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Lippincott MF, Schafer EC, Hindman AA, He W, Brauner R, Delaney A, Grinspon R, Hall JE, Hirschhorn JN, McElreavey K, Palmert MR, Rey R, Seminara SB, Salem RM, Chan YM. Contributions of common genetic variants to constitutional delay of puberty and idiopathic hypogonadotropic hypogonadism. J Clin Endocrinol Metab 2024:dgae166. [PMID: 38477512 DOI: 10.1210/clinem/dgae166] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
CONTEXT Constitutional delay of puberty (CDP) is highly heritable, but the genetic basis for CDP is largely unknown. Idiopathic hypogonadotropic hypogonadism (IHH) can be caused by rare genetic variants, but in about half of cases, no rare-variant cause is found. OBJECTIVE To determine whether common genetic variants that influence pubertal timing contribute to CDP and IHH. DESIGN Case-control study. PARTICIPANTS 80 individuals with CDP; 301 with normosmic IHH, and 348 with Kallmann syndrome; control genotyping data from unrelated studies. MAIN OUTCOME MEASURES Polygenic scores (PGS) based on genome-wide association studies for timing of male pubertal hallmarks and age at menarche (AAM). RESULTS The CDP cohort had higher PGS for male pubertal hallmarks and for AAM compared to controls (for male hallmarks, Cohen's d = 0.85, p = 1 × 10-16; for AAM, d = 0.67, p = 1 × 10-10). The normosmic IHH cohort also had higher PGS for male hallmarks compared to controls, but the difference was smaller (male hallmarks d = 0.20, p = 0.003; AAM d = 0.10, p = 0.055). No differences were seen for the KS cohort compared to controls (male hallmarks d = 0.04, p = 0.45; AAM d = -0.03, p = 0.86). CONCLUSIONS Common genetic variants that influence pubertal timing in the general population contribute strongly to the genetics of CDP, weakly to normosmic IHH, and potentially not at all to KS. These findings demonstrate that the common-variant genetics of CDP and normosmic IHH are largely but not entirely distinct.
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Affiliation(s)
- Margaret F Lippincott
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
| | - Evan C Schafer
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Anna A Hindman
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Wen He
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Raja Brauner
- Hôpital Fondation Adolphe de Rothschild and Université Paris Cité, Paris
| | - Angela Delaney
- Division of Endocrinology, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Romina Grinspon
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Janet E Hall
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Joel N Hirschhorn
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Mark R Palmert
- Division of Endocrinology, Hospital for Sick Children; Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON
| | - Rodolfo Rey
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Stephanie B Seminara
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Rany M Salem
- Herbert Wertheim School of Public Health & Human Longevity Science, University of San Diego, La Jolla, CA
| | - Yee-Ming Chan
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
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Farinha C, Barreto P, Coimbra R, Cachulo ML, Melo JB, Cunha-Vaz J, Lechanteur Y, Hoyng CB, Silva R. Common and rare genetic risk variants in age-related macular degeneration and genetic risk score in the Coimbra eye study. Acta Ophthalmol 2023; 101:185-199. [PMID: 36036675 DOI: 10.1111/aos.15232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/27/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022]
Abstract
PURPOSE To determine the contribution of common and rare genetic variants in age-related macular degeneration (AMD) in a Portuguese population from the Coimbra Eye Study (CES), and the genetic risk score (GRS). METHODS Participants underwent ophthalmologic examination and imaging. A centralized reading centre performed AMD staging. Genetic sequencing was carried out with the EYE-RISK assay. Sixty-nine single nucleotide polymorphisms (SNPs) were genotyped and tested for association with AMD. Case-control and progression-to-AMD analyses were performed using logistic regression to assess allelic odds ratio (OR) at a 95% confidence interval (CI) for each variant. GRS was calculated for cases/controls and progressors/non-progressors. Cumulative impact of rare variants was compared between cases/controls using logistic regression. RESULTS In case-control analysis (237 cases/640 controls) variants associated with risk of disease were: ARMS2 rs10490924, ARMS2_HTRA1 rs3750846, CFH rs35292876, SLC16A8 rs8135665, TGFBR1 rs1626340. Major risk variants ARMS2/HTRA1 rs3750846, CFH rs570618 and C3 rs2230199 had unexpected lower allele frequency (AF), and the highest risk-conferring variant was a rare variant, CFH rs35292876 (OR, 2.668; p-value = 0.021). In progression-to-AMD analysis (137 progressors/630 non-progressors), variants associated with risk of progression were ARMS2 rs10490924, ARMS2_HTRA1 rs3750846, CFH rs35292876. GRS of cases/controls was 1.124 ± 1.187 and 0.645 ± 1.124 (p-value < 0.001), and of progressors/non-progressors was 1.190 ± 1.178 and 0.669 ± 1.141 (p-value < 0.001). Higher proportion of pathogenic rare CFH variants was observed in cases (OR, 9.661; p-value < 0.001). CONCLUSIONS Both common and rare variants were associated with AMD, but a CFH rare variant conferred the highest risk of disease while three major risk variants had a lower-than-expected AF in our population originary from a geographic region with lower prevalence of AMD. GRS was still significantly higher in AMD patients. Damaging CFH rare variants were cumulatively more common in AMD cases.
