Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK. Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland. Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA. Harvard Medical School, Boston, Massachusetts, USA. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK. Gladstone Institutes, San Francisco, California, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. Genetics of Common Disorders Unit, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy. Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA. Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee, USA. Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, USA. Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, Indiana, USA. Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, USA. Department of Biological Psychology, VU University Amsterdam, Amsterdam, the Netherlands. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. Faculty of Medicine, University of Split, Split, Croatia. Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA. NHLBI's and Boston University's Framingham Heart Study, Framingham, Massachusetts, USA. Department of Twin Research and Genetic Epidemiology, King's College London, London, UK. National Institute for Health Research (NIHR) Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK. Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Trieste, Italy. School of Social and Community Medicine, University of Bristol, Bristol, UK. QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands. Institute of Genetics and Biophysics, CNR, Naples, Italy. MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK. Estonian Genome Center, University of Tartu, Tartu, Estonia. Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy. Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh, UK. Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK. Cancer Program, Broad Institute, Cambridge, Massachusetts, USA. Faculty of Medicine, University of Iceland, Reykjavik, Iceland. Icelandic Heart Association, Kopavogur, Iceland. Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands. Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany. Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy. Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany. Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain. Swiss Institute of Bioinformatics, Lausanne, Switzerland. Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland. Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA. Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark. Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. University of Tübingen, Tübingen, Germany. German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany. Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany. Institute for Prevention and Occupational Medicine of German Social Accident Insurance, Institute of Ruhr University Bochum (IPA), Bochum, Germany. Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy. Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA. Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia. Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA. Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA. Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. Academic Unit of Molecular Oncology, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK. Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA. Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands. Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands. Non-Communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK. Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland. David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, Los Angles, California, USA. Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA. Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland, USA. Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany. Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany. Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands. Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia. German Center for Diabetes Research, Neuherberg, Germany. Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France. Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA. Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany. Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Bethesda, Maryland, USA. Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA. Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands. Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA. Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK. Biocenter Oulu, University of Oulu, Oulu, Finland. Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu, Finland. Institute of Health Sciences, University of Oulu, Oulu, Finland. Unit of Primary Care, Oulu University Hospital, Oulu, Finland. Hebrew SeniorLife Institute for Aging Research, Boston, Massachusetts, USA. Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium. Vesalius Research Center (VRC), VIB, Leuven, Belgium. Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands. Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA. Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA. Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland. Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland. Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland. NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK. Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. Central Hospital of Augsburg, MONICA/KORA Myocardial Infarction Registry, Augsburg, Germany. Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Department of Electron Microscopy/Molecular Pathology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus. Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada. Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA. Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland. Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia. Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK. Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. National Institute for Health and Welfare, Helsinki, Finland. Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy. Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden. Division of Molecular Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands. Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia. Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK. Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany. Department of Public Health, University of Helsinki, Helsinki, Finland. Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee, USA. Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA. Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany. University Hospital of Lausanne, Lausanne, Switzerland. Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands. Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands. Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland. Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland. Department of Endocrinology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands. Department of Obstetrics and Gynecology, University Medicine Greifswald, Greifswald, Germany. Department of Biomedical Sciences, University of Sassari, Sassari, Italy. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands. Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark. Department of Obstetrics and Gynaecology, Campus Grosshadern, Ludwig Maximilians University, Munich, Germany. Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA. 23andMe, Inc., Mountain View, California, USA. Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, Massachusetts, USA. Department of Paediatrics, University of Cambridge, Cambridge, UK.

Nature genetics. 2017;(6):834-841

Abstract

The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project-imputed genotype data in up to ∼370,000 women, we identify 389 independent signals (P < 5 × 10-8) for age at menarche, a milestone in female pubertal development. In Icelandic data, these signals explain ∼7.4% of the population variance in age at menarche, corresponding to ∼25% of the estimated heritability. We implicate ∼250 genes via coding variation or associated expression, demonstrating significant enrichment in neural tissues. Rare variants near the imprinted genes MKRN3 and DLK1 were identified, exhibiting large effects when paternally inherited. Mendelian randomization analyses suggest causal inverse associations, independent of body mass index (BMI), between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men. In aggregate, our findings highlight the complexity of the genetic regulation of puberty timing and support causal links with cancer susceptibility.