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Martagón AJ, Bello-Chavolla OY, Arellano-Campos O, Almeda-Valdés P, Walford GA, Cruz-Bautista I, Gómez-Velasco DV, Mehta R, Muñoz-Hernández L, Sevilla-González M, Viveros-Ruiz TL, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Florez JC, Tusié-Luna MT, Aguilar-Salinas CA, Mercader JM, Huerta-Chagoya A, Moreno-Macías H, García-Ortiz H, Manning A, Caulkins L, Flannick J, Patterson N, Martínez-Hernández A, Centeno-Cruz F, Barajas-Olmos FM, Zerrweck C, Contreras-Cubas C, Mendoza-Caamal E, Revilla-Monsalve C, Islas Andrade S, Córdova E, Soberón X, González-Villalpando ME, Wilkens L, Le Marchand L, Monroe K, Kolonel L, Arellano-Campos O, Ordóñez-Sánchez ML, Rodríguez-Torres M, Segura-Kato Y, Rodríguez-Guillén R, Cruz-Bautista I, Muñoz-Hernández LL, Martagón AJ, Sevilla Gonzalez MDR, Gómez D, Almeda-Valdés P, Garay ME, Malacara Hernandez JM, Burtt NP, Cortes ML, Altshuler DM, Haiman CA, Aguilar-Salinas CA, González-Villalpando C, Orozco L, Tusié-Luna T, Florez JC. Mexican Carriers of the HNF1A p.E508K Variant Do Not Experience an Enhanced Response to Sulfonylureas. Diabetes Care 2018; 41:1726-1731. [PMID: 29844095 DOI: 10.2337/dc18-0384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/01/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To assess whether an ethnic-specific variant (p.E508K) in the maturity-onset diabetes of the young (MODY) gene hepatocyte nuclear factor-1α (HNF1A) found in Mexicans is associated with higher sensitivity to sulfonylureas, as documented in patients with MODY3. RESEARCH DESIGN AND METHODS We recruited 96 participants (46 variant carriers and 50 age- and sex-matched noncarriers). Response to glipizide (one 2.5-5.0-mg dose), metformin (four 500-mg doses), and an oral glucose challenge was evaluated using a previously validated protocol. Glucose and insulin levels and their areas under the curve (AUCs) were compared between groups. RESULTS Carriers of the p.E508K variant had a lower maximum insulin peak during the glipizide challenge as compared with noncarriers with diabetes (P < 0.05). Also, carriers had a lower insulin response after the oral glucose challenge. Following an oral glucose tolerance test in the presence of metformin, carriers of the p.E508K variant with diabetes had a lower maximum insulin peak and total and incremental insulin AUC value as compared with noncarriers with diabetes (P < 0.05). A similar but nonsignificant trend was seen in participants without type 2 diabetes. CONCLUSIONS Carriers of variant p.E508K in HNF1A have a reduced insulin response rather than the increased sensitivity to sulfonylureas seen in patients with MODY3.
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Affiliation(s)
- Alexandro J. Martagón
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo León, México
| | - Omar Yaxmehen Bello-Chavolla
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Plan de Estudios Combinados en Medicina, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Olimpia Arellano-Campos
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
| | - Paloma Almeda-Valdés
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Geoffrey A. Walford
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Ivette Cruz-Bautista
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Donají V. Gómez-Velasco
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
| | - Roopa Mehta
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Liliana Muñoz-Hernández
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
| | - Magdalena Sevilla-González
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
| | - Tannia L. Viveros-Ruiz
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
| | - María Luisa Ordoñez-Sánchez
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosario Rodríguez-Guillen
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jose C. Florez
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - María Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos A. Aguilar-Salinas
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición, Ciudad de México, México
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo León, México
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
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2
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Rusu V, Hoch E, Mercader JM, Tenen DE, Gymrek M, Hartigan CR, DeRan M, von Grotthuss M, Fontanillas P, Spooner A, Guzman G, Deik AA, Pierce KA, Dennis C, Clish CB, Carr SA, Wagner BK, Schenone M, Ng MCY, Chen BH, Centeno-Cruz F, Zerrweck C, Orozco L, Altshuler DM, Schreiber SL, Florez JC, Jacobs SBR, Lander ES. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms. Cell 2017; 170:199-212.e20. [PMID: 28666119 DOI: 10.1016/j.cell.2017.06.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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: 10/06/2016] [Revised: 03/16/2017] [Accepted: 06/08/2017] [Indexed: 01/08/2023]
Abstract
Type 2 diabetes (T2D) affects Latinos at twice the rate seen in populations of European descent. We recently identified a risk haplotype spanning SLC16A11 that explains ∼20% of the increased T2D prevalence in Mexico. Here, through genetic fine-mapping, we define a set of tightly linked variants likely to contain the causal allele(s). We show that variants on the T2D-associated haplotype have two distinct effects: (1) decreasing SLC16A11 expression in liver and (2) disrupting a key interaction with basigin, thereby reducing cell-surface localization. Both independent mechanisms reduce SLC16A11 function and suggest SLC16A11 is the causal gene at this locus. To gain insight into how SLC16A11 disruption impacts T2D risk, we demonstrate that SLC16A11 is a proton-coupled monocarboxylate transporter and that genetic perturbation of SLC16A11 induces changes in fatty acid and lipid metabolism that are associated with increased T2D risk. Our findings suggest that increasing SLC16A11 function could be therapeutically beneficial for T2D. VIDEO ABSTRACT.
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Affiliation(s)
- Victor Rusu
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Eitan Hoch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Metabolism Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Josep M Mercader
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08034 Barcelona, Spain
| | - Danielle E Tenen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Melissa Gymrek
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Michael DeRan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Marcin von Grotthuss
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Pierre Fontanillas
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexandra Spooner
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gaelen Guzman
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Amy A Deik
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kerry A Pierce
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Courtney Dennis
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Clary B Clish
- Metabolism Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Monica Schenone
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Brian H Chen
- Longitudinal Studies Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | | | | | | | - Carlos Zerrweck
- The Obesity Clinic at Hospital General Tlahuac, 13250 Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Tlalpan, 14610 Mexico City, Mexico
| | - David M Altshuler
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | | | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Metabolism Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Suzanne B R Jacobs
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Metabolism Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eric S Lander
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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3
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Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016; 536:285-91. [PMID: 27535533 PMCID: PMC5018207 DOI: 10.1038/nature19057] [Citation(s) in RCA: 7269] [Impact Index Per Article: 908.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/24/2016] [Indexed: 02/02/2023]
Abstract
Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.
