway-based scores were used to develop predictive models of TRD and non-response using gradient boosting in 70% of the sample (training) which were tested in the remaining 30% (testing), evaluating also the addition of clinical predictors. Independent replication was tested in STAR*D and GENDEP using exome array-based data. TRD and non-responders did not show higher risk to carry damaging variants compared to responders. Genes/pathways associated with TRD included those modulating cell survival and proliferation, neurodegeneration, and immune response. Genetic models showed significant prediction of TRD vs. response and they were improved by the addition of clinical predictors, but they were not significantly better than clinical predictors alone. Replication results were driven by clinical factors, except for a model developed in subjects treated with serotonergic antidepressants, which showed a clear improvement in prediction at the extremes of the genetic score distribution in STAR*D. These results suggested relevant biological mechanisms implicated in TRD and a new methodological approach to the prediction of TRD.
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209
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Zhang Y, Li M, Wang Q, Hsu JS, Deng W, Ma X, Ni P, Zhao L, Tian Y, Sham PC, Li T. A joint study of whole exome sequencing and structural MRI analysis in major depressive disorder. Psychol Med 2020; 50:384-395. [PMID: 30722798 DOI: 10.1017/s0033291719000072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading cause of disability worldwide and influenced by both environmental and genetic factors. Genetic studies of MDD have focused on common variants and have been constrained by the heterogeneity of clinical symptoms. METHODS We sequenced the exome of 77 cases and 245 controls of Han Chinese ancestry and scanned their brain. Burden tests of rare variants were performed first to explore the association between genes/pathways and MDD. Secondly, parallel Independent Component Analysis was conducted to investigate genetic underpinnings of gray matter volume (GMV) changes of MDD. RESULTS Two genes (CSMD1, p = 5.32×10-6; CNTNAP5, p = 1.32×10-6) and one pathway (Neuroactive Ligand Receptor Interactive, p = 1.29×10-5) achieved significance in burden test. In addition, we identified one pair of imaging-genetic components of significant correlation (r = 0.38, p = 9.92×10-6). The imaging component reflected decreased GMV in cases and correlated with intelligence quotient (IQ). IQ mediated the effects of GMV on MDD. The genetic component enriched in two gene sets, namely Singling by G-protein coupled receptors [false discovery rate (FDR) q = 3.23×10-4) and Alzheimer Disease Up (FDR q = 6.12×10-4). CONCLUSIONS Both rare variants analysis and imaging-genetic analysis found evidence corresponding with the neuroinflammation and synaptic plasticity hypotheses of MDD. The mediation of IQ indicates that genetic component may act on MDD through GMV alteration and cognitive impairment.
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Affiliation(s)
- Yamin Zhang
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Mingli Li
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Qiang Wang
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jacob Shujui Hsu
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wei Deng
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xiaohong Ma
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Peiyan Ni
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Liansheng Zhao
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yang Tian
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Pak Chung Sham
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tao Li
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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210
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van Loo KMJ, Becker AJ. Transcriptional Regulation of Channelopathies in Genetic and Acquired Epilepsies. Front Cell Neurosci 2020; 13:587. [PMID: 31992970 PMCID: PMC6971179 DOI: 10.3389/fncel.2019.00587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/23/2019] [Indexed: 01/03/2023] Open
Abstract
Epilepsy is a common neurological disorder characterized by recurrent uncontrolled seizures and has an idiopathic “genetic” etiology or a symptomatic “acquired” component. Genetic studies have revealed that many epilepsy susceptibility genes encode ion channels, including voltage-gated sodium, potassium and calcium channels. The high prevalence of ion channels in epilepsy pathogenesis led to the causative concept of “ion channelopathies,” which can be elicited by specific mutations in the coding or promoter regions of genes in genetic epilepsies. Intriguingly, expression changes of the same ion channel genes by augmentation of specific transcription factors (TFs) early after an insult can underlie acquired epilepsies. In this study, we review how the transcriptional regulation of ion channels in both genetic and acquired epilepsies can be controlled, and compare these epilepsy “ion channelopathies” with other neurodevelopmental disorders.
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Affiliation(s)
- Karen M J van Loo
- Department of Neuropathology, Section for Translational Epilepsy Research, University of Bonn Medical Center, Bonn, Germany
| | - Albert J Becker
- Department of Neuropathology, Section for Translational Epilepsy Research, University of Bonn Medical Center, Bonn, Germany
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211
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Oury C, Donis N, Marechal P. Can Body Fat Cause Aortic Stenosis?: Lessons From Genetics. J Am Coll Cardiol 2020; 75:177-179. [PMID: 31948646 DOI: 10.1016/j.jacc.2019.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Cécile Oury
- Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège Hospital, Department of Cardiology, CHU Sart Tilman, Liège, Belgium.
| | - Nathalie Donis
- Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège Hospital, Department of Cardiology, CHU Sart Tilman, Liège, Belgium
| | - Patrick Marechal
- Laboratory of Cardiology, GIGA Cardiovascular Sciences, University of Liège Hospital, Department of Cardiology, CHU Sart Tilman, Liège, Belgium
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212
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Xu Y, Liu X, Fu J, Wang H, Wang J, Huang C, Prasanna BM, Olsen MS, Wang G, Zhang A. Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants. PLANT COMMUNICATIONS 2020; 1:100005. [PMID: 33404534 PMCID: PMC7747995 DOI: 10.1016/j.xplc.2019.100005] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate of genetic gain needs to be accelerated to meet humanity's demand for agricultural products. In this regard, genomic selection (GS) has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due to livestock's significantly higher individual values and the greater reduction in generation interval that can be achieved in GS. Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects, along with significant cost reduction. Moreover, it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain. In addition, establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small- and medium-sized enterprises and agricultural research systems in developing countries. New strategies centered on GS for enhancing genetic gain need to be developed.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- CIMMYT-China Tropical Maize Research Center, Foshan University, Foshan 528231, China
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201400, China
| | - Xiaogang Liu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwu Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiankang Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changling Huang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Boddupalli M. Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S. Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Guoying Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Aimin Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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213
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Sleep deprivation, vigilant attention, and brain function: a review. Neuropsychopharmacology 2020; 45:21-30. [PMID: 31176308 PMCID: PMC6879580 DOI: 10.1038/s41386-019-0432-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/13/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022]
Abstract
Vigilant attention is a major component of a wide range of cognitive performance tasks. Vigilant attention is impaired by sleep deprivation and restored after rest breaks and (more enduringly) after sleep. The temporal dynamics of vigilant attention deficits across hours and days are driven by physiologic, sleep regulatory processes-a sleep homeostatic process and a circadian process. There is also evidence of a slower, allostatic process, which modulates the sleep homeostatic setpoint across days and weeks and is responsible for cumulative deficits in vigilant attention across consecutive days of sleep restriction. There are large inter-individual differences in vulnerability to sleep loss, and these inter-individual differences constitute a pronounced human phenotype. However, this phenotype is multi-dimensional; vulnerability in terms of vigilant attention impairment can be dissociated from vulnerability in terms of other cognitive processes such as attentional control. The vigilance decrement, or time-on-task effect-a decline in performance across the duration of a vigilant attention task-is characterized by progressively increasing response variability, which is exacerbated by sleep loss. This variability, while crucial to understanding the impact of sleep deprivation on performance in safety-critical tasks, is not well explained by top-down regulatory mechanisms, such as the homeostatic and circadian processes. A bottom-up, neuronal pathway-dependent mechanism involving use-dependent, local sleep may be the main driver of response variability. This bottom-up mechanism may also explain the dissociation between cognitive processes with regard to trait vulnerability to sleep loss.