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Affiliation(s)
- Cláudia Farinha
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal.,Ophthalmology Department, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, (iCBR- FMUC), University of Coimbra, Coimbra, Portugal
| | - Patricia Barreto
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal
| | - Rita Coimbra
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal
| | - Maria Luz Cachulo
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal.,Ophthalmology Department, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Joana Barbosa Melo
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - José Cunha-Vaz
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, (iCBR- FMUC), University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Yara Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Donders Institute for Brain Cognition and Behaviour, Nijmegan, Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Donders Institute for Brain Cognition and Behaviour, Nijmegan, Netherlands
| | - Rufino Silva
- AIBILI - Association for Innovation and Biomedical Research on Light and Image, Coimbra, Portugal.,Ophthalmology Department, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, (iCBR- FMUC), University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
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Upadhyai P, Shenoy PU, Banjan B, Albeshr MF, Mahboob S, Manzoor I, Das R. Exome-Wide Association Study Reveals Host Genetic Variants Likely Associated with the Severity of COVID-19 in Patients of European Ancestry. Life (Basel) 2022; 12:1300. [PMID: 36143338 PMCID: PMC9504138 DOI: 10.3390/life12091300] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Host genetic variability plays a pivotal role in modulating COVID-19 clinical outcomes. Despite the functional relevance of protein-coding regions, rare variants located here are less likely to completely explain the considerable numbers of acutely affected COVID-19 patients worldwide. Using an exome-wide association approach, with individuals of European descent, we sought to identify common coding variants linked with variation in COVID-19 severity. Herein, cohort 1 compared non-hospitalized (controls) and hospitalized (cases) individuals, and in cohort 2, hospitalized subjects requiring respiratory support (cases) were compared to those not requiring it (controls). 229 and 111 variants differed significantly between cases and controls in cohorts 1 and 2, respectively. This included FBXO34, CNTN2, and TMCC2 previously linked with COVID-19 severity using association studies. Overall, we report SNPs in 26 known and 12 novel candidate genes with strong molecular evidence implicating them in the pathophysiology of life-threatening COVID-19 and post-recovery sequelae. Of these few notable known genes include, HLA-DQB1, AHSG, ALOX5AP, MUC5AC, SMPD1, SPG7, SPEG,GAS6, and SERPINA12. These results enhance our understanding of the pathomechanisms underlying the COVID-19 clinical spectrum and may be exploited to prioritize biomarkers for predicting disease severity, as well as to improve treatment strategies in individuals of European ancestry.
