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Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility

Felix Day, Deborah Thompson, Hannes Helgason, Daniel Chasman, Hilary Finucane, Patrick Sulem, Katherine Ruth, Sean Whalen, Abhishek Sarkar, Eva Albrecht, Elisabeth Altmaier, Marzyeh Amini, Caterina Barbieri, Thibaud Boutin, Archie Campbell, Ellen Demerath, Ayush Giri, Chunyan He, Jouke Hottenga, Robert Karlsson, Ivana Kolcic, Po-Ru Loh, Kathryn Lunetta, Massimo Mangino, Brumat Marco, Gerorge McMahon, Sarah Medland, Ilja Nolte, Raymond Noordam, Teresa Nutile, Lavinia Paternoster, Natalia Perjakova, Eleonora Porcu, Lynda Rose, Katharina Schraut, Ayellet Segre, Albert Smith, Lisette Stolk, Alexander Teumer, Irene Andrulis, Stefania Bandinelli, Matthias Beckmann, Javier Benitez, Sven Bergmann, Murielle Bochud, Eric Boerwinkle, Stig Bojesen, Manjeet Bolla, Judith Brand, Hiltrud Braunch, Hermann Brenner, Linda Broer, Thomas Bruning, Julie Buring, Harry Campbell, Eulalia Catamo, Stephen Chanock, Georgia Chenevix-Trench, Tanguy Corre, Fergus Couch, Diana Cousminer, Angela Cox, Laura Crisponi, Kamila Czene, George Davey-Smith, Eco de Geus, Renne de Mutsert, Immaculata De Vivo, Joe Dennis, Peter Devilee, Isabel dos-Santos-Silva, Alison Dunning, Johan Eriksson, Peter Fasching, Lindsay Fernandez-Rhodes, Luigi Ferrucci, Dieter Flesch-Janys, Lude Franke, Marike Gabrielson, Ilaria Gandin, Graham Giles, Harald Grallert, Daniel Gudbjartsson, Pascal Guenel, Per Hall, Emily Hallberg, Ute Hamann, Tamara Harris, Catharina Hartman, Gerardo Heiss, Maartje Hooning, John Hopper, Frank Hu, David Hunter, Arfan Ikram, Hae Kyung Im, Marjo-Riitta Jarvelin, Peter Joshi, David Karasik, Zoltan Kutalik, Genevieve LaChance, Diether Lambrechts, Claudia Langenberg, Lenore Launer, Joop Laven, Stefania Lenarduzzi, Jingmei Li, Penelope Lind, Sara Lindstrom, YongMei Liu, Jianan Luan, Reedik Magi, Arto Mannermaa, Hamdi Mbarek, Mark McCarthy, Christa Meisinger, Thomas Meitinger, Cristina Menni, Andres Metspalu, Kyriaki Michailidou, Lili Milani, Roger Milne, Grant Montgomery, Anna Mulligan, Mike Nalls, Pau Navarro, Heli Nevanlinna, Dale Nyholt, Albertine Oldehinkel, Tracy O'Mara, Sandosh Padmanabhan, Aarno Palotie, Nancy Pedersen, Annette Peters, Julian Peto, Paul Pharoah, Anneli Pouta, Paolo Radice, Iffat Rahman, Susan Ring, Antonietta Robino, Frits Rosendaal, Igor Rudan, Rico Rueedi, Daniela Ruggiero, Cinzia Sala, Marjanka Schmidt, Robert Scott, Mitul Shah, Rossella Sorice, Melissa Southey, Ulla Sovio, Meir Stampfer, Maristella Steri, Konstantin Strauch, Toshiko Tanaka, Emmi Tikkanen, Nicholas Timpson, Michela Traglia, Therese Truong, Jonathan Tyrer, Andre Uitterlinden, Digna Velez Edwards, Veronique Vitart, Uwe Volker, Peter Vollenweider, Qin Wang, Elisabeth Widen, Ko Willems van Dijk, Gonneke Willemsen, Robert Winqvist, Bruce Wolffenbuttel, Jing Hua Zhao, Magdalena Zoledziewska, Marek Zygmunt, Behrooz Alizadeh, Dorret Boomsma, Marina Ciullo, Francesco Cucca, Tonu Esko, Nora Franceschini, Christian Gieger, Vilmundur Gudnason, Caroline Hayward, Peter Kraft, Debbie Lawlor, Patrik Magnusson, Nicholas Martin, Dennis Mook-Kanamori, Ellen Nohr, Ozren Polasek, David Porteous, Alkes Price, Paul Ridker, Harold Snieder, Tim Spector, Doris Stockl, Daniela Toniolo, Sheila Ulivi, Jenny Visser, Henry Volzke, Nicholas Wareham, James Wilson, The LifeLines Cohort Study, The InterAct Consortium, kConFab/AOCS Investigators, Endometrial Cancer Association Consortium, Ovarian Cancer Association Consortium, PRACTICAL consortium, Amanda Spurdle, Unnur Thorsteinsdottir, Katherine Pollard, Douglas Easton, Joyce Tung, Jenny Chang-Claude, David Hinds, Anna Murray, Joanne Murabito, Kari Stefansson, Ken Ong, John Perry
doi: http://dx.doi.org/10.1101/076794
Felix Day
University of Cambridge;
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Deborah Thompson
University of Cambridge;
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Hannes Helgason
deCODE genetics;
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Daniel Chasman
Brigham and Womens Hospital, Boston MA;
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Hilary Finucane
Harvard;
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Patrick Sulem
deCODE;
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Katherine Ruth
University of Exeter;
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Sean Whalen
Gladstone Institutes;
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Abhishek Sarkar
MIT;
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Eva Albrecht
Helmholtz Zentrum Munchen;
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Elisabeth Altmaier
Helmholtz Zentrum Munchen;
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Marzyeh Amini