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214
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Yang T, Kim J, Wu C, Ma Y, Wei P, Pan W. An adaptive test for meta-analysis of rare variant association studies. Genet Epidemiol 2020; 44:104-116. [PMID: 31830326 PMCID: PMC6980317 DOI: 10.1002/gepi.22273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/12/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Single genome-wide studies may be underpowered to detect trait-associated rare variants with moderate or weak effect sizes. As a viable alternative, meta-analysis is widely used to increase power by combining different studies. The power of meta-analysis critically depends on the underlying association patterns and heterogeneity levels, which are unknown and vary from locus to locus. However, existing methods mainly focus on one or only a few combinations of the association pattern and heterogeneity level, thus may lose power in many situations. To address this issue, we propose a general and unified framework by combining a class of tests including and beyond some existing ones, leading to high power across a wide range of scenarios. We demonstrate that the proposed test is more powerful than some existing methods in simulation studies, then show their performance with the NHLBI Exome-Sequencing Project (ESP) data. One gene (B4GALNT2) was found by our proposed test, but not by others, to be statistically significantly associated with plasma triglyceride. The signal was driven by African-ancestry subjects but it was previously reported to be associated with coronary artery disease among European-ancestry subjects. We implemented our method in an R package aSPUmeta, publicly available at https://github.com/ytzhong/metaRV and will be on CRAN soon.
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Affiliation(s)
- Tianzhong Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Junghi Kim
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Yiding Ma
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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215
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Liu L, Wang P, Meng J, Chen L, Zhu W, Ma W. A permutation method for detecting trend correlations in rare variant association studies. Genet Res (Camb) 2019; 101:e13. [PMID: 31831092 PMCID: PMC7044977 DOI: 10.1017/s0016672319000120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/25/2019] [Accepted: 11/07/2019] [Indexed: 01/14/2023] Open
Abstract
In recent years, there has been an increasing interest in detecting disease-related rare variants in sequencing studies. Numerous studies have shown that common variants can only explain a small proportion of the phenotypic variance for complex diseases. More and more evidence suggests that some of this missing heritability can be explained by rare variants. Considering the importance of rare variants, researchers have proposed a considerable number of methods for identifying the rare variants associated with complex diseases. Extensive research has been carried out on testing the association between rare variants and dichotomous, continuous or ordinal traits. So far, however, there has been little discussion about the case in which both genotypes and phenotypes are ordinal variables. This paper introduces a method based on the γ-statistic, called OV-RV, for examining disease-related rare variants when both genotypes and phenotypes are ordinal. At present, little is known about the asymptotic distribution of the γ-statistic when conducting association analyses for rare variants. One advantage of OV-RV is that it provides a robust estimation of the distribution of the γ-statistic by employing the permutation approach proposed by Fisher. We also perform extensive simulations to investigate the numerical performance of OV-RV under various model settings. The simulation results reveal that OV-RV is valid and efficient; namely, it controls the type I error approximately at the pre-specified significance level and achieves greater power at the same significance level. We also apply OV-RV for rare variant association studies of diastolic blood pressure.
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Affiliation(s)
- Lifeng Liu
- School of Mathematical Sciences, Heilongjiang University, Harbin150080, China
| | - Pengfei Wang
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun130024, China
| | - Jingbo Meng
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun130024, China
| | - Lili Chen
- School of Mathematical Sciences, Heilongjiang University, Harbin150080, China
| | - Wensheng Zhu
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun130024, China
| | - Weijun Ma
- School of Mathematical Sciences, Heilongjiang University, Harbin150080, China
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216
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Pallares LF. Searching for solutions to the missing heritability problem. eLife 2019; 8:53018. [PMID: 31799931 PMCID: PMC6892610 DOI: 10.7554/elife.53018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 01/04/2023] Open
Abstract
Rare genetic variants in yeast explain a large amount of phenotypic variation in a complex trait like growth.
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Affiliation(s)
- Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
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217
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Awika HO, Marconi TG, Bedre R, Mandadi KK, Avila CA. Minor alleles are associated with white rust ( Albugo occidentalis) susceptibility in spinach ( Spinacia oleracea). HORTICULTURE RESEARCH 2019; 6:129. [PMID: 31814982 PMCID: PMC6885047 DOI: 10.1038/s41438-019-0214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/29/2019] [Accepted: 11/03/2019] [Indexed: 05/05/2023]
Abstract
Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.
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Affiliation(s)
- Henry O. Awika
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Thiago G. Marconi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Plant Pathology and Microbiology, College Station, TX 77843 USA
| | - Carlos A. Avila
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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218
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Vlachos C, Kofler R. Optimizing the Power to Identify the Genetic Basis of Complex Traits with Evolve and Resequence Studies. Mol Biol Evol 2019; 36:2890-2905. [PMID: 31400203 PMCID: PMC6878953 DOI: 10.1093/molbev/msz183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Evolve and resequence (E&R) studies are frequently used to dissect the genetic basis of quantitative traits. By subjecting a population to truncating selection for several generations and estimating the allele frequency differences between selected and nonselected populations using next-generation sequencing (NGS), the loci contributing to the selected trait may be identified. The role of different parameters, such as, the population size or the number of replicate populations has been examined in previous works. However, the influence of the selection regime, that is the strength of truncating selection during the experiment, remains little explored. Using whole genome, individual based forward simulations of E&R studies, we found that the power to identify the causative alleles may be maximized by gradually increasing the strength of truncating selection during the experiment. Notably, such an optimal selection regime comes at no or little additional cost in terms of sequencing effort and experimental time. Interestingly, we also found that a selection regime which optimizes the power to identify the causative loci is not necessarily identical to a regime that maximizes the phenotypic response. Finally, our simulations suggest that an E&R study with an optimized selection regime may have a higher power to identify the genetic basis of quantitative traits than a genome-wide association study, highlighting that E&R is a powerful approach for finding the loci underlying complex traits.
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Affiliation(s)
- Christos Vlachos
- Institute für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
- Vienna Graduate School of Population Genetics, Wien, Austria
| | - Robert Kofler
- Institute für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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219
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Abstract
Although chronic obstructive pulmonary disease (COPD) risk is strongly influenced by cigarette smoking, genetic factors are also important determinants of COPD. In addition to Mendelian syndromes such as alpha-1 antitrypsin deficiency, many genomic regions that influence COPD susceptibility have been identified in genome-wide association studies. Similarly, multiple genomic regions associated with COPD-related phenotypes, such as quantitative emphysema measures, have been found. Identifying the functional variants and key genes within these association regions remains a major challenge. However, newly identified COPD susceptibility genes are already providing novel insights into COPD pathogenesis. Network-based approaches that leverage these genetic discoveries have the potential to assist in decoding the complex genetic architecture of COPD.