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Affiliation(s)
- Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Pooja U. Shenoy
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Bhavya Banjan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Mohammed F. Albeshr
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Irfan Manzoor
- Department of Biology, The College of Arts and Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
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Peyre H, Schoeler T, Liu C, Williams CM, Hoertel N, Havdahl A, Pingault JB. Combining multivariate genomic approaches to elucidate the comorbidity between autism spectrum disorder and attention deficit hyperactivity disorder. J Child Psychol Psychiatry 2021; 62:1285-1296. [PMID: 34235737 DOI: 10.1111/jcpp.13479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) are two highly heritable neurodevelopmental disorders. Several lines of evidence point towards the presence of shared genetic factors underlying ASD and ADHD. We conducted genomic analyses of common risk variants (i.e. single nucleotide polymorphisms, SNPs) shared by ASD and ADHD, and those specific to each disorder. METHODS With the summary data from two GWAS, one on ASD (N = 46,350) and another on ADHD (N = 55,374) individuals, we used genomic structural equation modelling and colocalization analysis to identify SNPs shared by ASD and ADHD and SNPs specific to each disorder. Functional genomic analyses were then conducted on shared and specific common genetic variants. Finally, we performed a bidirectional Mendelian randomization analysis to test whether the shared genetic risk between ASD and ADHD was interpretable in terms of reciprocal relationships between ASD and ADHD. RESULTS We found that 37.5% of the SNPs associated with ASD (at p < 1e-6) colocalized with ADHD SNPs and that 19.6% of the SNPs associated with ADHD colocalized with ASD SNPs. We identified genes mapped to SNPs that are specific to ASD or ADHD and that are shared by ASD and ADHD, including two novel genes INSM1 and PAX1. Our bidirectional Mendelian randomization analyses indicated that the risk of ASD was associated with an increased risk of ADHD and vice versa. CONCLUSIONS Using multivariate genomic analyses, the present study uncovers shared and specific genetic variants associated with ASD and ADHD. Further functional investigation of genes mapped to those shared variants may help identify pathophysiological pathways and new targets for treatment.
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Affiliation(s)
- Hugo Peyre
- Department of Clinical, Educational and Health Psychology, University College London, London, UK.,Laboratoire de Sciences Cognitives et Psycholinguistique (ENS, EHESS, CNRS), Ecole Normale Supérieure, PSL University, Paris, France.,Neurodiderot, INSERM UMR 1141, Paris Diderot University, Paris, France.,Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Tabea Schoeler
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Chaoyu Liu
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Camille Michèle Williams
- Laboratoire de Sciences Cognitives et Psycholinguistique (ENS, EHESS, CNRS), Ecole Normale Supérieure, PSL University, Paris, France
| | - Nicolas Hoertel
- INSERM UMR 894, Psychiatry and Neurosciences Center, Paris Descartes University, PRES Sorbonne Paris Cité, Paris, France.,Department of Psychiatry, Corentin Celton Hospital, APHP, Issy-les-Moulineaux, Paris Descartes University, PRES Sorbonne Paris Cité, Paris, France
| | - Alexandra Havdahl
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jean-Baptiste Pingault
- Department of Clinical, Educational and Health Psychology, University College London, London, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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Aygün N, Elwell AL, Liang D, Lafferty MJ, Cheek KE, Courtney KP, Mory J, Hadden-Ford E, Krupa O, de la Torre-Ubieta L, Geschwind DH, Love MI, Stein JL. Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis. Am J Hum Genet 2021; 108:1647-1668. [PMID: 34416157 PMCID: PMC8456186 DOI: 10.1016/j.ajhg.2021.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/28/2020] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
Interpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing quantitative trait locus (e/sQTL) analyses is generally performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements active during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs, and allele-specific expression in cultured cells representing two major developmental stages, primary human neural progenitors (n = 85) and their sorted neuronal progeny (n = 74), identifying numerous loci not detected in either bulk developing cortical wall or adult cortex. Using colocalization and genetic imputation via transcriptome-wide association, we uncover cell-type-specific regulatory mechanisms underlying risk for brain-relevant traits that are active during neocortical differentiation. Specifically, we identified a progenitor-specific eQTL for CENPW co-localized with common variant associations for cortical surface area and educational attainment.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Angela L Elwell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Lafferty
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry E Cheek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenan P Courtney
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Mory
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellie Hadden-Ford
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Weigl K, Chang-Claude J, Hsu L, Hoffmeister M, Brenner H. Establishing a valid approach for estimating familial risk of cancer explained by common genetic variants. Int J Cancer 2020; 146:68-75. [PMID: 31483856 PMCID: PMC7121903 DOI: 10.1002/ijc.32664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/21/2019] [Revised: 07/31/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022]
Abstract
We critically examined existing approaches for the estimation of the excess familial risk of cancer that can be attributed to identified common genetic risk variants and propose an alternative, more straightforward approach for calculating this proportion using well-established epidemiological methodology. We applied the underlying equations of the traditional approaches and the new epidemiological approach for colorectal cancer (CRC) in a large population-based case-control study in Germany with 4,447 cases and 3,480 controls, who were recruited from 2003 to 2016 and for whom interview, medical and genomic data were available. Having a family history of CRC (FH) was associated with a 1.77-fold risk increase in our study population (95% CI 1.52-2.07). Traditional approaches yielded estimates of the FH-associated risk explained by 97 common genetics variants from 9.6% to 23.1%, depending on various assumptions. Our alternative approach resulted in smaller and more consistent estimates of this proportion, ranging from 5.4% to 14.3%. Commonly employed methods may lead to strongly divergent and possibly exaggerated estimates of excess familial risk of cancer explained by associated known common genetic variants. Our results suggest that familial risk and risk associated with known common genetic variants might reflect two complementary major sources of risk.