University of Groningen;
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Caterina Barbieri
IRCCS San Raffaele Scientific Institute;
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Thibaud Boutin
University of Edinburgh;
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Archie Campbell
University of Edinburgh;
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Ellen Demerath
Minnesotta University;
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Ayush Giri
Vanderbilt University;
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Chunyan He
Indiana University;
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Jouke Hottenga
Vrije Universiteit Amsterdam;
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Robert Karlsson
Karolinska Institutet;
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Ivana Kolcic
University of Split;
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Po-Ru Loh
Harvard;
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Kathryn Lunetta
Boston University;
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Massimo Mangino
Kings College London;
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Brumat Marco
University of Trieste;
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Gerorge McMahon
University of Bristol;
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Sarah Medland
QIMR;
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Ilja Nolte
University of Groningen;
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Raymond Noordam
Leiden University;
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Teresa Nutile
Institute of Genetics and Biophysics - CNR;
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Lavinia Paternoster
University of Bristol;
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Natalia Perjakova
University of Tartu;
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Eleonora Porcu
Institute of Genetics and Biomedical Research, National Research Council, Cagliari;
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Lynda Rose
Brigham and Womens Hospital;
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Katharina Schraut
University of Edinburgh;
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Ayellet Segre
Broad Institute;
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Albert Smith
Icelandic Heart Association;
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Lisette Stolk
Erasmus MC;
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Alexander Teumer
University Medicine Greifswald;
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Irene Andrulis
Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital;
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Stefania Bandinelli
Azienda Sanitaria Firenze (ASF);
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Matthias Beckmann
Friedrich-Alexander University Erlangen-Nuremberg;
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Javier Benitez
Spanish National Cancer Research Centre;
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Sven Bergmann
University of Lausanne;
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Murielle Bochud
University of Lausanne;
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Eric Boerwinkle
University of Texas;
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Stig Bojesen
Copenhagen University Hospital;
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Manjeet Bolla
University of Cambridge;
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Judith Brand
Karolinska Institutet;
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Hiltrud Braunch
Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology;
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Hermann Brenner
German Cancer Research Center (DKFZ);
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Linda Broer
Erasmus MC;
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Thomas Bruning
Institute of the Ruhr University Bochum;
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Julie Buring
Brigham and Womens Hospital;
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Harry Campbell
University of Edinburgh;
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Eulalia Catamo
IRCCS Burlo Garofolo, Trieste;
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Stephen Chanock
National Cancer Institute, Bethesda;
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Georgia Chenevix-Trench
QIMR;
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Tanguy Corre
University of Lausanne;
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Fergus Couch
Mayo Clinic, Rochester;
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Diana Cousminer