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Affiliation(s)
- Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;
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220
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Bai WY, Zhu XW, Cong PK, Zhang XJ, Richards JB, Zheng HF. Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity. Brief Bioinform 2019; 21:bbz108. [PMID: 32002535 DOI: 10.1093/bib/bbz108] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022] Open
Abstract
Here, 622 imputations were conducted with 394 customized reference panels for Han Chinese and European populations. Besides validating the fact that imputation accuracy could always benefit from the increased panel size when the reference panel was population specific, the results brought two new thoughts. First, when the haplotype size of the reference panel was fixed, the imputation accuracy of common and low-frequency variants (Minor Allele Frequency (MAF) > 0.5%) decreased while the population diversity of the reference panel increased, but for rare variants (MAF < 0.5%), a small fraction of diversity in panel could improve imputation accuracy. Second, when the haplotype size of the reference panel was increased with extra population-diverse samples, the imputation accuracy of common variants (MAF > 5%) for the European population could always benefit from the expanding sample size. However, for the Han Chinese population, the accuracy of all imputed variants reached the highest when reference panel contained a fraction of an extra diverse sample (8-21%). In addition, we evaluated the imputation performances in the existing reference panels, such as the Haplotype Reference Consortium (HRC), 1000 Genomes Project Phase 3 and the China, Oxford and Virginia Commonwealth University Experimental Research on Genetic Epidemiology (CONVERGE). For the European population, the HRC panel showed the best performance in our analysis. For the Han Chinese population, we proposed an optimum imputation reference panel constituent ratio if researchers would like to customize their own sequenced reference panel, but a high-quality and large-scale Chinese reference panel was still needed. Our findings could be generalized to the other populations with conservative genome; a tool was provided to investigate other populations of interest (https://github.com/Abyss-bai/reference-panel-reconstruction).
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Affiliation(s)
- Wei-Yang Bai
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Xiao-Wei Zhu
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Pei-Kuan Cong
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Xue-Jun Zhang
- Institute of Dermatology and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Hou-Feng Zheng
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
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221
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Fournier T, Abou Saada O, Hou J, Peter J, Caudal E, Schacherer J. Extensive impact of low-frequency variants on the phenotypic landscape at population-scale. eLife 2019; 8:49258. [PMID: 31647416 PMCID: PMC6892612 DOI: 10.7554/elife.49258] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) allow to dissect complex traits and map genetic variants, which often explain relatively little of the heritability. One potential reason is the preponderance of undetected low-frequency variants. To increase their allele frequency and assess their phenotypic impact in a population, we generated a diallel panel of 3025 yeast hybrids, derived from pairwise crosses between natural isolates and examined a large number of traits. Parental versus hybrid regression analysis showed that while most phenotypic variance is explained by additivity, a third is governed by non-additive effects, with complete dominance having a key role. By performing GWAS on the diallel panel, we found that associated variants with low frequency in the initial population are overrepresented and explain a fraction of the phenotypic variance as well as an effect size similar to common variants. Overall, we highlighted the relevance of low-frequency variants on the phenotypic variation.
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Affiliation(s)
- Téo Fournier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jackson Peter
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Elodie Caudal
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
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222
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Bloom JS, Boocock J, Treusch S, Sadhu MJ, Day L, Oates-Barker H, Kruglyak L. Rare variants contribute disproportionately to quantitative trait variation in yeast. eLife 2019; 8:49212. [PMID: 31647408 PMCID: PMC6892613 DOI: 10.7554/elife.49212] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/23/2019] [Indexed: 11/24/2022] Open
Abstract
How variants with different frequencies contribute to trait variation is a central question in genetics. We use a unique model system to disentangle the contributions of common and rare variants to quantitative traits. We generated ~14,000 progeny from crosses among 16 diverse yeast strains and identified thousands of quantitative trait loci (QTLs) for 38 traits. We combined our results with sequencing data for 1011 yeast isolates to show that rare variants make a disproportionate contribution to trait variation. Evolutionary analyses revealed that this contribution is driven by rare variants that arose recently, and that negative selection has shaped the relationship between variant frequency and effect size. We leveraged the structure of the crosses to resolve hundreds of QTLs to single genes. These results refine our understanding of trait variation at the population level and suggest that studies of rare variants are a fertile ground for discovery of genetic effects.
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Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, United States
| | - James Boocock
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, United States
| | - Sebastian Treusch
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, United States
| | - Meru J Sadhu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, United States
| | - Laura Day
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Holly Oates-Barker
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, United States
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223
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Conley D, Sotoudeh R, Laidley T. Birth Weight and Development: Bias or Heterogeneity by Polygenic Risk Factors? POPULATION RESEARCH AND POLICY REVIEW 2019. [DOI: 10.1007/s11113-019-09559-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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224
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Povysil G, Petrovski S, Hostyk J, Aggarwal V, Allen AS, Goldstein DB. Rare-variant collapsing analyses for complex traits: guidelines and applications. Nat Rev Genet 2019; 20:747-759. [PMID: 31605095 DOI: 10.1038/s41576-019-0177-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/11/2022]
Abstract
The first phase of genome-wide association studies (GWAS) assessed the role of common variation in human disease. Advances optimizing and economizing high-throughput sequencing have enabled a second phase of association studies that assess the contribution of rare variation to complex disease in all protein-coding genes. Unlike the early microarray-based studies, sequencing-based studies catalogue the full range of genetic variation, including the evolutionarily youngest forms. Although the experience with common variants helped establish relevant standards for genome-wide studies, the analysis of rare variation introduces several challenges that require novel analysis approaches.
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Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.,Department of Medicine, The University of Melbourne, Austin Health and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
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225
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Zeng Z, Bromberg Y. Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives. Front Genet 2019; 10:914. [PMID: 31649718 PMCID: PMC6791167 DOI: 10.3389/fgene.2019.00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput experimentation have put the exploration of genome sequences at the forefront of precision medicine. In an effort to interpret the sequencing data, numerous computational methods have been developed for evaluating the effects of genome variants. Interestingly, despite the fact that every person has as many synonymous (sSNV) as non-synonymous single nucleotide variants, our ability to predict their effects is limited. The paucity of experimentally tested sSNV effects appears to be the limiting factor in development of such methods. Here, we summarize the details and evaluate the performance of nine existing computational methods capable of predicting sSNV effects. We used a set of observed and artificially generated variants to approximate large scale performance expectations of these tools. We note that the distribution of these variants across amino acid and codon types suggests purifying evolutionary selection retaining generated variants out of the observed set; i.e., we expect the generated set to be enriched for deleterious variants. Closer inspection of the relationship between the observed variant frequencies and the associated prediction scores identifies predictor-specific scoring thresholds of reliable effect predictions. Notably, across all predictors, the variants scoring above these thresholds were significantly more often generated than observed. which confirms our assumption that the generated set is enriched for deleterious variants. Finally, we find that while the methods differ in their ability to identify severe sSNV effects, no predictor appears capable of definitively recognizing subtle effects of such variants on a large scale.