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Affiliation(s)
- Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center of Tumor Diseases (NCT), Heidelberg, Germany
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He Y, Theodoratou E, Li X, Din FV, Vaughan‐Shaw P, Svinti V, Farrington SM, Campbell H, Dunlop MG, Timofeeva M. Effects of common genetic variants associated with colorectal cancer risk on survival outcomes after diagnosis: A large population-based cohort study. Int J Cancer 2019; 145:2427-2432. [PMID: 31271446 PMCID: PMC6771941 DOI: 10.1002/ijc.32550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Received: 05/03/2019] [Revised: 06/06/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
Genome-wide association studies have thus far identified 130 genetic variants linked to colorectal cancer (CRC) risk (r2 < 0.2). Given their implication in disease causation, and thus plausible biologically effects on cancer-relevant biological pathways, we investigated whether these variants are associated with CRC prognosis and also whether they might provide predictive value for survival outcome. We conducted the analysis in a well-characterized population-based study of 5,675 patients after CRC diagnosis in Scotland. None of the genetic risk variants were associated with either overall survival (OS) or CRC-specific survival. Next, we combined the variants in a polygenic risk score, but again we observed no association between survival outcome and overall genetic susceptibility to CRC risk-as defined by common genetic variants (OS: hazard ratio = 1.00, 95% confidence interval = 0.96-1.05). Furthermore, we found no incremental increase in the discriminative performance when adding these genetic variants to the baseline CRC-survival predictive model of age, sex and stage at diagnosis. Given that our study is well-powered (>0.88) to detect effects on survival for 74% of the variants, we conclude that effects of common variants associated with CRC risk which have been identified to date are unlikely to have clinically relevant effect on survival outcomes for patients diagnosed with CRC.
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Affiliation(s)
- Yazhou He
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Xue Li
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Farhat V.N. Din
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Peter Vaughan‐Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Susan M. Farrington
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Harry Campbell
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and Informatics, The University of EdinburghEdinburghUnited Kingdom
| | - Malcolm G. Dunlop
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Maria Timofeeva
- Cancer Research UK Edinburgh CentreMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Colon Cancer Genetics Group, Medical Research Council Human Genetics UnitMedical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of EdinburghEdinburghUnited Kingdom
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Smeland OB, Wang Y, Frei O, Li W, Hibar DP, Franke B, Bettella F, Witoelar A, Djurovic S, Chen CH, Thompson PM, Dale AM, Andreassen OA. Genetic Overlap Between Schizophrenia and Volumes of Hippocampus, Putamen, and Intracranial Volume Indicates Shared Molecular Genetic Mechanisms. Schizophr Bull 2018; 44:854-864. [PMID: 29136250 PMCID: PMC6007549 DOI: 10.1093/schbul/sbx148] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Schizophrenia (SCZ) is associated with differences in subcortical brain volumes and intracranial volume (ICV). However, little is known about the underlying etiology of these brain alterations. Here, we explored whether brain structure volumes and SCZ share genetic risk factors. Using conditional false discovery rate (FDR) analysis, we integrated genome-wide association study (GWAS) data on SCZ (n = 82315) and GWAS data on 7 subcortical brain volumes and ICV (n = 11840). By conditioning the FDR on overlapping associations, this statistical approach increases power to discover genetic loci. To assess the credibility of our approach, we studied the identified loci in larger GWAS samples on ICV (n = 26577) and hippocampal volume (n = 26814). We observed polygenic overlap between SCZ and volumes of hippocampus, putamen, and ICV. Based on conjunctional FDR < 0.05, we identified 2 loci shared between SCZ and ICV implicating genes FOXO3 (rs10457180) and ITIH4 (rs4687658), 2 loci shared between SCZ and hippocampal volume implicating SLC4A10 (rs4664442) and SPATS2L (rs1653290), and 2 loci shared between SCZ and volume of putamen implicating DCC (rs4632195) and DLG2 (rs11233632). The loci shared between SCZ and hippocampal volume or ICV had not reached significance in the primary GWAS on brain phenotypes. Proving our point of increased power, 2 loci did reach genome-wide significance with ICV (rs10457180) and hippocampal volume (rs4664442) in the larger GWAS. Three of the 6 identified loci are novel for SCZ. Altogether, the findings provide new insights into the relationship between SCZ and brain structure volumes, suggesting that their genetic architectures are not independent.
