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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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Williams CM, Peyre H, Ramus F. Brain volumes, thicknesses, and surface areas as mediators of genetic factors and childhood adversity on intelligence. Cereb Cortex 2022; 33:5885-5895. [PMID: 36533516 DOI: 10.1093/cercor/bhac468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
Although genetic and environmental factors influence general intelligence (g-factor), few studies examined the neuroanatomical measures mediating environmental and genetic effects on intelligence. Here, we investigate the brain volumes, cortical mean thicknesses, and cortical surface areas mediating the effects of the g-factor polygenic score (gPGS) and childhood adversity on the g-factor in the UK Biobank. We first examined the global and regional brain measures that contribute to the g-factor. Most regions contributed to the g-factor through global brain size. Parieto-frontal integration theory (P-FIT) regions were not more associated with the g-factor than non-PFIT regions. After adjusting for global brain size and regional associations, only a few regions predicted intelligence and were included in the mediation analyses. We conducted mediation analyses on global measures, regional volumes, mean thicknesses, and surface areas, separately. Total brain volume mediated 7.04% of the gPGS' effect on the g-factor and 2.50% of childhood adversity's effect on the g-factor. In comparison, the fraction of the gPGS and childhood adversity's effects mediated by individual regional volumes, surfaces, and mean thicknesses was 10-15 times smaller. Therefore, genetic and environmental effects on intelligence may be mediated to a larger extent by other brain properties.
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Affiliation(s)
- Camille M Williams
- Laboratoire de Sciences Cognitives et Psycholinguistique, Département d'Études Cognitives, École Normale Supérieure, EHESS, CNRS, PSL University, 29 rue d'ulm, 75005, Paris, France
| | - Hugo Peyre
- Laboratoire de Sciences Cognitives et Psycholinguistique, Département d'Études Cognitives, École Normale Supérieure, EHESS, CNRS, PSL University, 29 rue d'ulm, 75005, Paris, France
- INSERM UMR 1141, Paris Diderot University, 48 Bd Sérurier, 75019, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, 48 Bd Sérurier, 75019, Paris, France
| | - Franck Ramus
- Laboratoire de Sciences Cognitives et Psycholinguistique, Département d'Études Cognitives, École Normale Supérieure, EHESS, CNRS, PSL University, 29 rue d'ulm, 75005, Paris, France
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Cefalù AB, Spina R, Noto D, Rabacchi C, Giammanco A, Simone ML, Brucato F, Scrimali C, Gueli-Alletti MG, Barbagallo CM, Tarugi P, Averna MR. Comparison of two polygenic risk score to identify non-monogenic primary hypocholesterolemias in a large cohort of Italian hypocholesterolemic subjects. J Clin Lipidol 2022; 16:530-537. [DOI: 10.1016/j.jacl.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/08/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
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Auwerx C, Lepamets M, Sadler MC, Patxot M, Stojanov M, Baud D, Mägi R, Porcu E, Reymond A, Kutalik Z, Metspalu A, Milani L, Mägi R, Nelis M. The individual and global impact of copy-number variants on complex human traits. Am J Hum Genet 2022; 109:647-668. [PMID: 35240056 PMCID: PMC9069145 DOI: 10.1016/j.ajhg.2022.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/09/2022] [Indexed: 12/25/2022] Open
Abstract
The impact of copy-number variations (CNVs) on complex human traits remains understudied. We called CNVs in 331,522 UK Biobank participants and performed genome-wide association studies (GWASs) between the copy number of CNV-proxy probes and 57 continuous traits, revealing 131 signals spanning 47 phenotypes. Our analysis recapitulated well-known associations (e.g., 1q21 and height), revealed the pleiotropy of recurrent CNVs (e.g., 26 and 16 traits for 16p11.2-BP4-BP5 and 22q11.21, respectively), and suggested gene functionalities (e.g., MARF1 in female reproduction). Forty-eight CNV signals (38%) overlapped with single-nucleotide polymorphism (SNP)-GWASs signals for the same trait. For instance, deletion of PDZK1, which encodes a urate transporter scaffold protein, decreased serum urate levels, while deletion of RHD, which encodes the Rhesus blood group D antigen, associated with hematological traits. Other signals overlapped Mendelian disorder regions, suggesting variable expressivity and broad impact of these loci, as illustrated by signals mapping to Rotor syndrome (SLCO1B1/3), renal cysts and diabetes syndrome (HNF1B), or Charcot-Marie-Tooth (PMP22) loci. Total CNV burden negatively impacted 35 traits, leading to increased adiposity, liver/kidney damage, and decreased intelligence and physical capacity. Thirty traits remained burden associated after correcting for CNV-GWAS signals, pointing to a polygenic CNV architecture. The burden negatively correlated with socio-economic indicators, parental lifespan, and age (survivorship proxy), suggesting a contribution to decreased longevity. Together, our results showcase how studying CNVs can expand biological insights, emphasizing the critical role of this mutational class in shaping human traits and arguing in favor of a continuum between Mendelian and complex diseases.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Maarja Lepamets
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia; Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Marie C Sadler
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Miloš Stojanov
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - David Baud
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland.