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Affiliation(s)
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,School of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia,Institute for Neuroscience and Muscle Research, Childrens Hospital at Westmead, Sydney, NSW, Australia
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric V Minikel
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Kaitlin E Samocha
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Fennell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - James S Ware
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,National Heart and Lung Institute, Imperial College London, London, UK,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, UK,MRC Clinical Sciences Centre, Imperial College London, London, UK
| | - Andrew J Hill
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel P Birnbaum
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack A Kosmicki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Laramie E Duncan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karol Estrada
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fengmei Zhao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Zou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joanne Berghout
- Mouse Genome Informatics, Jackson Laboratory, Bar Harbor, ME, USA,Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | - Mark DePristo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Menachem Fromer
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jackie Goldstein
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Howrigan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Kiezun
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mitja I Kurki
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Gen—mica, Mexico City, Mexico
| | - Gina M Peloso
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan Poplin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuel A Rivas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Samuel A Rose
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Douglas M Ruderfer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khalid Shakir
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Christine Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett P Thomas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Tiao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Tusie-Luna
- Molecular Biology and Genomic Medicine Unit, Instituto Nacional de Ciencias M_dicas y Nutrici—n, Mexico City, Mexico
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University,Samsung Medical Center, Seoul, Republic of Korea
| | - Dongmei Yu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - David M Altshuler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Vertex Pharmaceuticals, Boston, MA, USA
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Danesh
- Department of Public Health and Primary Care, Strangeways Research Laboratory, Cambridge, UK
| | - Stacey Donnelly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Stacey B Gabriel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory, State University of New York,Upstate Medical University, Syracuse, NY, USA,Department of Psychiatry and Behavioral Sciences, State University of New York,Upstate Medical University, Syracuse, NY, USA,Department of Neuroscience and Physiology, State University of New York,Upstate Medical University, Syracuse, NY, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Foundation Trust, Oxford, UK
| | - Dermot McGovern
- Inflammatory Bowel Disease and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Shaun M Purcell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,Center for Non-Communicable Diseases, Karachi, , Pakistan
| | - Jeremiah M Scharf
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Ming T Tsuang
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Hugh C Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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4
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Clapham KR, Chu AY, Wessel J, Natarajan P, Flannick J, Rivas MA, Sartori S, Mehran R, Baber U, Fuster V, Scott RA, Rader DJ, Boehnke M, McCarthy MI, Altshuler DM, Kathiresan S, Peloso GM. A null mutation in ANGPTL8 does not associate with either plasma glucose or type 2 diabetes in humans. BMC Endocr Disord 2016; 16:7. [PMID: 26822414 PMCID: PMC4730725 DOI: 10.1186/s12902-016-0088-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/22/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Experiments in mice initially suggested a role for the protein angiopoietin-like 8 (ANGPTL8) in glucose homeostasis. However, subsequent experiments in model systems have challenged this proposed role. We sought to better understand the importance of ANGPTL8 in human glucose homeostasis by examining the association of a null mutation in ANGPTL8 with fasting glucose levels and risk for type 2 diabetes. METHODS A naturally-occurring null mutation in human ANGPTL8 (rs145464906; c.361C > T; p.Q121X) is carried by ~1 in 1000 individuals of European ancestry and is associated with higher levels of plasma high-density lipoprotein cholesterol, suggesting that this mutation has functional significance. We examined the association of p.Q121X with fasting glucose levels and risk for type 2 diabetes in up to 95,558 individuals (14,824 type 2 diabetics and 80,734 controls). RESULTS We found no significant association of p.Q121X with either fasting glucose or type 2 diabetes (p-value = 0.90 and 0.65, respectively). Given our sample sizes, we had >98 % power to detect at least a 0.23 mmol/L effect on plasma glucose and >95 % power to detect a 70 % increase in risk for type 2 diabetes. CONCLUSION Disruption of ANGPTL8 function in humans does not seem to have a large effect on measures of glucose tolerance.
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Affiliation(s)
- Katharine R Clapham
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Audrey Y Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- National Heart, Lung, and Blood Institute (NHLBI) Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indianapolis, IN, 46202, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Pradeep Natarajan
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Manuel A Rivas
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Samantha Sartori
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Roxana Mehran
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Usman Baber
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Valentin Fuster
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0SL, UK
| | - Daniel J Rader
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - David M Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sekar Kathiresan
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Gina M Peloso
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.
- , 801 Massachusetts Ave, Crosstown Center, Third Floor, Boston, MA, 02118, USA.
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5
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Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JAL, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJW, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJR, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med 2015; 7:270ra6. [PMID: 25589632 DOI: 10.1126/scitranslmed.3010134] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The recent discovery of heterozygous human mutations that truncate full-length titin (TTN, an abundant structural, sensory, and signaling filament in muscle) as a common cause of end-stage dilated cardiomyopathy (DCM) promises new prospects for improving heart failure management. However, realization of this opportunity has been hindered by the burden of TTN-truncating variants (TTNtv) in the general population and uncertainty about their consequences in health or disease. To elucidate the effects of TTNtv, we coupled TTN gene sequencing with cardiac phenotyping in 5267 individuals across the spectrum of cardiac physiology and integrated these data with RNA and protein analyses of human heart tissues. We report diversity of TTN isoform expression in the heart, define the relative inclusion of TTN exons in different isoforms (using the TTN transcript annotations available at http://cardiodb.org/titin), and demonstrate that these data, coupled with the position of the TTNtv, provide a robust strategy to discriminate pathogenic from benign TTNtv. We show that TTNtv is the most common genetic cause of DCM in ambulant patients in the community, identify clinically important manifestations of TTNtv-positive DCM, and define the penetrance and outcomes of TTNtv in the general population. By integrating genetic, transcriptome, and protein analyses, we provide evidence for a length-dependent mechanism of disease. These data inform diagnostic criteria and management strategies for TTNtv-positive DCM patients and for TTNtv that are identified as incidental findings.