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Affiliation(s)
- Zishuo Zeng
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, United States
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Genetics, Rutgers University, Human Genetics Institute, Piscataway, NJ, United States
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Update on the Role of the Non-Canonical Wnt/Planar Cell Polarity Pathway in Neural Tube Defects. Cells 2019; 8:cells8101198. [PMID: 31590237 PMCID: PMC6829399 DOI: 10.3390/cells8101198] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/26/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
Neural tube defects (NTDs), including spina bifida and anencephaly, represent the most severe and common malformations of the central nervous system affecting 0.7–3 per 1000 live births. They result from the failure of neural tube closure during the first few weeks of pregnancy. They have a complex etiology that implicate a large number of genetic and environmental factors that remain largely undetermined. Extensive studies in vertebrate models have strongly implicated the non-canonical Wnt/planar cell polarity (PCP) signaling pathway in the pathogenesis of NTDs. The defects in this pathway lead to a defective convergent extension that is a major morphogenetic process essential for neural tube elongation and subsequent closure. A large number of genetic studies in human NTDs have demonstrated an important role of PCP signaling in their etiology. However, the relative contribution of this pathway to this complex etiology awaits a better picture of the complete genetic architecture of these defects. The emergence of new genome technologies and bioinformatics pipelines, complemented with the powerful tool of animal models for variant interpretation as well as significant collaborative efforts, will help to dissect the complex genetics of NTDs. The ultimate goal is to develop better preventive and counseling strategies for families affected by these devastating conditions.
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Knobloch TJ, Peng J, Hade EM, Cohn DE, Ruffin MT, Schiano MA, Calhoun BC, McBee WC, Lesnock JL, Gallion HH, Pollock J, Lu B, Oghumu S, Zhang Z, Sears MT, Ogbemudia BE, Perrault JT, Weghorst LC, Strawser E, DeGraffinreid CR, Paskett ED, Weghorst CM. Inherited alterations of TGF beta signaling components in Appalachian cervical cancers. Cancer Causes Control 2019; 30:1087-1100. [PMID: 31435875 PMCID: PMC6768402 DOI: 10.1007/s10552-019-01221-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 08/15/2019] [Indexed: 12/18/2022]
Abstract
PURPOSE This study examined targeted genomic variants of transforming growth factor beta (TGFB) signaling in Appalachian women. Appalachian women with cervical cancer were compared to healthy Appalachian counterparts to determine whether these polymorphic alleles were over-represented within this high-risk cancer population, and whether lifestyle or environmental factors modified the aggregate genetic risk in these Appalachian women. METHODS Appalachian women's survey data and blood samples from the Community Awareness, Resources, and Education (CARE) CARE I and CARE II studies (n = 163 invasive cervical cancer cases, 842 controls) were used to assess gene-environment interactions and cancer risk. Polymorphic allele frequencies and socio-behavioral demographic measurements were compared using t tests and χ2 tests. Multivariable logistic regression was used to evaluate interaction effects between genomic variance and demographic, behavioral, and environmental characteristics. RESULTS Several alleles demonstrated significant interaction with smoking (TP53 rs1042522, TGFB1 rs1800469), alcohol consumption (NQO1 rs1800566), and sexual intercourse before the age of 18 (TGFBR1 rs11466445, TGFBR1 rs7034462, TGFBR1 rs11568785). Interestingly, we noted a significant interaction between "Appalachian self-identity" variables and NQO1 rs1800566. Multivariable logistic regression of cancer status in an over-dominant TGFB1 rs1800469/TGFBR1 rs11568785 model demonstrated a 3.03-fold reduction in cervical cancer odds. Similar decreased odds (2.78-fold) were observed in an over-dominant TGFB1 rs1800469/TGFBR1 rs7034462 model in subjects who had no sexual intercourse before age 18. CONCLUSIONS This study reports novel associations between common low-penetrance alleles in the TGFB signaling cascade and modified risk of cervical cancer in Appalachian women. Furthermore, our unexpected findings associating Appalachian identity and NQO1 rs1800566 suggests that the complex environmental exposures that contribute to Appalachian self-identity in Appalachian cervical cancer patients represent an emerging avenue of scientific exploration.
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Affiliation(s)
- Thomas J Knobloch
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| | - Juan Peng
- Department of Biomedical Informatics, Center for Biostatistics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Erinn M Hade
- Department of Biomedical Informatics, Center for Biostatistics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - David E Cohn
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wexner Medical Center, College of Medicine, The Ohio State University Columbus, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Mack T Ruffin
- Department of Family and Community Medicine, Milton S. Hershey Medical Center, Penn State University, Hersey, PA, 17033, USA
| | - Michael A Schiano
- Department of Obstetrics & Gynecology, West Virginia University, Charleston, WV, 26505, USA
- Charleston Area Medical Center Health System, Charleston, WV, 25302, USA
| | - Byron C Calhoun
- Department of Obstetrics & Gynecology, West Virginia University, Charleston, WV, 26505, USA
- Charleston Area Medical Center Health System, Charleston, WV, 25302, USA
| | | | | | | | - Jondavid Pollock
- Wheeling Hospital, Schiffler Cancer Center, Wheeling, WV, 26003, USA
| | - Bo Lu
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Steve Oghumu
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Zhaoxia Zhang
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Marta T Sears
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Joseph T Perrault
- Division of Cancer Prevention and Control, Wexner Medical Center, College of Medicine, The Ohio State University Columbus, Columbus, OH, 43210, USA
| | - Logan C Weghorst
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Erin Strawser
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Cecilia R DeGraffinreid
- Division of Cancer Prevention and Control, Wexner Medical Center, College of Medicine, The Ohio State University Columbus, Columbus, OH, 43210, USA
| | - Electra D Paskett
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- Division of Cancer Prevention and Control, Wexner Medical Center, College of Medicine, The Ohio State University Columbus, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Christopher M Weghorst
- College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
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228
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Thompson PA, Bishop DVM, Eising E, Fisher SE, Newbury DF. Generalized Structured Component Analysis in candidate gene association studies: applications and limitations. Wellcome Open Res 2019; 4:142. [PMID: 33521327 PMCID: PMC7818107 DOI: 10.12688/wellcomeopenres.15396.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/15/2024] Open
Abstract
Background: Generalized Structured Component Analysis (GSCA) is a component-based alternative to traditional covariance-based structural equation modelling. This method has previously been applied to test for association between candidate genes and clinical phenotypes, contrasting with traditional genetic association analyses that adopt univariate testing of many individual single nucleotide polymorphisms (SNPs) with correction for multiple testing. Methods: We first evaluate the ability of the GSCA method to replicate two previous findings from a genetics association study of developmental language disorders. We then present the results of a simulation study to test the validity of the GSCA method under more restrictive data conditions, using smaller sample sizes and larger numbers of SNPs than have previously been investigated. Finally, we compare GSCA performance against univariate association analysis conducted using PLINK v1.9. Results: Results from simulations show that power to detect effects depends not just on sample size, but also on the ratio of SNPs with effect to number of SNPs tested within a gene. Inclusion of many SNPs in a model dilutes true effects. Conclusions: We propose that GSCA is a useful method for replication studies, when candidate SNPs have been identified, but should not be used for exploratory analysis.