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Symonds JD, Elliott KS, Shetty J, Armstrong M, Brunklaus A, Cutcutache I, Diver LA, Dorris L, Gardiner S, Jollands A, Joss S, Kirkpatrick M, McLellan A, MacLeod S, O'Regan M, Page M, Pilley E, Pilz DT, Stephen E, Stewart K, Ashrafian H, Knight JC, Zuberi SM. Early childhood epilepsies: epidemiology, classification, aetiology, and socio-economic determinants. Brain 2021; 144:2879-2891. [PMID: 34687210 PMCID: PMC8557326 DOI: 10.1093/brain/awab162] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/22/2021] [Accepted: 03/24/2021] [Indexed: 11/14/2022] Open
Abstract
Epilepsies of early childhood are frequently resistant to therapy and often associated with cognitive and behavioural comorbidity. Aetiology focused precision medicine, notably gene-based therapies, may prevent seizures and comorbidities. Epidemiological data utilizing modern diagnostic techniques including whole genome sequencing and neuroimaging can inform diagnostic strategies and therapeutic trials. We present a 3-year, multicentre prospective cohort study, involving all children under 3 years of age in Scotland presenting with epilepsies. We used two independent sources for case identification: clinical reporting and EEG record review. Capture-recapture methodology was then used to improve the accuracy of incidence estimates. Socio-demographic and clinical details were obtained at presentation, and 24 months later. Children were extensively investigated for aetiology. Whole genome sequencing was offered for all patients with drug-resistant epilepsy for whom no aetiology could yet be identified. Multivariate logistic regression modelling was used to determine associations between clinical features, aetiology, and outcome. Three hundred and ninety children were recruited over 3 years. The adjusted incidence of epilepsies presenting in the first 3 years of life was 239 per 100 000 live births [95% confidence interval (CI) 216-263]. There was a socio-economic gradient to incidence, with a significantly higher incidence in the most deprived quintile (301 per 100 000 live births, 95% CI 251-357) compared with the least deprived quintile (182 per 100 000 live births, 95% CI 139-233), χ2 odds ratio = 1.7 (95% CI 1.3-2.2). The relationship between deprivation and incidence was only observed in the group without identified aetiology, suggesting that populations living in higher deprivation areas have greater multifactorial risk for epilepsy. Aetiology was determined in 54% of children, and epilepsy syndrome was classified in 54%. Thirty-one per cent had an identified genetic cause for their epilepsy. We present novel data on the aetiological spectrum of the most commonly presenting epilepsies of early childhood. Twenty-four months after presentation, 36% of children had drug-resistant epilepsy (DRE), and 49% had global developmental delay (GDD). Identification of an aetiology was the strongest determinant of both DRE and GDD. Aetiology was determined in 82% of those with DRE, and 75% of those with GDD. In young children with epilepsy, genetic testing should be prioritized as it has the highest yield of any investigation and is most likely to inform precision therapy and prognosis. Epilepsies in early childhood are 30% more common than previously reported. Epilepsies of undetermined aetiology present more frequently in deprived communities. This likely reflects increased multifactorial risk within these populations.
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Affiliation(s)
- Joseph D Symonds
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK.,Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8QQ, UK
| | - Katherine S Elliott
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jay Shetty
- Department of Paediatric Neurosciences, Royal Hospital for Sick Children, Sciennes Road, Edinburgh EH9 1LF, UK
| | | | - Andreas Brunklaus
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK.,Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Louise A Diver
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospitals, Glasgow G51 4TF, UK
| | - Liam Dorris
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK.,Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sarah Gardiner
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospitals, Glasgow G51 4TF, UK
| | - Alice Jollands
- Paediatric Neurology, Tayside Children's Hospital, Dundee DD1 9SY, UK
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospitals, Glasgow G51 4TF, UK
| | - Martin Kirkpatrick
- Paediatric Neurology, Tayside Children's Hospital, Dundee DD1 9SY, UK.,School of Medicine, University of Dundee DD1 9SY, UK
| | - Ailsa McLellan
- Department of Paediatric Neurosciences, Royal Hospital for Sick Children, Sciennes Road, Edinburgh EH9 1LF, UK
| | - Stewart MacLeod
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Mary O'Regan
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK.,Paediatric Neurology, Crumlin Children's Hospital, Cooley Rd, Crumlin, Dublin D12 N512, Ireland
| | | | - Elizabeth Pilley
- Department of Paediatric Neurosciences, Royal Hospital for Sick Children, Sciennes Road, Edinburgh EH9 1LF, UK.,Paediatric Neurology, Tayside Children's Hospital, Dundee DD1 9SY, UK
| | - Daniela T Pilz
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospitals, Glasgow G51 4TF, UK
| | - Elma Stephen
- Paediatric Neurology, Royal Aberdeen Children's Hospital, Aberdeen AB25 2ZG, UK
| | - Kirsty Stewart
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospitals, Glasgow G51 4TF, UK
| | - Houman Ashrafian
- Division of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK.,Department of Experimental Therapeutics, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow G51 4TF, UK.,Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8QQ, UK
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