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Affiliation(s)
- Angharad M Roberts
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK. National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - James S Ware
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Daniel S Herman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sebastian Schafer
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - John Baksi
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Alexander G Bick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rachel J Buchan
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Roddy Walsh
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Shibu John
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Samuel Wilkinson
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Francesco Mazzarotto
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Leanne E Felkin
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Sungsam Gong
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Jason Flannick
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stacey B Gabriel
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David M Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter S Macdonald
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Matthias Heinig
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Anne M Keogh
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Christopher S Hayward
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Nicholas R Banner
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Hill End Road, Harefield, Middlesex UB9 6JH, UK
| | - Dudley J Pennell
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Declan P O'Regan
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Tan Ru San
- National Heart Centre Singapore, Singapore 169609, Singapore
| | - Antonio de Marvao
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Timothy J W Dawes
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK
| | - Ankur Gulati
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Emma J Birks
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. Department of Medicine, University of Louisville and Jewish Hospital, Louisville, KY 40202, USA
| | - Magdi H Yacoub
- National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Michael Radke
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany. German Centre for Cardiovascular Research, 13347 Berlin, Germany
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Christopher J O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA. Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Sanjay K Prasad
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK
| | - Paul J R Barton
- National Institute for Health Research (NIHR) Cardiovascular Biomedical Research Unit at Royal Brompton & Harefield National Health Service (NHS) Foundation Trust and Imperial College London, London SW3 6NP, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK
| | - Diane Fatkin
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia. Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany. German Centre for Cardiovascular Research, 13347 Berlin, Germany. Charité-Universitätsmedizin, 10117 Berlin, Germany
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Stuart A Cook
- Clinical Sciences Centre, Medical Research Council (MRC), Imperial College London, London W12 0NN, UK. National Heart & Lung Institute, Imperial College London, London SW3 6NP, UK. National Heart Centre Singapore, Singapore 169609, Singapore. Duke-National University of Singapore, Singapore 169857, Singapore.
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6
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Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet 2014; 10:e1004494. [PMID: 25078778 PMCID: PMC4117444 DOI: 10.1371/journal.pgen.1004494] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/14/2014] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10⁻¹¹⁷). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
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Affiliation(s)
- Elaine T. Lim
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Würtz
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Aki S. Havulinna
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karola Rehnström
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Michael Inouye
- Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tuuli Lappalainen
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Stanford Center for Computational, Evolutionary and Human Genomics, Stanford, California, United States of America
| | - Yingleong Chan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Rany M. Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alisa Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Claes Ladenvall
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Marko Salmi
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Stefan Blankenberg
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Svati Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Benjamin Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, Utah, United States of America
| | - Ruth McPherson
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Gerald K. Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Muredach P. Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Domenico Girelli
- University of Verona School of Medicine, Department of Medicine, Verona, Italy
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Nathan O. Stitziel
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Leif Groop
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- National Institute for Health and Welfare, Dept of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David M. Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecilia M. Lindgren
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | | | - Nelson B. Freimer
- University of California Los Angeles Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tanja Zeller
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sirpa Jalkanen
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Seppo Koskinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- Department of Biometry, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
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7
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Ito K, Bick AG, Flannick J, Friedman DJ, Genovese G, Parfenov MG, Depalma SR, Gupta N, Gabriel SB, Taylor HA, Fox ER, Newton-Cheh C, Kathiresan S, Hirschhorn JN, Altshuler DM, Pollak MR, Wilson JG, Seidman JG, Seidman C. Increased burden of cardiovascular disease in carriers of APOL1 genetic variants. Circ Res 2014; 114:845-50. [PMID: 24379297 PMCID: PMC3982584 DOI: 10.1161/circresaha.114.302347] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [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] [Indexed: 01/26/2023]
Abstract
RATIONALE Two distinct alleles in the gene encoding apolipoprotein L1 (APOL1), a major component of high-density lipoprotein, confer protection against Trypanosoma brucei rhodesiense infection and also increase risk for chronic kidney disease. Approximately 14% of Americans with African ancestry carry 2 APOL1 risk alleles, accounting for the high chronic kidney disease burden in this population. OBJECTIVE We tested whether APOL1 risk alleles significantly increase risk for atherosclerotic cardiovascular disease (CVD) in African Americans. METHODS AND RESULTS We sequenced APOL1 in 1959 randomly selected African American participants in the Jackson Heart Study (JHS) and evaluated associations between APOL1 genotypes and renal and cardiovascular phenotypes. Previously identified association between APOL1 genotypes and chronic kidney disease was confirmed (P=2.4×10(-6)). Among JHS participants with 2 APOL1 risk alleles, we observed increased risk for CVD (50/763 events among participants without versus 37/280 events among participants with 2 risk alleles; odds ratio, 2.17; P=9.4×10(-4)). We replicated this novel association of APOL1 genotype with CVD in Women's Health Initiative (WHI) participants (66/292 events among participants without versus 37/101 events among participants with 2 risk alleles; odds ratio, 1.98; P=8.37×10(-3); JHS and WHI combined, P=8.5×10(-5); odds ratio, 2.12). The increased risk for CVD conferred by APOL1 alleles was robust to correction for both traditional CVD risk factors and chronic kidney disease. CONCLUSIONS APOL1 variants contribute to atherosclerotic CVD risk, indicating a genetic component to cardiovascular health disparities in individuals of African ancestry. The considerable population of African Americans with 2 APOL1 risk alleles may benefit from intensive interventions to reduce CVD.
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Affiliation(s)
- Kaoru Ito
- From the Department of Genetics, Harvard Medical School, Boston, MA (K.I., A.G.B., M.G.P., S.R.D., J.N.H., J.G.S., C.S.); Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge (K.I., A.G.B., J.F., G.G., N.G., S.B.G., C.N.-C., S.K., J.N.H., D.M.A., M.R.P., J.G.S., C.S.); Center for Human Genetic Research, Massachusetts General Hospital, Boston (J.F., C.N.-C., S.K., D.M.A.); Division of Nephrology, Department of Medicine (D.J.F., G.G., M.R.P.) and Center for Vascular Biology Research, Department of Medicine (D.J.F.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA; Departments of Medicine (H.A.T., E.R.F.) and Physiology and Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson; Jackson State University, MS (H.A.T.); Tougaloo College, MS (H.A.T.); Cardiology Division, Massachusetts General Hospital, Boston (C.N.-C., S.K.); Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital, Boston, MA (J.N.H.); and Howard Hughes Medical Institute and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (C.S.)
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8
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Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I. DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. Am J Hum Genet 2011; 88:706-717. [PMID: 21620352 DOI: 10.1016/j.ajhg.2011.04.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/13/2011] [Accepted: 04/26/2011] [Indexed: 02/01/2023] Open
Abstract
Rare variants affecting phenotype pose a unique challenge for human genetics. Although genome-wide association studies have successfully detected many common causal variants, they are underpowered in identifying disease variants that are too rare or population-specific to be imputed from a general reference panel and thus are poorly represented on commercial SNP arrays. We set out to overcome these challenges and detect association between disease and rare alleles using SNP arrays by relying on long stretches of genomic sharing that are identical by descent. We have developed an algorithm, DASH, which builds upon pairwise identical-by-descent shared segments to infer clusters of individuals likely to be sharing a single haplotype. DASH constructs a graph with nodes representing individuals and links on the basis of such segments spanning a locus and uses an iterative minimum cut algorithm to identify densely connected components. We have applied DASH to simulated data and diverse GWAS data sets by constructing haplotype clusters and testing them for association. In simulations we show this approach to be significantly more powerful than single-marker testing in an isolated population that is from Kosrae, Federated States of Micronesia and has abundant IBD, and we provide orthogonal information for rare, recent variants in the outbred Wellcome Trust Case-Control Consortium (WTCCC) data. In both cohorts, we identified a number of haplotype associations, five such loci in the WTCCC data and ten in the isolated, that were conditionally significant beyond any individual nearby markers. We have replicated one of these loci in an independent European cohort and identified putative structural changes in low-pass whole-genome sequence of the cluster carriers.