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Affiliation(s)
- Paul A. Thompson
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Else Eising
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Montessorilaan 3, Nijmegen, 6525 HR, The Netherlands
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK
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El-Soda M, Neris Moreira C, Goredema-Matongera N, Jamar D, Koornneef M, Aarts MGM. QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:410. [PMID: 31533608 PMCID: PMC6751748 DOI: 10.1186/s12870-019-1996-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/29/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability. RESULTS Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus. CONCLUSION We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
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Affiliation(s)
- Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613 Egypt
| | - Charles Neris Moreira
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Nakai Goredema-Matongera
- Department of Research and Specialist Services, Maize Breeding Programme, Crop Breeding Institute, P. O. Box CY550 Causeway, Harare, Zimbabwe
| | - Diaan Jamar
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mark G. M. Aarts
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Contribution of Four Polymorphisms in Renin-Angiotensin-Aldosterone-Related Genes to Hypertension in a Thai Population. Int J Hypertens 2019; 2019:4861081. [PMID: 31511791 PMCID: PMC6710803 DOI: 10.1155/2019/4861081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/16/2019] [Indexed: 01/19/2023] Open
Abstract
Introduction The roles of genes in the renin-angiotensin-aldosterone system (RAAS) in hypertension, including angiotensin-converting enzyme (ACE), angiotensinogen (AGT), angiotensin II receptor type 1 (AGTR1), and aldosterone synthase (CYP11B2), have been widely studied across different ethnicities, but there has been no such investigation in Thai population. Materials and Methods Using 4,150 Thais recorded in the Electricity Generating Authority of Thailand (EGAT) study, we examined the association of rs1799752, rs699, rs5186, and rs1799998 located in or near ACE, AGT, AGTR1, and CYP11B2 genes in hypertension. We investigated their roles in hypertension using multivariate logistic regression and further examined their roles in blood pressure (BP) using quantile regression. Sex, age, and BMI were adjusted as potential confounders. Results We did not observe associations between hypertension and rs1799752 (P=0.422), rs699 (P=0.36), rs5186 (P=0.49), and rs1799998 (P=0.71). No evidence of association between these SNPs and BP was found across an entire distribution. A nonlinear relationship between age and BP was observed. Conclusion In Thai population, our study showed no evidence of association between RAAS-related genes and hypertension. While our study is the first and largest study to investigate the role of RAAS-related genes in hypertension in Thai population, restricted statistical power due to limited sample size is a limitation.
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231
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Cai L, He L. Placebo effects and the molecular biological components involved. Gen Psychiatr 2019; 32:e100089. [PMID: 31552390 PMCID: PMC6738668 DOI: 10.1136/gpsych-2019-100089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Pharmacologically inactive substances have been used in medicine for more than 700 years and can trigger beneficial responses in the human body, which is referred to as the placebo effects or placebo responses. This effect is robust enough to influence psychosocial and physiological responses to the placebo and to active treatments in many settings, which has led to increased interest from researchers. In this article, we summarise the history of placebo, the characteristics of placebo effects and recent advancements reported from the studies on placebo effects and highlight placebome studies to identify various molecular biological components associated with placebo effects. Although placebos have a long history, the placebome concept is still in its infancy. Although behavioural, neurobiological and genetic studies have identified that molecules in the dopamine, opioid, serotonin and endocannabinoid systems might be targets of the placebo effect, placebome studies with a no-treatment control (NTC) are necessary to identify whole-genome genetic targets. Although bioinformatics analysis has identified the molecular placebome module, placebome studies with NTCs are also required to validate the related findings.
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Affiliation(s)
- Lei Cai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center of Genetics and Development, Shanghai Jiaotong University, Shanghai 200240, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center of Genetics and Development, Shanghai Jiaotong University, Shanghai 200240, China
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232
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Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays. G3-GENES GENOMES GENETICS 2019; 9:3023-3033. [PMID: 31337639 PMCID: PMC6723120 DOI: 10.1534/g3.119.400549] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modern improvement of complex traits in agricultural species relies on successful associations of heritable molecular variation with observable phenotypes. Historically, this pursuit has primarily been based on easily measurable genetic markers. The recent advent of new technologies allows assaying and quantifying biological intermediates (hereafter endophenotypes) which are now readily measurable at a large scale across diverse individuals. The usefulness of endophenotypes for delineating the regulatory landscape of the genome and genetic dissection of complex trait variation remains underexplored in plants. The work presented here illustrated the utility of a large-scale (299-genotype and seven-tissue) gene expression resource to dissect traits across multiple levels of biological organization. Using single-tissue- and multi-tissue-based transcriptome-wide association studies (TWAS), we revealed that about half of the functional variation acts through altered transcript abundance for maize kernel traits, including 30 grain carotenoid abundance traits, 20 grain tocochromanol abundance traits, and 22 field-measured agronomic traits. Comparing the efficacy of TWAS with genome-wide association studies (GWAS) and an ensemble approach that combines both GWAS and TWAS, we demonstrated that results of TWAS in combination with GWAS increase the power to detect known genes and aid in prioritizing likely causal genes. Using a variance partitioning approach in the largely independent maize Nested Association Mapping (NAM) population, we also showed that the most strongly associated genes identified by combining GWAS and TWAS explain more heritable variance for a majority of traits than the heritability captured by the random genes and the genes identified by GWAS or TWAS alone. This not only improves the ability to link genes to phenotypes, but also highlights the phenotypic consequences of regulatory variation in plants.
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233
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Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019; 98:76. [PMID: 31544798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spirometry based measurement of lung function is a global initiative for chronic obstructive lung disease (GOLD) standard to diagnose chronic obstructive pulmonary disease (COPD), one of the leading causes of mortality worldwide. The environmental and behavioural risk factors for COPD includes tobacco smoking, air pollutants and biomass fuel exposure, which can induce one or more abnormal lung function patterns. While smoking remains the primary risk factor, only 15-20% smokers develop COPD, indicating that the genetic factors are also likely to play a role. According to the study of Global Burden of Disease 2015, ∼174 million people across the world have COPD. From a comprehensive literature search conducted using the 'PubMed' and 'GWAS Catalogue' databases, and reviewing the literature available, only a limited number of studies were identified which had attempted to investigate the genetics of COPD and lung volumes, implying a huge research gap. With the advent of genomewide association studies several genetic variants linked to lung function and COPD, like HHIP, HTR4, ADAM19 and GSTCD etc., have been found and validated in different population groups, suggesting their potential role in determining lung volume and risk for COPD. This article aims at reviewing the present knowledge of the genetics of lung function and COPD.
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Affiliation(s)
- Astha Ranjan
- Department of Anthropology, University of Delhi, Delhi 110 007, India.
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234
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Can H, Kal U, Ozyigit II, Paksoy M, Turkmen O. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 2019; 98:86. [PMID: 31544799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.
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Affiliation(s)
- Hasan Can
- Faculty of Agriculture, Department of Field Crops and Horticulture, Kyrgyz-Turkish Manas University, Bishkek 720038, Kyrgyzstan.