Children's Hospital of Philadelphia;
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Angela Cox
University of Sheffield;
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Laura Crisponi
National Research Council, Cagliari;
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Kamila Czene
Karolinska Institutet;
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George Davey-Smith
University of Bristol;
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Eco de Geus
Vrije Universiteit Amsterdam;
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Renne de Mutsert
Leiden University;
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Immaculata De Vivo
Harvard University;
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Joe Dennis
University of Cambridge;
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Peter Devilee
Leiden University Medical Center;
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Isabel dos-Santos-Silva
London School of Hygiene and Tropical Medicine;
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Alison Dunning
University of Cambridge;
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Johan Eriksson
Helsinki University;
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Peter Fasching
University Hospital Erlangen;
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Lindsay Fernandez-Rhodes
University of North Carolina;
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Luigi Ferrucci
National Institute on Aging;
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Dieter Flesch-Janys
University Medical Center Hamburg-Eppendorf;
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Lude Franke
University of Groningen;
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Marike Gabrielson
Karolinska Institutet;
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Ilaria Gandin
University of Trieste;
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Graham Giles
Cancer Council Victoria, Melbourne;
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Harald Grallert
Helmholtz Zentrum Munchen;
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Daniel Gudbjartsson
deCODE;
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Pascal Guenel
University Paris-Sud;
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Per Hall
Karolinska Institutet;
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Emily Hallberg
Mayo Clinic, Rochester;
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Ute Hamann
German Cancer Research Center (DKFZ);
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Tamara Harris
National Institute on Aging;
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Catharina Hartman
University of Groningen;
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Gerardo Heiss
University of North Carolina;
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Maartje Hooning
Erasmus MC;
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John Hopper
The University of Melbourne;
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Frank Hu
Harvard Medical School;
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David Hunter
Harvard Medical School;
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Arfan Ikram
Erasmus MC;
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Hae Kyung Im
University of Chicago;
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Marjo-Riitta Jarvelin
Imperial College London;
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Peter Joshi
University of Edinburgh;
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David Karasik
Hebrew SeniorLife Institute for Aging Research, Boston;
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Zoltan Kutalik
University of Lausanne;
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Genevieve LaChance
Kings College London;
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Diether Lambrechts
Vesalius Research Center, VIB;
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Claudia Langenberg
University of Cambridge;
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Lenore Launer
National Institute on Aging;
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Joop Laven
Erasmus MC;
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Stefania Lenarduzzi
IRCCS Burlo Garofolo, Trieste, Italy;
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Jingmei Li
Karolinska Institutet;
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Penelope Lind
QIMR;
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Sara Lindstrom
University of Washington;
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YongMei Liu
Wake Forest;
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Jianan Luan