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Affiliation(s)
- Alexander Gusev
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Eimear E Kenny
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Jennifer K Lowe
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jaqueline Salit
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Richa Saxena
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Cardiovascular Disease Prevention Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David M Altshuler
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey M Friedman
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Jan L Breslow
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA.
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9
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Im KM, Kirchhoff T, Wang X, Green T, Chow CY, Vijai J, Korn J, Gaudet MM, Fredericksen Z, Shane Pankratz V, Guiducci C, Crenshaw A, McGuffog L, Kartsonaki C, Morrison J, Healey S, Sinilnikova OM, Mai PL, Greene MH, Piedmonte M, Rubinstein WS, Hogervorst FB, Rookus MA, Collée JM, Hoogerbrugge N, van Asperen CJ, Meijers-Heijboer HEJ, Van Roozendaal CE, Caldes T, Perez-Segura P, Jakubowska A, Lubinski J, Huzarski T, Blecharz P, Nevanlinna H, Aittomäki K, Lazaro C, Blanco I, Barkardottir RB, Montagna M, D'Andrea E, Devilee P, Olopade OI, Neuhausen SL, Peissel B, Bonanni B, Peterlongo P, Singer CF, Rennert G, Lejbkowicz F, Andrulis IL, Glendon G, Ozcelik H, Toland AE, Caligo MA, Beattie MS, Chan S, Domchek SM, Nathanson KL, Rebbeck TR, Phelan C, Narod S, John EM, Hopper JL, Buys SS, Daly MB, Southey MC, Terry MB, Tung N, Hansen TVO, Osorio A, Benitez J, Durán M, Weitzel JN, Garber J, Hamann U, Peock S, Cook M, Oliver CT, Frost D, Platte R, Evans DG, Eeles R, Izatt L, Paterson J, Brewer C, Hodgson S, Morrison PJ, Porteous M, Walker L, Rogers MT, Side LE, Godwin AK, Schmutzler RK, Wappenschmidt B, Laitman Y, Meindl A, Deissler H, Varon-Mateeva R, Preisler-Adams S, Kast K, Venat-Bouvet L, Stoppa-Lyonnet D, Chenevix-Trench G, Easton DF, Klein RJ, Daly MJ, Friedman E, Dean M, Clark AG, Altshuler DM, Antoniou AC, Couch FJ, Offit K, Gold B. Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers. Hum Genet 2011; 130:685-99. [PMID: 21597964 DOI: 10.1007/s00439-011-1003-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 04/20/2011] [Indexed: 11/26/2022]
Abstract
Three founder mutations in BRCA1 and BRCA2 contribute to the risk of hereditary breast and ovarian cancer in Ashkenazi Jews (AJ). They are observed at increased frequency in the AJ compared to other BRCA mutations in Caucasian non-Jews (CNJ). Several authors have proposed that elevated allele frequencies in the surrounding genomic regions reflect adaptive or balancing selection. Such proposals predict long-range linkage disequilibrium (LD) resulting from a selective sweep, although genetic drift in a founder population may also act to create long-distance LD. To date, few studies have used the tools of statistical genomics to examine the likelihood of long-range LD at a deleterious locus in a population that faced a genetic bottleneck. We studied the genotypes of hundreds of women from a large international consortium of BRCA1 and BRCA2 mutation carriers and found that AJ women exhibited long-range haplotypes compared to CNJ women. More than 50% of the AJ chromosomes with the BRCA1 185delAG mutation share an identical 2.1 Mb haplotype and nearly 16% of AJ chromosomes carrying the BRCA2 6174delT mutation share a 1.4 Mb haplotype. Simulations based on the best inference of Ashkenazi population demography indicate that long-range haplotypes are expected in the context of a genome-wide survey. Our results are consistent with the hypothesis that a local bottleneck effect from population size constriction events could by chance have resulted in the large haplotype blocks observed at high frequency in the BRCA1 and BRCA2 regions of Ashkenazi Jews.
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Affiliation(s)
- Kate M Im
- Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute, Frederick, MD, USA
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10
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Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Kang HM, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL, Pe'er I. Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Hum Mol Genet 2010; 20:827-39. [PMID: 21118897 DOI: 10.1093/hmg/ddq510] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The potential benefits of using population isolates in genetic mapping, such as reduced genetic, phenotypic and environmental heterogeneity, are offset by the challenges posed by the large amounts of direct and cryptic relatedness in these populations confounding basic assumptions of independence. We have evaluated four representative specialized methods for association testing in the presence of relatedness; (i) within-family (ii) within- and between-family and (iii) mixed-models methods, using simulated traits for 2906 subjects with known genome-wide genotype data from an extremely isolated population, the Island of Kosrae, Federated States of Micronesia. We report that mixed models optimally extract association information from such samples, demonstrating 88% power to rank the true variant as among the top 10 genome-wide with 56% achieving genome-wide significance, a >80% improvement over the other methods, and demonstrate that population isolates have similar power to non-isolate populations for observing variants of known effects. We then used the mixed-model method to reanalyze data for 17 published phenotypes relating to metabolic traits and electrocardiographic measures, along with another 8 previously unreported. We replicate nine genome-wide significant associations with known loci of plasma cholesterol, high-density lipoprotein, low-density lipoprotein, triglycerides, thyroid stimulating hormone, homocysteine, C-reactive protein and uric acid, with only one detected in the previous analysis of the same traits. Further, we leveraged shared identity-by-descent genetic segments in the region of the uric acid locus to fine-map the signal, refining the known locus by a factor of 4. Finally, we report a novel associations for height (rs17629022, P< 2.1 × 10⁻⁸).