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Ruisch IH, Dietrich A, Glennon JC, Buitelaar JK, Hoekstra PJ. Interplay between genome-wide implicated genetic variants and environmental factors related to childhood antisocial behavior in the UK ALSPAC cohort. Eur Arch Psychiatry Clin Neurosci 2019; 269:741-752. [PMID: 30569215 PMCID: PMC6689282 DOI: 10.1007/s00406-018-0964-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
We investigated gene-environment (G × E) interactions related to childhood antisocial behavior between polymorphisms implicated by recent genome-wide association studies (GWASs) and two key environmental adversities (maltreatment and smoking during pregnancy) in a large population cohort (ALSPAC). We also studied the MAOA candidate gene and addressed comorbid attention-deficit/hyperactivity disorder (ADHD). ALSPAC is a large, prospective, ethnically homogeneous British cohort. Our outcome consisted of mother-rated conduct disorder symptom scores at age 7;9 years. G × E interactions were tested in a sex-stratified way (α = 0.0031) for four GWAS-implicated variants (for males, rs4714329 and rs9471290; for females, rs2764450 and rs11215217), and a length polymorphism near the MAOA-promoter region. We found that males with rs4714329-GG (P = 0.0015) and rs9471290-AA (P = 0.0001) genotypes were significantly more susceptible to effects of smoking during pregnancy in relation to childhood antisocial behavior. Females with the rs11215217-TC genotype (P = 0.0018) were significantly less susceptible to effects of maltreatment, whereas females with the MAOA-HL genotype (P = 0.0002) were more susceptible to maltreatment effects related to antisocial behavior. After adjustment for comorbid ADHD symptomatology, aforementioned G × E's remained significant, except for rs11215217 × maltreatment, which retained only nominal significance. Genetic variants implicated by recent GWASs of antisocial behavior moderated associations of smoking during pregnancy and maltreatment with childhood antisocial behavior in the general population. While we also found a G × E interaction between the candidate gene MAOA and maltreatment, we were mostly unable to replicate the previous results regarding MAOA-G × E's. Future studies should, in addition to genome-wide implicated variants, consider polygenic and/or multimarker analyses and take into account potential sex stratification.
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Affiliation(s)
- I. Hyun Ruisch
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - Jeffrey C. Glennon
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands
| | - Jan K. Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Reinier Postlaan 12, 6525GC Nijmegen, The Netherlands
| | - Pieter J. Hoekstra
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
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Can H, Kal U, Ozyigit II, Paksoy M, Turkmen O. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 2019. [DOI: 10.1007/s12041-019-1129-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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237
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Cerrone M, Remme CA, Tadros R, Bezzina CR, Delmar M. Beyond the One Gene-One Disease Paradigm: Complex Genetics and Pleiotropy in Inheritable Cardiac Disorders. Circulation 2019; 140:595-610. [PMID: 31403841 DOI: 10.1161/circulationaha.118.035954] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inheritable cardiac disorders, which may be associated with cardiomyopathic changes, are often associated with increased risk of sudden death in the young. Early linkage analysis studies in Mendelian forms of these diseases, such as hypertrophic cardiomyopathy and long-QT syndrome, uncovered large-effect genetic variants that contribute to the phenotype. In more recent years, through genotype-phenotype studies and methodological advances in genetics, it has become evident that most inheritable cardiac disorders are not monogenic but, rather, have a complex genetic basis wherein multiple genetic variants contribute (oligogenic or polygenic inheritance). Conversely, studies on genes underlying these disorders uncovered pleiotropic effects, with a single gene affecting multiple and apparently unrelated phenotypes. In this review, we explore these 2 phenomena: on the one hand, the evidence that variants in multiple genes converge to generate one clinical phenotype, and, on the other, the evidence that variants in one gene can lead to apparently unrelated phenotypes. Although multiple conditions are addressed to illustrate these concepts, the experience obtained in the study of long-QT syndrome, Brugada syndrome, and arrhythmogenic cardiomyopathy, and in the study of functions related to SCN5A (the gene coding for the α-subunit of the most abundant sodium channel in the heart) and PKP2 (the gene coding for the desmosomal protein plakophilin-2), as well, is discussed in more detail.
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Affiliation(s)
- Marina Cerrone
- Leon H. Charney Division of Cardiology (M.C., M.D.), NYU School of Medicine, New York.,Inherited Arrhythmias Clinic and Heart Rhythm Center, Leon H. Charney Division of Cardiology (M.C.), NYU School of Medicine, New York
| | - Carol Ann Remme
- Inherited Arrhythmias Clinic and Heart Rhythm Center, Leon H. Charney Division of Cardiology (M.C.), NYU School of Medicine, New York
| | - Rafik Tadros
- Amsterdam UMC, University of Amsterdam, Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, AMC Heart Center, The Netherlands (C.A.R., C.R.B.)
| | - Connie R Bezzina
- Inherited Arrhythmias Clinic and Heart Rhythm Center, Leon H. Charney Division of Cardiology (M.C.), NYU School of Medicine, New York
| | - Mario Delmar
- Leon H. Charney Division of Cardiology (M.C., M.D.), NYU School of Medicine, New York
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238
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Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019. [DOI: 10.1007/s12041-019-1119-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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GWEHS: A Genome-Wide Effect Sizes and Heritability Screener. Genes (Basel) 2019; 10:genes10080558. [PMID: 31344961 PMCID: PMC6723621 DOI: 10.3390/genes10080558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022] Open
Abstract
During the last decade, there has been a huge development of Genome-Wide Association Studies (GWAS), and thousands of loci associated to complex traits have been detected. These efforts have led to the creation of public databases of GWAS results, making a huge source of information available on the genetic background of many diverse traits. Here we present GWEHS (Genome-Wide Effect size and Heritability Screener), an open-source online application to screen loci associated to human complex traits and diseases from the NHGRI-EBI GWAS Catalog. This application provides a way to explore the distribution of effect sizes of loci affecting these traits, as well as their contribution to heritability. Furthermore, it allows for making predictions on the change in the expected mean effect size, as well as in the heritability as new loci are found. The application enables inferences on whether the additive contribution of loci expected to be discovered in the future will be able to explain the estimates of familial heritability for the different traits. We illustrate the use of this tool, compare some of the results obtained with those from a previous meta-analysis, and discuss its uses and limitations.
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240
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Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180248. [PMID: 31154982 PMCID: PMC6560268 DOI: 10.1098/rstb.2018.0248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, University of Texas Arlington, Arlington, TX 76019, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - João F. R. Tonini
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Kathrin Näpflin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Torres
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | - Frank Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY 10024, USA
| | - Julia A. Clarke
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | | | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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241
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Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y. Power and sample size calculations for high-throughput sequencing-based experiments. Brief Bioinform 2019; 19:1247-1255. [PMID: 28605403 DOI: 10.1093/bib/bbx061] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/22/2022] Open
Abstract
Power/sample size (power) analysis estimates the likelihood of successfully finding the statistical significance in a data set. There has been a growing recognition of the importance of power analysis in the proper design of experiments. Power analysis is complex, yet necessary for the success of large studies. It is important to design a study that produces statistically accurate and reliable results. Power computation methods have been well established for both microarray-based gene expression studies and genotyping microarray-based genome-wide association studies. High-throughput sequencing (HTS) has greatly enhanced our ability to conduct biomedical studies at the highest possible resolution (per nucleotide). However, the complexity of power computations is much greater for sequencing data than for the simpler genotyping array data. Research on methods of power computations for HTS-based studies has been recently conducted but is not yet well known or widely used. In this article, we describe the power computation methods that are currently available for a range of HTS-based studies, including DNA sequencing, RNA-sequencing, microbiome sequencing and chromatin immunoprecipitation sequencing. Most importantly, we review the methods of power analysis for several types of sequencing data and guide the reader to the relevant methods for each data type.
