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Zorkoltseva IV, Elgaeva EE, Belonogova NM, Kirichenko AV, Svishcheva GR, Freidin MB, Williams FMK, Suri P, Tsepilov YA, Axenovich TI. Multi-Trait Exome-Wide Association Study of Back Pain-Related Phenotypes. Genes (Basel) 2023; 14:1962. [PMID: 37895311 PMCID: PMC10606006 DOI: 10.3390/genes14101962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Back pain (BP) is a major contributor to disability worldwide, with heritability estimated at 40-60%. However, less than half of the heritability is explained by common genetic variants identified by genome-wide association studies. More powerful methods and rare and ultra-rare variant analysis may offer additional insight. This study utilized exome sequencing data from the UK Biobank to perform a multi-trait gene-based association analysis of three BP-related phenotypes: chronic back pain, dorsalgia, and intervertebral disc disorder. We identified the SLC13A1 gene as a contributor to chronic back pain via loss-of-function (LoF) and missense variants. This gene has been previously detected in two studies. A multi-trait approach uncovered the novel FSCN3 gene and its impact on back pain through LoF variants. This gene deserves attention because it is only the second gene shown to have an effect on back pain due to LoF variants and represents a promising drug target for back pain therapy.
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Affiliation(s)
- Irina V. Zorkoltseva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
| | - Elizaveta E. Elgaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nadezhda M. Belonogova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
| | - Anatoliy V. Kirichenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
| | - Gulnara R. Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Maxim B. Freidin
- Department of Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK;
| | - Pradeep Suri
- Seattle Epidemiologic Research and Information Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
- Division of Rehabilitation Care Services, Seattle, WA 98208, USA
- Clinical Learning, Evidence, and Research Center, University of Washington, Seattle, WA 98195, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
| | - Tatiana I. Axenovich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.V.Z.); (E.E.E.); (N.M.B.); (A.V.K.); (G.R.S.); (Y.A.T.)
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Zuber V, Grinberg NF, Gill D, Manipur I, Slob EAW, Patel A, Wallace C, Burgess S. Combining evidence from Mendelian randomization and colocalization: Review and comparison of approaches. Am J Hum Genet 2022; 109:767-782. [PMID: 35452592 PMCID: PMC7612737 DOI: 10.1016/j.ajhg.2022.04.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mendelian randomization and colocalization are two statistical approaches that can be applied to summarized data from genome-wide association studies (GWASs) to understand relationships between traits and diseases. However, despite similarities in scope, they are different in their objectives, implementation, and interpretation, in part because they were developed to serve different scientific communities. Mendelian randomization assesses whether genetic predictors of an exposure are associated with the outcome and interprets an association as evidence that the exposure has a causal effect on the outcome, whereas colocalization assesses whether two traits are affected by the same or distinct causal variants. When considering genetic variants in a single genetic region, both approaches can be performed. While a positive colocalization finding typically implies a non-zero Mendelian randomization estimate, the reverse is not generally true: there are several scenarios which would lead to a non-zero Mendelian randomization estimate but lack evidence for colocalization. These include the existence of distinct but correlated causal variants for the exposure and outcome, which would violate the Mendelian randomization assumptions, and a lack of strong associations with the outcome. As colocalization was developed in the GWAS tradition, typically evidence for colocalization is concluded only when there is strong evidence for associations with both traits. In contrast, a non-zero estimate from Mendelian randomization can be obtained despite only nominally significant genetic associations with the outcome at the locus. In this review, we discuss how the two approaches can provide complementary information on potential therapeutic targets.