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Affiliation(s)
- Eimear E Kenny
- Department of Computer Science, Columbia University, 505 Computer Science Building, 1214 Amsterdam Ave.: Mailcode 0401, New York, NY 10027-7003, USA
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11
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Gaudet MM, Kirchhoff T, Green T, Vijai J, Korn JM, Guiducci C, Segrè AV, McGee K, McGuffog L, Kartsonaki C, Morrison J, Healey S, Sinilnikova OM, Stoppa-Lyonnet D, Mazoyer S, Gauthier-Villars M, Sobol H, Longy M, Frenay M, GEMO Study Collaborators, Hogervorst FBL, Rookus MA, Collée JM, Hoogerbrugge N, van Roozendaal KEP, Piedmonte M, Rubinstein W, Nerenstone S, Van Le L, Blank SV, Caldés T, de la Hoya M, Nevanlinna H, Aittomäki K, Lazaro C, Blanco I, Arason A, Johannsson OT, Barkardottir RB, Devilee P, Olopade OI, Neuhausen SL, Wang X, Fredericksen ZS, Peterlongo P, Manoukian S, Barile M, Viel A, Radice P, Phelan CM, Narod S, Rennert G, Lejbkowicz F, Flugelman A, Andrulis IL, Glendon G, Ozcelik H, Toland AE, Montagna M, D'Andrea E, Friedman E, Laitman Y, Borg A, Beattie M, Ramus SJ, Domchek SM, Nathanson KL, Rebbeck T, Spurdle AB, Chen X, Holland H, John EM, Hopper JL, Buys SS, Daly MB, Southey MC, Terry MB, Tung N, Overeem Hansen TV, Nielsen FC, Greene MI, Mai PL, Osorio A, Durán M, Andres R, Benítez J, Weitzel JN, Garber J, Hamann U, Peock S, Cook M, Oliver C, Frost D, Platte R, Evans DG, Lalloo F, Eeles R, Izatt L, Walker L, Eason J, Barwell J, Godwin AK, Schmutzler RK, Wappenschmidt B, Engert S, Arnold N, Gadzicki D, Dean M, Gold B, Klein RJ, Couch FJ, Chenevix-Trench G, Easton DF, Daly MJ, Antoniou AC, Altshuler DM, Offit K. Common genetic variants and modification of penetrance of BRCA2-associated breast cancer. PLoS Genet 2010; 6:e1001183. [PMID: 21060860 PMCID: PMC2965747 DOI: 10.1371/journal.pgen.1001183] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 09/28/2010] [Indexed: 01/12/2023] Open
Abstract
The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors. To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers, we undertook a two-staged genome-wide association study in BRCA2 mutation carriers. In stage 1 using the Affymetrix 6.0 platform, 592,163 filtered SNPs genotyped were available on 899 young (<40 years) affected and 804 unaffected carriers of European ancestry. Associations were evaluated using a survival-based score test adjusted for familial correlations and stratified by country of the study and BRCA2*6174delT mutation status. The genomic inflation factor (λ) was 1.011. The stage 1 association analysis revealed multiple variants associated with breast cancer risk: 3 SNPs had p-values<10(-5) and 39 SNPs had p-values<10(-4). These variants included several previously associated with sporadic breast cancer risk and two novel loci on chromosome 20 (rs311499) and chromosome 10 (rs16917302). The chromosome 10 locus was in ZNF365, which contains another variant that has recently been associated with breast cancer in an independent study of unselected cases. In stage 2, the top 85 loci from stage 1 were genotyped in 1,264 cases and 1,222 controls. Hazard ratios (HR) and 95% confidence intervals (CI) for stage 1 and 2 were combined and estimated using a retrospective likelihood approach, stratified by country of residence and the most common mutation, BRCA2*6174delT. The combined per allele HR of the minor allele for the novel loci rs16917302 was 0.75 (95% CI 0.66-0.86, ) and for rs311499 was 0.72 (95% CI 0.61-0.85, ). FGFR2 rs2981575 had the strongest association with breast cancer risk (per allele HR = 1.28, 95% CI 1.18-1.39, ). These results indicate that SNPs that modify BRCA2 penetrance identified by an agnostic approach thus far are limited to variants that also modify risk of sporadic BRCA2 wild-type breast cancer.
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Affiliation(s)
- Mia M. Gaudet
- Department of Epidemiology and Population Health and Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Tomas Kirchhoff
- Clinical Genetics Service, Department of Medicine, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Todd Green
- Broad Institute of Harvard and Massachusetts Institute of Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Joshua M. Korn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Candace Guiducci
- Broad Institute of Harvard and Massachusetts Institute of Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ayellet V. Segrè
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kate McGee
- Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute – Frederick, Frederick, Maryland, United States of America
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Christiana Kartsonaki
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Morrison
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sue Healey
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Hospitalier Universitaire de Lyon/Centre Léon Bérard, Lyon, France
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Service de Génétique, INSERM U830, F-75248, Université Paris Descartes, Paris, France
- Service de Genetique Oncologique, Institut Curie, Paris, France
| | - Sylvie Mazoyer
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | | | - Hagay Sobol
- Département Oncologie génétique, Prévention et Dépistage, INSERM CIC-P9502, Institut Paoli-Calmettes/Université d'Aix-Marseille II, Marseille, France
| | | | | | - GEMO Study Collaborators
- GEMO Study - Cancer Genetics Network “Groupe Génétique et Cancer”, Fédération Nationale des Centres de Lutte Contre le Cancer, Paris, France
| | | | - Matti A. Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J. Margriet Collée
- Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | - Marion Piedmonte
- Gynecologic Oncology Group Statistical and Data Center, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Wendy Rubinstein
- NorthShore University Health System, Evanston, Illinois, United States of America
| | - Stacy Nerenstone
- Central Connecticut Cancer Consortium, Hartford Hospital, Hartford, Connecticut, United States of America
| | - Linda Van Le
- University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephanie V. Blank
- New York University School of Medicine, New York, New York, United States of America
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, Madrid, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Adalgeir Arason
- Department of Oncology, Landspitali–LSH, Reykjavik, Iceland
- Department of Pathology, Landspitali–LSH, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Oskar T. Johannsson
- Department of Oncology, Landspitali–LSH, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rosa B. Barkardottir
- Department of Oncology, Landspitali–LSH, Reykjavik, Iceland
- Department of Pathology, Landspitali–LSH, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Peter Devilee
- Department of Human Genetics and Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Olofunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Susan L. Neuhausen
- Department of Population Sciences, the Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Zachary S. Fredericksen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Paolo Peterlongo
- Unit of Genetic Susceptibility to Cancer, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Alessandra Viel
- Division of Experimental Oncology 1, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano (PN), Italy
| | - Paolo Radice
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | | | - Steven Narod
- Women's College Research Institute, Toronto, Canada
| | - Gad Rennert
- CHS National Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- CHS National Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Anath Flugelman
- CHS National Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Irene L. Andrulis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
- Cancer Care Ontario, Ontario Cancer Genetics Network, University of Toronto, Toronto, Canada
| | - Gord Glendon
- Cancer Care Ontario, Ontario Cancer Genetics Network, University of Toronto, Toronto, Canada
| | - Hilmi Ozcelik
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
- Cancer Care Ontario, Ontario Cancer Genetics Network, University of Toronto, Toronto, Canada
| | - OCGN
- Cancer Care Ontario, Ontario Cancer Genetics Network, University of Toronto, Toronto, Canada
| | - Amanda E. Toland
- Departments of Molecular Virology, Immunology, and Medical Genetics and Internal Medicine, Ohio State University, Columbus, Ohio, United States of America