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Affiliation(s)
- Olav B Smeland
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Neurosciences, University of California San Diego, La Jolla, CA,To whom correspondence should be addressed; Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Kirkeveien 166, 0424 Oslo, Norway; tel: +1-858-568-4915, fax: +47-230-273-33, e-mail:
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Radiology, University of California San Diego, La Jolla, CA,Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA
| | - Oleksandr Frei
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Wen Li
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Derrek P Hibar
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA
| | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway,NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Chi-Hua Chen
- Department of Radiology, University of California San Diego, La Jolla, CA,Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA
| | - Anders M Dale
- Department of Neurosciences, University of California San Diego, La Jolla, CA,Department of Radiology, University of California San Diego, La Jolla, CA,Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA,Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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Weigl K, Chang-Claude J, Knebel P, Hsu L, Hoffmeister M, Brenner H. Strongly enhanced colorectal cancer risk stratification by combining family history and genetic risk score. Clin Epidemiol 2018; 10:143-152. [PMID: 29403313 PMCID: PMC5783152 DOI: 10.2147/clep.s145636] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background and aim Family history (FH) and genetic risk scores (GRSs) are increasingly used for risk stratification for colorectal cancer (CRC) screening. However, they were mostly considered alternatively rather than jointly. The aim of this study was to assess the potential of individual and joint risk stratification for CRC by FH and GRS. Patients and methods A GRS was built based on the number of risk alleles in 53 previously identified single-nucleotide polymorphisms among 2,363 patients with a first diagnosis of CRC and 2,198 controls in DACHS [colorectal cancer: chances for prevention through screening], a population-based case-control study in Germany. Associations between GRS and FH with CRC risk were quantified by multiple logistic regression. Results A total of 316 cases (13.4%) and 214 controls (9.7%) had a first-degree relative (FDR) with CRC (adjusted odds ratio [aOR] 1.86, 95% CI 1.52–2.29). A GRS in the highest decile was associated with a 3.0-fold increased risk of CRC (aOR 3.00, 95% CI 2.24–4.02) compared with the lowest decile. This association was tentatively more pronounced in older age groups. FH and GRS were essentially unrelated, and their joint consideration provided more accurate risk stratification than risk stratification based on each of the variables individually. For example, risk was 6.1-fold increased in the presence of both FH in a FDR and a GRS in the highest decile (aOR 6.14, 95% CI 3.47–10.84) compared to persons without FH and a GRS in the lowest decile. Conclusion Both FH and the so far identified genetic variants carry essentially independent risk information and in combination provide great potential for CRC risk stratification.
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Affiliation(s)
- Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg.,University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg
| | - Phillip Knebel
- Department for General, Visceral and Transplantation Surgery, University Heidelberg, Heidelberg, Germany
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
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Abstract
Pathogenic mutations in BRCA1 and BRCA2 are associated with high risks of breast and ovarian cancer. However, penetrance estimates for mutation carriers have been found to vary substantially between studies, and the observed differences in risk are consistent with the hypothesis that genetic and environmental factors modify cancer risks for women with these mutations. Direct evidence that this is the case has emerged in the past decade, through large-scale international collaborative efforts. Here, we describe the methodological challenges in the identification and characterisation of these risk-modifying factors, review the latest evidence on genetic and lifestyle/hormonal risk factors that modify breast and ovarian cancer risks for women with BRCA1 and BRCA2 mutations and outline the implications of these findings for cancer risk prediction. We also review the unresolved issues in this area of research and identify strategies of clinical implementation so that women with BRCA1 and BRCA2 mutations are no longer counselled on the basis of 'average' risk estimates.
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Affiliation(s)
- Roger L Milne
- Cancer Epidemiology CentreCancer Council Victoria, Melbourne, Australia Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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Abstract
Endometriosis is a heritable complex disorder that is influenced by multiple genetic and environmental factors. Identification of these genetic factors will aid a better understanding of the underlying biology of the disease. In this article, we describe different methods of studying genetic variation of endometriosis, summarize results from genetic studies performed to date and provide recommendations for future studies to uncover additional factors contributing to the heritable component of endometriosis.