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Affiliation(s)
- Verena Zuber
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK; UK Dementia Research Institute at Imperial College, Imperial College London, London, UK
| | | | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Clinical Pharmacology and Therapeutics Section, Institute of Medical and Biomedical Education and Institute for Infection and Immunity, St George's, University of London, London, UK; Clinical Pharmacology Group, Pharmacy and Medicines Directorate, St George's University Hospitals NHS Foundation Trust, London, UK; Genetics Department, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Ichcha Manipur
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eric A W Slob
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Ashish Patel
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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Byun J, Han Y, Ostrom QT, Edelson J, Walsh KM, Pettit RW, Bondy ML, Hung RJ, McKay JD, Amos CI. The Shared Genetic Architectures Between Lung Cancer and Multiple Polygenic Phenotypes in Genome-Wide Association Studies. Cancer Epidemiol Biomarkers Prev 2021; 30:1156-1164. [PMID: 33771847 PMCID: PMC9108090 DOI: 10.1158/1055-9965.epi-20-1635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Prior genome-wide association studies have identified numerous lung cancer risk loci and reveal substantial etiologic heterogeneity across histologic subtypes. Analyzing the shared genetic architecture underlying variation in complex traits can elucidate common genetic etiologies across phenotypes. Exploring pairwise genetic correlations between lung cancer and other polygenic traits can reveal the common genetic etiology of correlated phenotypes. METHODS Using cross-trait linkage disequilibrium score regression, we estimated the pairwise genetic correlation and heritability between lung cancer and multiple traits using publicly available summary statistics. Identified genetic relationships were also examined after excluding genomic regions known to be associated with smoking behaviors, a major risk factor for lung cancer. RESULTS We observed several traits showing moderate single nucleotide polymorphism-based heritability and significant genetic correlations with lung cancer. We observed highly significant correlations between the genetic architectures of lung cancer and emphysema/chronic bronchitis across all histologic subtypes, as well as among lung cancer occurring among smokers. Our analyses revealed highly significant positive correlations between lung cancer and paternal history of lung cancer. We also observed a strong negative correlation with parental longevity. We observed consistent directions in genetic patterns after excluding genomic regions associated with smoking behaviors. CONCLUSIONS This study identifies numerous phenotypic traits that share genomic architecture with lung carcinogenesis and are not fully accounted for by known smoking-associated genomic loci. IMPACT These findings provide new insights into the etiology of lung cancer by identifying traits that are genetically correlated with increased risk of lung cancer.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Quinn T Ostrom
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jacob Edelson
- Department of Medicine, Center for Biomedical Informatics Research, Stanford University, Stanford, California
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Stanford, California
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Canada
| | - James D McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
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Rommelse NNJ, Franke B, Geurts HM, Hartman CA, Buitelaar JK. Shared heritability of attention-deficit/hyperactivity disorder and autism spectrum disorder. Eur Child Adolesc Psychiatry 2010; 19:281-95. [PMID: 20148275 PMCID: PMC2839489 DOI: 10.1007/s00787-010-0092-x] [Citation(s) in RCA: 392] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 01/08/2010] [Indexed: 01/17/2023]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) are both highly heritable neurodevelopmental disorders. Evidence indicates both disorders co-occur with a high frequency, in 20-50% of children with ADHD meeting criteria for ASD and in 30-80% of ASD children meeting criteria for ADHD. This review will provide an overview on all available studies [family based, twin, candidate gene, linkage, and genome wide association (GWA) studies] shedding light on the role of shared genetic underpinnings of ADHD and ASD. It is concluded that family and twin studies do provide support for the hypothesis that ADHD and ASD originate from partly similar familial/genetic factors. Only a few candidate gene studies, linkage studies and GWA studies have specifically addressed this co-occurrence, pinpointing to some promising pleiotropic genes, loci and single nucleotide polymorphisms (SNPs), but the research field is in urgent need for better designed and powered studies to tackle this complex issue. We propose that future studies examining shared familial etiological factors for ADHD and ASD use a family-based design in which the same phenotypic (ADHD and ASD), candidate endophenotypic, and environmental measurements are obtained from all family members. Multivariate multi-level models are probably best suited for the statistical analysis.
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Affiliation(s)
- Nanda N J Rommelse
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Reinier Postlaan 10, Nijmegen, The Netherlands.
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