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - Emma D'Andrea
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto, IRCCS, Padua, Italy
- Department of Oncology and Surgical Sciences, University of Padua, Padua, Italy
| | - Eitan Friedman
- The Susan Levy Gertner Oncogenetics Unit, Institute of Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Yael Laitman
- The Susan Levy Gertner Oncogenetics Unit, Institute of Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Ake Borg
- Department of Oncology, Lund University, Lund, Sweden
| | - Mary Beattie
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Susan J. Ramus
- Gynaecological Oncology Unit, UCL EGA Institute for Women's Health, University College London, United Kingdom
| | - Susan M. Domchek
- Department of Oncology, The Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katherine L. Nathanson
- Department of Cell and Molecular Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Tim Rebbeck
- Center for Clinical Epidemiology and Biostatistics, Department of Biostatistics and Epidemiology, The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Amanda B. Spurdle
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Xiaoqing Chen
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - Helene Holland
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia
| | - kConFab
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - John L. Hopper
- Centre for Genetic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Saundra S. Buys
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary B. Daly
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Melissa C. Southey
- Centre for Genetic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Nadine Tung
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Thomas V. Overeem Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospitalet, Copenhagen, Denmark
| | - Finn C. Nielsen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospitalet, Copenhagen, Denmark
| | - Mark I. Greene
- Clinical Genetics Branch, National Cancer Institute, Rockville, Maryland, United States of America
| | - Phuong L. Mai
- Clinical Genetics Branch, National Cancer Institute, Rockville, Maryland, United States of America
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Mercedes Durán
- Institute of Biology and Molecular Genetics, Universidad de Valladolid (IBGM-UVA), Valladolid, Spain
| | - Raquel Andres
- Oncology Service, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - Javier Benítez
- Human Genetics Group and Genotyping Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jeffrey N. Weitzel
- City of Hope Cancer Center, Duarte, California, United States of America
| | - Judy Garber
- Dana Farber Cancer Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Margaret Cook
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Clare Oliver
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Radka Platte
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - D. Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, United Kingdom
| | - Jacqueline Eason
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Julian Barwell
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Andrew K. Godwin
- Women's Cancer Program, Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Rita K. Schmutzler
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Stefanie Engert
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts University Kiel, Kiel, Germany
| | - Dorothea Gadzicki
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - Michael Dean
- Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute – Frederick, Frederick, Maryland, United States of America
| | - Bert Gold
- Center for Cancer Research, Cancer Inflammation Program, Human Genetics Section, National Cancer Institute – Frederick, Frederick, Maryland, United States of America
| | - Robert J. Klein
- Program in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Mark J. Daly
- Broad Institute of Harvard and Massachusetts Institute of Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - David M. Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
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12
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Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PIW, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJR, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467:52-8. [PMID: 20811451 DOI: 10.1038/nature09298] [Citation(s) in RCA: 2019] [Impact Index Per Article: 144.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 06/21/2010] [Indexed: 12/24/2022]
Abstract
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of <or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.
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Affiliation(s)
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- Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA.
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13
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Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. Eur J Hum Genet 2010; 18:309-16. [PMID: 19844264 PMCID: PMC2987223 DOI: 10.1038/ejhg.2009.180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [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: 05/22/2009] [Revised: 08/11/2009] [Accepted: 09/11/2009] [Indexed: 01/16/2023] Open
Abstract
The architecture of natural variation present in a contemporary population is a result of multiple population genetic forces, including population bottleneck and expansion, selection, drift, and admixture. We seek to untangle the contribution of admixture to genetic diversity on the Micronesian island of Kosrae. Toward this goal, we used a complete genetic approach by combining a dense genome-wide map of 100,000 single-nucleotide polymorphisms (SNPs) with data from uniparental markers from the mitochondrial genome and the nonrecombining portion of the Y chromosome. These markers were typed in approximately 3200 individuals from Kosrae, representing 80% of the adult population of the island. We developed novel software that uses SNP data to delineate ancestry for individual segments of the genome. Through this analysis, we determined that 39% of Kosraens have some European ancestry. However, the vast majority of admixed individuals (77%) have European alleles spanning less than 10% of their genomes. Data from uniparental markers show most of this admixture to be male, introduced in the late nineteenth century. Furthermore, pedigree analysis shows that the majority of European admixture on Kosrae is because of the contribution of one individual. This approach shows the benefit of combining information from autosomal and uniparental polymorphisms and provides new methodology for determining ancestry in a population.
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Affiliation(s)
- Penelope E Bonnen
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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14
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Greenway SC, Pereira AC, Lin JC, DePalma SR, Israel SJ, Mesquita SM, Ergul E, Conta JH, Korn JM, McCarroll SA, Gorham JM, Gabriel S, Altshuler DM, Quintanilla-Dieck MDL, Artunduaga MA, Eavey RD, Plenge RM, Shadick NA, Weinblatt ME, De Jager PL, Hafler DA, Breitbart RE, Seidman JG, Seidman CE. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet 2009; 41:931-5. [PMID: 19597493 PMCID: PMC2747103 DOI: 10.1038/ng.415] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 06/03/2009] [Indexed: 11/17/2022]
Abstract
Tetralogy of Fallot (TOF), the most common severe congenital heart malformation, occurs sporadically, without other anomaly, and from unknown cause in 70% of cases. A genome-wide survey of 114 TOF patients and their unaffected parents identified 11 de novo copy number variants (CNVs) that were absent or extremely rare (<0.1%) in 2,265 controls. A second, independent TOF cohort (n = 398) was then examined for additional CNVs at these loci. In 1% (5/512, p = 0.0002, OR = 22.3) of non-syndromic sporadic TOF cases we identified CNVs at chromosome 1q21.1. Recurrent CNVs were also identified at 3p25.1, 7p21.3 and 22q11.2. CNVs in a single TOF case occurred at six loci, two that encode known (NOTCH1, JAG1) disease genes. Our data predicts that at least 10% (4.5–15.5, 95% CI) of sporadic, non-syndromic TOF reflects de novo CNVs and implicates mutations within these loci as etiologic in other cases of TOF.