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Affiliation(s)
- Nilufer Rahmioglu
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Grant W Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Krina T Zondervan
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Nuffield Department of Obstetrics & Gynaecology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
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Abstract
Though extensively characterized clinically, the causes of autism spectrum disorder (ASD) remain a mystery. ASD is known to have a strong genetic basis, but it is genetically very heterogeneous. Recent studies have estimated that de novo disruptive mutations in hundreds of genes may contribute to ASD. However, it is unclear how it is possible for mutations in so many different genes to contribute to ASD. Recent findings suggest that many of the mutations disrupt genes involved in transcription regulation that are expressed prenatally in the developing brain. De novo disruptive mutations are also more frequent in girls with ASD, despite the fact that ASD is more prevalent in boys. In this paper, we hypothesize that loss of robustness may contribute to ASD. Loss of phenotypic robustness may be caused by mutations that disrupt capacitors that operate in the developing brain. This may lead to the release of cryptic genetic variation that contributes to ASD. Reduced robustness is consistent with the observed variability in expressivity and incomplete penetrance. It is also consistent with the hypothesis that the development of the female brain is more robust, and it may explain the higher rate and severity of disruptive de novo mutations in girls with ASD.
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Affiliation(s)
- Reut Suliman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Eyal Ben-David
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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Ntalla I, Panoutsopoulou K, Vlachou P, Southam L, William Rayner N, Zeggini E, Dedoussis GV. Replication of established common genetic variants for adult BMI and childhood obesity in Greek adolescents: the TEENAGE study. Ann Hum Genet 2013; 77:268-74. [PMID: 23347264 PMCID: PMC3652032 DOI: 10.1111/ahg.12012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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] [Received: 08/31/2012] [Accepted: 11/26/2012] [Indexed: 01/23/2023]
Abstract
Multiple genetic loci have been associated with body mass index (BMI) and obesity. The aim of this study was to investigate the effects of established adult BMI and childhood obesity loci in a Greek adolescent cohort. For this purpose, 34 variants were selected for investigation in 707 (55.9% females) adolescents of Greek origin aged 13.42 ± 0.88 years. Cumulative effects of variants were assessed by calculating a genetic risk score (GRS-34) for each subject. Variants at the FTO, TMEM18, FAIM2, RBJ, ZNF608 and QPCTL loci yielded nominal evidence for association with BMI and/or overweight risk (p < 0.05). Variants at TFAP2B and NEGR1 loci showed nominal association (p < 0.05) with BMI and/or overweight risk in males and females respectively. Even though we did not detect any genome-wide significant associations, 27 out of 34 variants yielded directionally consistent effects with those reported by large-scale meta-analyses (binomial sign p = 0.0008). The GRS-34 was associated with both BMI (beta = 0.17 kg/m(2) /allele; p < 0.001) and overweight risk (OR = 1.09/allele; 95% CI: 1.04-1.16; p = 0.001). In conclusion, we replicate associations of established BMI and childhood obesity variants in a Greek adolescent cohort and confirm directionally consistent effects for most of them.
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Affiliation(s)
- Ioanna Ntalla
- Harokopio University of Athens, Department of Nutrition and Dietetics, 17671 Athens, Greece.