University of Cambridge;
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Reedik Magi
University of Tartu;
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Arto Mannermaa
University of Eastern Finland;
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Hamdi Mbarek
Vrije Universiteit Amsterdam;
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Mark McCarthy
University of Oxford;
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Christa Meisinger
Helmholtz Zentrum Munchen;
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Thomas Meitinger
Helmholtz Zentrum Munchen;
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Cristina Menni
Kings College London;
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Andres Metspalu
University of Tartu;
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Kyriaki Michailidou
University of Cambridge;
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Lili Milani
University of Tartu;
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Roger Milne
Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne;
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Grant Montgomery
QIMR;
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Anna Mulligan
University of Toronto;
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Mike Nalls
National Institute on Aging;
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Pau Navarro
University of Edinburgh;
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Heli Nevanlinna
University of Helsinki;
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Dale Nyholt
Queensland University of Technology;
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Albertine Oldehinkel
University of Groningen;
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Tracy O'Mara
QIMR;
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Sandosh Padmanabhan
University of Glasgow;
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Aarno Palotie
Harvard Medical School;
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Nancy Pedersen
Karolinska Institutet;
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Annette Peters
Helmholtz Zentrum Munchen;
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Julian Peto
London School of Hygiene and Tropical Medicine;
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Paul Pharoah
University of Cambridge;
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Anneli Pouta
National Institute for Health and Welfare, Finland;
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Paolo Radice
Istituto Nazionale dei Tumori (INT), Milan;
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Iffat Rahman
Karolinska Institutet;
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Susan Ring
University of Bristol;
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Antonietta Robino
IRCCS Burlo Garofolo, Trieste, Italy;
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Frits Rosendaal
Leiden University;
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Igor Rudan
University of Edinburgh;
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Rico Rueedi
University of Lausanne;
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Daniela Ruggiero
CNR, via Pietro Castellino 111, 80131, Naples;
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Cinzia Sala
Vita-Salute San Raffaele University;
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Marjanka Schmidt
The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital;
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Robert Scott
University of Cambridge;
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Mitul Shah
University of Cambridge;
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Rossella Sorice
NR, via Pietro Castellino 111, 80131, Naples;
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Melissa Southey
The University of Melbourne;
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Ulla Sovio
Imperial College London;
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Abstract