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Affiliation(s)
- Steven C Greenway
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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15
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Smith JG, Lowe JK, Kovvali S, Maller JB, Salit J, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Breslow JL, Newton-Cheh C. Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. Heart Rhythm 2009; 6:634-41. [PMID: 19389651 DOI: 10.1016/j.hrthm.2009.02.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 02/11/2009] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cardiac conduction, as assessed by electrocardiographic PR interval and QRS duration, is an important electrophysiological trait and a determinant of arrhythmia risk. OBJECTIVE We sought to identify common genetic determinants of these measures. METHODS We examined 1604 individuals from the island of Kosrae, Federated States of Micronesia, an isolated founder population. We adjusted for covariates and estimated the heritability of quantitative electrocardiographic QRS duration and PR interval and, secondarily, its subcomponents, P-wave duration and PR segment. Finally, we performed a genome-wide association study (GWAS) in a subset of 1262 individuals genotyped using the Affymetrix GeneChip Human Mapping 500K microarray. RESULTS The heritability of PR interval was 34% (standard error [SE] 5%, P = 4 x 10(-18)); of PR segment, 31% (SE 6%, P = 3.2 x 10(-13)); and of P-wave duration, 17% (SE 5%, P = 5.8 x 10(-6)), but the heritablility of QRS duration was only 3% (SE 4%, P = .20). Hence, GWAS was performed only for the PR interval and its subcomponents. A total of 338,049 single nucleotide polymorphisms (SNPs) passed quality filters. For the PR interval, the most significantly associated SNPs were located in and downstream of the alpha-subunit of the cardiac voltage-gated sodium channel gene SCN5A, with a 4.8 ms (SE 1.0) or 0.23 standard deviation increase in adjusted PR interval for each minor allele copy of rs7638909 (P = 1.6 x 10(-6), minor allele frequency 0.40). These SNPs were also associated with P-wave duration (P = 1.5 x 10(-4)) and PR segment (P = .01) but not with QRS duration (P > or =.22). CONCLUSIONS The PR interval and its subcomponents showed substantial heritability in a South Pacific islander population and were associated with common genetic variation in SCN5A.
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Affiliation(s)
- J Gustav Smith
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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16
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Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS, Wahlstrand B, Hedner T, Corella D, Tai ES, Ordovas JM, Berglund G, Vartiainen E, Jousilahti P, Hedblad B, Taskinen MR, Newton-Cheh C, Salomaa V, Peltonen L, Groop L, Altshuler DM, Orho-Melander M. Erratum: Corrigendum: Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008. [DOI: 10.1038/ng1108-1384a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Kathiresan S, Melander O, Anevski D, Guiducci C, Burtt NP, Roos C, Hirschhorn JN, Berglund G, Hedblad B, Groop L, Altshuler DM, Newton-Cheh C, Orho-Melander M. Polymorphisms associated with cholesterol and risk of cardiovascular events. N Engl J Med 2008; 358:1240-9. [PMID: 18354102 DOI: 10.1056/nejmoa0706728] [Citation(s) in RCA: 497] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Common single-nucleotide polymorphisms (SNPs) that are associated with blood low-density lipoprotein (LDL) or high-density lipoprotein (HDL) cholesterol modestly affect lipid levels. We tested the hypothesis that a combination of such SNPs contributes to the risk of cardiovascular disease. METHODS We studied SNPs at nine loci in 5414 subjects from the cardiovascular cohort of the Malmö Diet and Cancer Study. We first validated the association between SNPs and either LDL or HDL cholesterol and subsequently created a genotype score on the basis of the number of unfavorable alleles. We used Cox proportional-hazards models to determine the time to the first cardiovascular event in relation to the genotype score. RESULTS All nine SNPs showed replication of an association with levels of either LDL or HDL cholesterol. With increasing genotype scores, the level of LDL cholesterol increased from 152 mg to 171 mg per deciliter (3.9 to 4.4 mmol per liter), whereas HDL cholesterol decreased from 60 mg to 51 mg per deciliter (1.6 to 1.3 mmol per liter). During follow-up (median, 10.6 years), 238 subjects had a first cardiovascular event. The genotype score was associated with incident cardiovascular disease in models adjusted for covariates including baseline lipid levels (P<0.001). The use of the genotype score did not improve the clinical risk prediction, as assessed by the C statistic. However, there was a significant improvement in risk classification with the use of models that included the genotype score, as compared with those that did not include the genotype score. CONCLUSIONS A genotype score of nine validated SNPs that are associated with modulation in levels of LDL or HDL cholesterol was an independent risk factor for incident cardiovascular disease. The score did not improve risk discrimination but did modestly improve clinical risk reclassification for individual subjects beyond standard clinical factors.
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Affiliation(s)
- Sekar Kathiresan
- Cardiovascular Disease Prevention Center, Cardiology Division, Massachusetts General Hospital, MA 02114, USA.
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18
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Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. Challenges and standards in integrating surveys of structural variation. Nat Genet 2007; 39:S7-15. [PMID: 17597783 PMCID: PMC2698291 DOI: 10.1038/ng2093] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research.
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Affiliation(s)
- Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14-701, Ontario M5G 1L7, Canada.
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19
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Abstract
The central goal of human genetics is to understand the inherited basis of human variation in phenotypes, elucidating human physiology, evolution and disease. Rare mutations have been found underlying two thousand mendelian diseases; more recently, it has become possible to assess systematically the contribution of common SNPs to complex disease. The known role of copy-number alterations in sporadic genomic disorders, combined with emerging information about inherited copy-number variation, indicate the importance of systematically assessing copy-number variants (CNVs), including common copy-number polymorphisms (CNPs), in disease. Here we discuss evidence that CNVs affect phenotypes, directions for basic knowledge to support clinical study of CNVs, the challenge of genotyping CNPs in clinical cohorts, the use of SNPs as markers for CNPs and statistical challenges in testing CNVs for association with disease. Critical needs are high-resolution maps of common CNPs and techniques that accurately determine the allelic state of affected individuals.