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Devan WJ, Falcone GJ, Anderson CD, Jagiella JM, Schmidt H, Hansen BM, Jimenez-Conde J, Giralt-Steinhauer E, Cuadrado-Godia E, Soriano C, Ayres AM, Schwab K, Kassis SB, Valant V, Pera J, Urbanik A, Viswanathan A, Rost NS, Goldstein JN, Freudenberger P, Stögerer EM, Norrving B, Tirschwell DL, Selim M, Brown DL, Silliman SL, Worrall BB, Meschia JF, Kidwell CS, Montaner J, Fernandez-Cadenas I, Delgado P, Greenberg SM, Roquer J, Lindgren A, Slowik A, Schmidt R, Woo D, Rosand J, Biffi A. Heritability estimates identify a substantial genetic contribution to risk and outcome of intracerebral hemorrhage. Stroke 2013; 44:1578-83. [PMID: 23559261 DOI: 10.1161/strokeaha.111.000089] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Previous studies suggest that genetic variation plays a substantial role in occurrence and evolution of intracerebral hemorrhage (ICH). Genetic contribution to disease can be determined by calculating heritability using family-based data, but such an approach is impractical for ICH because of lack of large pedigree-based studies. However, a novel analytic tool based on genome-wide data allows heritability estimation from unrelated subjects. We sought to apply this method to provide heritability estimates for ICH risk, severity, and outcome. METHODS We analyzed genome-wide genotype data for 791 ICH cases and 876 controls, and determined heritability as the proportion of variation in phenotype attributable to captured genetic variants. Contribution to heritability was separately estimated for the APOE (encoding apolipoprotein E) gene, an established genetic risk factor, and for the rest of the genome. Analyzed phenotypes included ICH risk, admission hematoma volume, and 90-day mortality. RESULTS ICH risk heritability was estimated at 29% (SE, 11%) for non-APOE loci and at 15% (SE, 10%) for APOE. Heritability for 90-day ICH mortality was 41% for non-APOE loci and 10% (SE, 9%) for APOE. Genetic influence on hematoma volume was also substantial: admission volume heritability was estimated at 60% (SE, 70%) for non-APOEloci and at 12% (SE, 4%) for APOE. CONCLUSIONS Genetic variation plays a substantial role in ICH risk, outcome, and hematoma volume. Previously reported risk variants account for only a portion of inherited genetic influence on ICH pathophysiology, pointing to additional loci yet to be identified.
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Affiliation(s)
- William J Devan
- Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, CPZN-6818, Boston, MA 02114, USA
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15
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Walford G, Green T, Neale B, Isakova T, Rotter J, Grant S, Fox C, Pankow J, Wilson J, Meigs J, Siscovick D, Bowden D, Daly M, Florez J. Common genetic variants differentially influence the transition from clinically defined states of fasting glucose metabolism. Diabetologia 2012; 55:331-9. [PMID: 22038522 PMCID: PMC3589986 DOI: 10.1007/s00125-011-2353-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 10/06/2011] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS Common genetic variants have been associated with type 2 diabetes. We hypothesised that a subset of these variants may have different effects on the transition from normal fasting glucose (NFG) to impaired fasting glucose (IFG) than on that from IFG to diabetes. METHODS We identified 16 type 2 diabetes risk variants from the Illumina Broad Candidate-gene Association Resource (CARe) array genotyped in 26,576 CARe participants. Participants were categorised at baseline as NFG, IFG or type 2 diabetic (n = 16,465, 8,017 or 2,291, respectively). Using Cox proportional hazards and likelihood ratio tests (LRTs), we compared rates of progression by genotype for 4,909 (NFG to IFG) and 1,518 (IFG to type 2 diabetes) individuals, respectively. We then performed multinomial regression analyses at baseline, comparing the risk of assignment to the NFG, IFG or diabetes groups by genotype. RESULTS The rate of progression from NFG to IFG was significantly greater in participants carrying the risk allele at MTNR1B (p = 1 × 10(-4)), nominally greater at GCK and SLC30A8 (p < 0.05) and nominally smaller at IGF2BP2 (p = 0.01) than the rate of progression from IFG to diabetes by the LRT. Results of the baseline, multinomial regression model were consistent with these findings. CONCLUSIONS/INTERPRETATION Common genetic risk variants at GCK, SLC30A8, IGF2BP2 and MTNR1B influence to different extents the development of IFG and the transition from IFG to type 2 diabetes. Our findings may have implications for understanding the genetic contribution of these variants to the development of IFG and type 2 diabetes.
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Affiliation(s)
- G.A. Walford
- Center for Human Genetic Research, Simches Research Building - CPZN 5.250, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - T. Green
- Center for Human Genetic Research, Simches Research Building - CPZN 5.250, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - B. Neale
- Center for Human Genetic Research, Simches Research Building - CPZN 5.250, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - T. Isakova
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Renal Unit, Massachusetts General Hospital, Boston, MA, USA
| | - J.I. Rotter
- Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - S.F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - C.S. Fox
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - J.S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - J.G. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Medicine, V.A. Medical Center, Jackson, MS, USA
| | - J.B. Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - D.S. Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - D.W. Bowden
- Department of Biochemistry, Centers for Human Genomics and Diabetes Research, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - M.J. Daly
- Center for Human Genetic Research, Simches Research Building - CPZN 5.250, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - J.C. Florez
- Center for Human Genetic Research, Simches Research Building - CPZN 5.250, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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