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Affiliation(s)
- Chung-I Li
- Department of Statistics, National Cheng Kung University in Taiwan
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, USA
| | | | - Yu Shyr
- Department of Biostatistics, Vanderbilt University, USA
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University
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242
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López-Cortegano E, Caballero A. Inferring the Nature of Missing Heritability in Human Traits Using Data from the GWAS Catalog. Genetics 2019; 212:891-904. [PMID: 31123044 PMCID: PMC6614893 DOI: 10.1534/genetics.119.302077] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/11/2019] [Indexed: 02/07/2023] Open
Abstract
Thousands of genes responsible for many diseases and other common traits in humans have been detected by Genome Wide Association Studies (GWAS) in the last decade. However, candidate causal variants found so far usually explain only a small fraction of the heritability estimated by family data. The most common explanation for this observation is that the missing heritability corresponds to variants, either rare or common, with very small effect, which pass undetected due to a lack of statistical power. We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the observed distribution of locus effects for a set of 42 complex traits and to quantify their contribution to narrow-sense heritability. With the data at hand, we were able to predict the expected distribution of locus effects for 16 traits and diseases, their expected contribution to heritability, and the missing number of loci yet to be discovered to fully explain the familial heritability estimates. Our results indicate that, for 6 out of the 16 traits, the additive contribution of a great number of loci is unable to explain the familial (broad-sense) heritability, suggesting that the gap between GWAS and familial estimates of heritability may not ever be closed for these traits. In contrast, for the other 10 traits, the additive contribution of hundreds or thousands of loci yet to be found could potentially explain the familial heritability estimates, if this were the case. Computer simulations are used to illustrate the possible contribution from nonadditive genetic effects to the gap between GWAS and familial estimates of heritability.
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Affiliation(s)
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Spain
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243
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Vidmar L, Maver A, Drulović J, Sepčić J, Novaković I, Ristič S, Šega S, Peterlin B. Multiple Sclerosis patients carry an increased burden of exceedingly rare genetic variants in the inflammasome regulatory genes. Sci Rep 2019; 9:9171. [PMID: 31235738 PMCID: PMC6591387 DOI: 10.1038/s41598-019-45598-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/03/2019] [Indexed: 12/17/2022] Open
Abstract
The role of rare genetic variation and the innate immune system in the etiology of multiple sclerosis (MS) is being increasingly recognized. Recently, we described several rare variants in the NLRP1 gene, presumably conveying an increased risk for familial MS. In the present study we aimed to assess rare genetic variation in the inflammasome regulatory network. We performed whole exome sequencing of 319 probands, comprising patients with familial MS, sporadic MS and control subjects. 62 genes involved in the NLRP1/NLRP3 inflammasome regulation were screened for potentially pathogenic rare genetic variation. Aggregate mutational burden was analyzed, considering the variants' predicted pathogenicity and frequency in the general population. We demonstrate an increased (p = 0.00004) variant burden among MS patients which was most pronounced for the exceedingly rare variants with high predicted pathogenicity. These variants were found in inflammasome genes (NLRP1/3, CASP1), genes mediating inflammasome inactivation via auto and mitophagy (RIPK2, MEFV), and genes involved in response to infection with DNA viruses (POLR3A, DHX58, IFIH1) and to type-1 interferons (TYK2, PTPRC). In conclusion, we present new evidence supporting the importance of rare genetic variation in the inflammasome signaling pathway and its regulation via autophagy and interferon-β to the etiology of MS.
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Affiliation(s)
- Lovro Vidmar
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jelena Drulović
- Clinic of Neurology, CCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Juraj Sepčić
- Postgraduate Study, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ivana Novaković
- Faculty of Medicine, University of Belgrade, Institute of Human Genetics, 26 Visegradska, Belgrade, Serbia
| | - Smiljana Ristič
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Šega
- Division of Neurology, University Medical Centre Ljubljana, Zaloška 2, 1000, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia.
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244
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Otyama PI, Wilkey A, Kulkarni R, Assefa T, Chu Y, Clevenger J, O'Connor DJ, Wright GC, Dezern SW, MacDonald GE, Anglin NL, Cannon EKS, Ozias-Akins P, Cannon SB. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics 2019; 20:481. [PMID: 31185892 PMCID: PMC6558826 DOI: 10.1186/s12864-019-5824-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/21/2019] [Indexed: 12/03/2022] Open
Abstract
Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. Results LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. Conclusions Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. Electronic supplementary material The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul I Otyama
- Agronomy Department, Iowa State University, Ames, IA, USA
| | - Andrew Wilkey
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Roshan Kulkarni
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Teshale Assefa
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Ye Chu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Josh Clevenger
- Mars-Wrigley Confectionery, Center for Applied Genetic Technologies, Athens, GA, USA
| | | | | | | | | | | | | | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA - Agricultural Research Service, 1017 Crop Genome Lab 819 Wallace Rd, Ames, IA, 50011-4014, USA.
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245
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Frei O, Holland D, Smeland OB, Shadrin AA, Fan CC, Maeland S, O'Connell KS, Wang Y, Djurovic S, Thompson WK, Andreassen OA, Dale AM. Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation. Nat Commun 2019; 10:2417. [PMID: 31160569 PMCID: PMC6547727 DOI: 10.1038/s41467-019-10310-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Accumulating evidence from genome wide association studies (GWAS) suggests an abundance of shared genetic influences among complex human traits and disorders, such as mental disorders. Here we introduce a statistical tool, MiXeR, which quantifies polygenic overlap irrespective of genetic correlation, using GWAS summary statistics. MiXeR results are presented as a Venn diagram of unique and shared polygenic components across traits. At 90% of SNP-heritability explained for each phenotype, MiXeR estimates that 8.3 K variants causally influence schizophrenia and 6.4 K influence bipolar disorder. Among these variants, 6.2 K are shared between the disorders, which have a high genetic correlation. Further, MiXeR uncovers polygenic overlap between schizophrenia and educational attainment. Despite a genetic correlation close to zero, the phenotypes share 8.3 K causal variants, while 2.5 K additional variants influence only educational attainment. By considering the polygenicity, discoverability and heritability of complex phenotypes, MiXeR analysis may improve our understanding of cross-trait genetic architectures.
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Affiliation(s)
- Oleksandr Frei
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway.
| | - Dominic Holland
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA.,Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olav B Smeland
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway
| | - Chun Chieh Fan
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA.,Department of Cognitive Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Steffen Maeland
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway
| | - Kevin S O'Connell
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway.,Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway.,NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | - Wesley K Thompson
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, 92093, USA.,Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Capital Region of Denmark, Roskilde, 4000, Denmark
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway
| | - Anders M Dale
- Center for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA, 92037, USA. .,Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA. .,Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA. .,Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA.
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246
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Flood PJ. Using natural variation to understand the evolutionary pressures on plant photosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:68-73. [PMID: 31284076 DOI: 10.1016/j.pbi.2019.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Photosynthesis is the gateway of the Sun's energy into the biosphere and the source of the ozone layer; thus it is both provider and protector of life as we know it. Despite its pivotal role we know surprisingly little about the genetic basis of variation in photosynthesis and the selective pressures giving rise to or maintaining this variation. In this review, I will briefly summarise our current knowledge of intraspecific and interspecific variation in photosynthesis to understand the main selective constraints on photosynthesis and what this means for the future of nature and agriculture in a changing world.