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Affiliation(s)
- Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
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20
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Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM, Eichler EE. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet 2006; 79:275-90. [PMID: 16826518 PMCID: PMC1559496 DOI: 10.1086/505653] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/04/2006] [Indexed: 11/04/2022] Open
Abstract
Studies of copy-number variation and linkage disequilibrium (LD) have typically excluded complex regions of the genome that are rich in duplications and prone to rearrangement. In an attempt to assess the heritability and LD of copy-number polymorphisms (CNPs) in duplication-rich regions of the genome, we profiled copy-number variation in 130 putative "rearrangement hotspot regions" among 269 individuals of European, Yoruba, Chinese, and Japanese ancestry analyzed by the International HapMap Consortium. Eighty-four hotspot regions, corresponding to 257 bacterial artificial chromosome (BAC) probes, showed evidence of copy-number differences. Despite a predisposing genetic architecture, no polymorphism was ever observed in the remaining 46 "rearrangement hotspots," and we suggest these represent excellent candidate sites for pathogenic rearrangements. We used a combination of BAC-based and high-density customized oligonucleotide arrays to resolve the molecular basis of structural rearrangements. For common variants (frequency >10%), we observed a distinct bias against copy-number losses, suggesting that deletions are subject to purifying selection. Heritability estimates did not differ significantly from 1.0 among the majority (30 of 34) of loci analyzed, consistent with normal Mendelian inheritance. Some of the CNPs in duplication-rich regions showed strong LD with nearby single-nucleotide polymorphisms (SNPs) and were observed to segregate on ancestral SNP haplotypes. However, LD with the best available SNP markers was weaker than has been reported for deletion polymorphisms in less complex regions of the genome. These observations may be accounted for by a low density of SNP data in duplicated regions, challenges in mapping and typing the CNPs, and the possibility that CNPs in these regions have rearranged on multiple haplotype backgrounds. Our results underscore the need for complete maps of genetic variation in duplication-rich regions of the genome.
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Affiliation(s)
- Devin P Locke
- Department of Genome Sciences, University of Washington and Howard Hughes Medical Institute, Seattle, WA 98195, USA
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21
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Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C. Copy number variation: new insights in genome diversity. Genome Res 2006. [PMID: 16809666 DOI: 10.1101/gr.3677206.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA copy number variation has long been associated with specific chromosomal rearrangements and genomic disorders, but its ubiquity in mammalian genomes was not fully realized until recently. Although our understanding of the extent of this variation is still developing, it seems likely that, at least in humans, copy number variants (CNVs) account for a substantial amount of genetic variation. Since many CNVs include genes that result in differential levels of gene expression, CNVs may account for a significant proportion of normal phenotypic variation. Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases.
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Affiliation(s)
- Jennifer L Freeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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22
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Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C. Copy number variation: new insights in genome diversity. Genome Res 2006; 16:949-61. [PMID: 16809666 DOI: 10.1101/gr.3677206] [Citation(s) in RCA: 545] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA copy number variation has long been associated with specific chromosomal rearrangements and genomic disorders, but its ubiquity in mammalian genomes was not fully realized until recently. Although our understanding of the extent of this variation is still developing, it seems likely that, at least in humans, copy number variants (CNVs) account for a substantial amount of genetic variation. Since many CNVs include genes that result in differential levels of gene expression, CNVs may account for a significant proportion of normal phenotypic variation. Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases.
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Affiliation(s)
- Jennifer L Freeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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Pe’er I, Chretien YR, de Bakker PIW, Barrett JC, Daly MJ, Altshuler DM. Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet 2006; 78:588-603. [PMID: 16532390 PMCID: PMC1424697 DOI: 10.1086/502803] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 01/20/2006] [Indexed: 01/07/2023] Open
Abstract
Genetic association studies of common disease often rely on linkage disequilibrium (LD) along the human genome and in the population under study. Although understanding the characteristics of this correlation has been the focus of many large-scale surveys (culminating in genomewide haplotype maps), the results of different studies have yielded wide-ranging estimates. Since understanding these differences (and whether they can be reconciled) has important implications for whole-genome association studies, in this article we dissect biases in these estimations that are due to known aspects of study design and analytic methodology. In particular, we document in the empirical data that the long-known complicating effects of allele frequency, marker density, and sample size largely reconcile all large-scale surveys. Two exceptions are an underappraisal of redundancy among single-nucleotide polymorphisms (SNPs) when evaluation is limited to short regions (as in candidate-gene resequencing studies) and an inflation in the extent of LD in HapMap phase I, which is likely due to oversampling of specific haplotypes in the creation of the public SNP map. Understanding these factors can guide the understanding of empirical LD surveys and has implications for genetic association studies.
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Affiliation(s)
- Itsik Pe’er
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
| | - Yves R. Chretien
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
| | - Paul I. W. de Bakker
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
| | - Jeffrey C. Barrett
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
| | - Mark J. Daly
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
| | - David M. Altshuler
- Center for Human Genetic Research, Department of Molecular Biology, and Diabetes Unit, Massachusetts General Hospital, and Departments of Genetics and Medicine, Harvard Medical School, Boston; Broad Institute of M.I.T. and Harvard and Harvard-M.I.T. Division of Health Sciences and Technology, Cambridge, MA; and Wellcome Trust Genome Campus, Oxford, United Kingdom
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McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM. Common deletion polymorphisms in the human genome. Nat Genet 2006; 38:86-92. [PMID: 16468122 DOI: 10.1038/ng1696] [Citation(s) in RCA: 566] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies.
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Affiliation(s)
- Steven A McCarroll
- Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
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Memisoglu A, Hu FB, Hankinson SE, Liu S, Meigs JB, Altshuler DM, Hunter DJ, Manson JE. Prospective study of the association between the proline to alanine codon 12 polymorphism in the PPARgamma gene and type 2 diabetes. Diabetes Care 2003; 26:2915-7. [PMID: 14514601 DOI: 10.2337/diacare.26.10.2915] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To determine whether the Pro12Ala polymorphism in the PPARgamma gene was associated with risk of type 2 diabetes in the Nurses' Health Study. RESEARCH DESIGN AND METHODS The study was a nested case-control study of 387 incident cases of type 2 diabetes and 771 matching control subjects nested within the Nurses' Health Study, a prospective cohort study. Association between PPARgamma genotype and incident type 2 diabetes was estimated using logistic regression. RESULTS Carriers of the PPARgamma variant 12Ala allele had reduced risk of type 2 diabetes compared with noncarriers. Unadjusted and adjusted odds ratios of type 2 diabetes were 0.74 (95% CI 0.55-1.00) and 0.72 (0.52-0.99), respectively. CONCLUSIONS The results of this study provide further support for an inverse association between the PPARgamma variant 12Ala allele and risk of type 2 diabetes.
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Affiliation(s)
- Asli Memisoglu
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
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