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Affiliation(s)
- Pádraic J Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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247
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Jakobson CM, Jarosz DF. Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships. Cell Syst 2019; 8:363-379.e3. [PMID: 31054809 PMCID: PMC6560647 DOI: 10.1016/j.cels.2019.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/25/2019] [Accepted: 04/05/2019] [Indexed: 01/09/2023]
Abstract
The statistical complexity of heredity has long been evident, but its molecular origins remain elusive. To investigate, we charted 90 comprehensive genotype-to-phenotype maps in a large population of wild diploid yeast. In contrast to long-standing assumptions, all types of genetic variation contributed similarly to phenotype. Causal synonymous and regulatory variants exhibited distinct molecular signatures, as did nonlinearities in heterozygote fitness that likely contribute to hybrid vigor. Highly pleiotropic variants altered disordered sequences within signaling hubs, and their effects correlated across environments-even when antagonistic-suggesting that large fitness gains bring concomitant costs. Natural genetic networks defined by the causal loci differed from those determined by precise gene deletions or protein-protein interactions. Finally, we found that traits that would appear omnigenic in less powered studies do in fact have finite genetic determinants. Integrating these molecular principles will be crucial as genome reading and writing become routine in research, industry, and medicine.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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248
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Inglés M, Mas-Bargues C, Gimeno-Mallench L, Cruz-Guerrero R, García-García FJ, Gambini J, Borrás C, Rodríguez-Mañas L, Viña J. Relation Between Genetic Factors and Frailty in Older Adults. J Am Med Dir Assoc 2019; 20:1451-1457. [PMID: 31078485 DOI: 10.1016/j.jamda.2019.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/03/2019] [Accepted: 03/16/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Frailty is a geriatric syndrome that identifies individuals at higher risk of disability, institutionalization, and death. We previously reported that frailty is related to oxidative stress and cognitive impairment-related biomarkers. The aim of this study was to determine whether frailty is associated with genetic variants. DESIGN Longitudinal population-based cohort of 2488 community-dwelling people from Toledo, Spain, aged 65 years or older. SETTING AND PARTICIPANTS We obtained blood samples from 78 individuals with frailty and 74 nonfrail individuals who were nonfrail (according to Fried criteria) from the Toledo Study of Healthy Ageing and extracted DNA using the Chemagic DNA blood kit. MEASURES Sample genotyping was carried out by means of Axiom Exome 319 Genotyping Array (Thermo Fisher Scientific), which contains 295,988 markers [single-nucleotide polymorphisms (SNPs) and rare variants], and transferred to the GeneTitan Instrument (Affymetrix). RESULTS We found 15 SNPs (P < .001), 18 genes (P < .005), and 4 pathways (P < .05) related to cytokine-cytokine receptor interaction, natural killer cell-mediated cytotoxicity, regulation of autophagy, and renin-angiotensin system as the most strongly associated with frailty. CONCLUSIONS/IMPLICATIONS The specific genetic features related to energy metabolism, biological processes regulation, cognition, and inflammation highlighted by this preliminary analysis offer useful insights for finding biologically meaningful biomarkers of frailty that allow early diagnosis and treatment. Further research is needed to confirm our novel findings in a larger population. Indeed, the EU-funded FRAILOMICS research effort will address this question.
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Affiliation(s)
- Marta Inglés
- Freshage Research Group, Department of Physiotherapy, Faculty of Physiotherapy, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain
| | - Cristina Mas-Bargues
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain
| | - Lucia Gimeno-Mallench
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain
| | - Raquel Cruz-Guerrero
- CIBERER- Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Juan Gambini
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain
| | - Consuelo Borrás
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain.
| | - Leocadio Rodríguez-Mañas
- Department of Geriatric Medicine, Hospital Universitario de Getafe and CIBERFES (CIBER of Frailty and Healthy Ageing), Getafe, Spain
| | - Jose Viña
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, CIBERFES-ISCIII, INCLIVA, Valencia, Spain
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249
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Li X, Wu D, Cui Y, Liu B, Walter H, Schumann G, Li C, Jiang T. Reliable heritability estimation using sparse regularization in ultrahigh dimensional genome-wide association studies. BMC Bioinformatics 2019; 20:219. [PMID: 31039742 PMCID: PMC6492418 DOI: 10.1186/s12859-019-2792-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Data from genome-wide association studies (GWASs) have been used to estimate the heritability of human complex traits in recent years. Existing methods are based on the linear mixed model, with the assumption that the genetic effects are random variables, which is opposite to the fixed effect assumption embedded in the framework of quantitative genetics theory. Moreover, heritability estimators provided by existing methods may have large standard errors, which calls for the development of reliable and accurate methods to estimate heritability. RESULTS In this paper, we first investigate the influences of the fixed and random effect assumption on heritability estimation, and prove that these two assumptions are equivalent under mild conditions in the theoretical aspect. Second, we propose a two-stage strategy by first performing sparse regularization via cross-validated elastic net, and then applying variance estimation methods to construct reliable heritability estimations. Results on both simulated data and real data show that our strategy achieves a considerable reduction in the standard error while reserving the accuracy. CONCLUSIONS The proposed strategy allows for a reliable and accurate heritability estimation using GWAS data. It shows the promising future that reliable estimations can still be obtained with even a relatively restricted sample size, and should be especially useful for large-scale heritability analyses in the genomics era.
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Affiliation(s)
- Xin Li
- School of Mathematical Sciences, Zhejiang University, 38 Zheda Road, Hangzhou, 310027 China
| | - Dongya Wu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049 China
| | - Yue Cui
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
| | - Bing Liu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS) and MRC-SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Chong Li
- School of Mathematical Sciences, Zhejiang University, 38 Zheda Road, Hangzhou, 310027 China
| | - Tianzi Jiang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, 95 East Zhongguancun Road, Beijing, 100190 China
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, 4 Section 2 North Jianshe Road, Chengdu, 610054 China
- The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049 China
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250
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Wang C, Deng S, Sun L, Li L, Hu YQ. A nonparametric test for association with multiple loci in the retrospective case-control study. Stat Methods Med Res 2019; 29:589-602. [PMID: 30987531 DOI: 10.1177/0962280219842892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genome-wide association studies aim at identifying common or rare variants associated with common diseases and explaining more heritability. It is well known that common diseases are influenced by multiple single nucleotide polymorphisms (SNPs) that are usually correlated in location or function. In order to powerfully detect association signals, it is highly desirable to take account of correlations or linkage disequilibrium (LD) information among multiple SNPs in testing for association. In this article, we propose a test SLIDE that depicts the difference of the average multi-locus genotypes between cases and controls and derive its variance-covariance matrix in the retrospective design. This matrix is composed of the pairwise LD between SNPs. Thus SLIDE can borrow the strength from an external database in the population of interest with a few thousands to hundreds of thousands individuals to improve the power for detecting association. Extensive simulations show that SLIDE has apparent superiority over the existing methods, especially in the situation involving both common and rare variants, both protective and deleterious variants. Furthermore, the efficiency of the proposed method is demonstrated in the application to the data from the Wellcome Trust Case Control Consortium.
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Affiliation(s)
- Chan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biostatistics, Fudan University, Shanghai, China.,Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Shufang Deng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biostatistics, Fudan University, Shanghai, China
| | - Leiming Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biostatistics, Fudan University, Shanghai, China
| | - Liming Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biostatistics, Fudan University, Shanghai, China
| | - Yue-Qing Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Biostatistics, Fudan University, Shanghai, China.,Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China
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