The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Here, we analyse 1000-Genome reference panel imputed genotype data on up to ~370,000 women and identify 389 independent signals (all P<5x10-8) for age at menarche, a notable milestone in female pubertal development. In Icelandic data from deCODE, these signals explain ~7.4% of the population variance in age at menarche, corresponding to one quarter of the estimated heritability. We implicate over 250 genes via coding variation or associated gene expression, and demonstrate enrichment across genes active in neural tissues. We identify multiple rare variants near the imprinted genes MKRN3 and DLK1 that exhibit large effects on menarche only when paternally inherited. Disproportionate effects of variants on early or late puberty timing are observed: single variant and heritability estimates are larger for early than late puberty timing in females. The opposite pattern is seen in males, with larger estimates for late than early puberty timing. Mendelian randomization analyses indicate causal inverse associations, independent of BMI, between puberty timing and risks for breast and endometrial cancers in women, and prostate cancer in men. In aggregate, our findings reveal new complexity in the genetic regulation of puberty timing and support new causal links with adult cancer risks.

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The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
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  • Posted September 23, 2016.

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Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility
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Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility
Felix Day, Deborah Thompson, Hannes Helgason, Daniel Chasman, Hilary Finucane, Patrick Sulem, Katherine Ruth, Sean Whalen, Abhishek Sarkar, Eva Albrecht, Elisabeth Altmaier, Marzyeh Amini, Caterina Barbieri, Thibaud Boutin, Archie Campbell, Ellen Demerath, Ayush Giri, Chunyan He, Jouke Hottenga, Robert Karlsson, Ivana Kolcic, Po-Ru Loh, Kathryn Lunetta, Massimo Mangino, Brumat Marco, Gerorge McMahon, Sarah Medland, Ilja Nolte, Raymond Noordam, Teresa Nutile, Lavinia Paternoster, Natalia Perjakova, Eleonora Porcu, Lynda Rose, Katharina Schraut, Ayellet Segre, Albert Smith, Lisette Stolk, Alexander Teumer, Irene Andrulis, Stefania Bandinelli, Matthias Beckmann, Javier Benitez, Sven Bergmann, Murielle Bochud, Eric Boerwinkle, Stig Bojesen, Manjeet Bolla, Judith Brand, Hiltrud Braunch, Hermann Brenner, Linda Broer, Thomas Bruning, Julie Buring, Harry Campbell, Eulalia Catamo, Stephen Chanock, Georgia Chenevix-Trench, Tanguy Corre, Fergus Couch, Diana Cousminer, Angela Cox, Laura Crisponi, Kamila Czene, George Davey-Smith, Eco de Geus, Renne de Mutsert, Immaculata De Vivo, Joe Dennis, Peter Devilee, Isabel dos-Santos-Silva, Alison Dunning, Johan Eriksson, Peter Fasching, Lindsay Fernandez-Rhodes, Luigi Ferrucci, Dieter Flesch-Janys, Lude Franke, Marike Gabrielson, Ilaria Gandin, Graham Giles, Harald Grallert, Daniel Gudbjartsson, Pascal Guenel, Per Hall, Emily Hallberg, Ute Hamann, Tamara Harris, Catharina Hartman, Gerardo Heiss, Maartje Hooning, John Hopper, Frank Hu, David Hunter, Arfan Ikram, Hae Kyung Im, Marjo-Riitta Jarvelin, Peter Joshi, David Karasik, Zoltan Kutalik, Genevieve LaChance, Diether Lambrechts, Claudia Langenberg, Lenore Launer, Joop Laven, Stefania Lenarduzzi, Jingmei Li, Penelope Lind, Sara Lindstrom, YongMei Liu, Jianan Luan, Reedik Magi, Arto Mannermaa, Hamdi Mbarek, Mark McCarthy, Christa Meisinger, Thomas Meitinger, Cristina Menni, Andres Metspalu, Kyriaki Michailidou, Lili Milani, Roger Milne, Grant Montgomery, Anna Mulligan, Mike Nalls, Pau Navarro, Heli Nevanlinna, Dale Nyholt, Albertine Oldehinkel, Tracy O'Mara, Sandosh Padmanabhan, Aarno Palotie, Nancy Pedersen, Annette Peters, Julian Peto, Paul Pharoah, Anneli Pouta, Paolo Radice, Iffat Rahman, Susan Ring, Antonietta Robino, Frits Rosendaal, Igor Rudan, Rico Rueedi, Daniela Ruggiero, Cinzia Sala, Marjanka Schmidt, Robert Scott, Mitul Shah, Rossella Sorice, Melissa Southey, Ulla Sovio, Meir Stampfer, Maristella Steri, Konstantin Strauch, Toshiko Tanaka, Emmi Tikkanen, Nicholas Timpson, Michela Traglia, Therese Truong, Jonathan Tyrer, Andre Uitterlinden, Digna Velez Edwards, Veronique Vitart, Uwe Volker, Peter Vollenweider, Qin Wang, Elisabeth Widen, Ko Willems van Dijk, Gonneke Willemsen, Robert Winqvist, Bruce Wolffenbuttel, Jing Hua Zhao, Magdalena Zoledziewska, Marek Zygmunt, Behrooz Alizadeh, Dorret Boomsma, Marina Ciullo, Francesco Cucca, Tonu Esko, Nora Franceschini, Christian Gieger, Vilmundur Gudnason, Caroline Hayward, Peter Kraft, Debbie Lawlor, Patrik Magnusson, Nicholas Martin, Dennis Mook-Kanamori, Ellen Nohr, Ozren Polasek, David Porteous, Alkes Price, Paul Ridker, Harold Snieder, Tim Spector, Doris Stockl, Daniela Toniolo, Sheila Ulivi, Jenny Visser, Henry Volzke, Nicholas Wareham, James Wilson, The LifeLines Cohort Study, The InterAct Consortium, kConFab/AOCS Investigators, Endometrial Cancer Association Consortium, Ovarian Cancer Association Consortium, PRACTICAL consortium, Amanda Spurdle, Unnur Thorsteinsdottir, Katherine Pollard, Douglas Easton, Joyce Tung, Jenny Chang-Claude, David Hinds, Anna Murray, Joanne Murabito, Kari Stefansson, Ken Ong, John Perry
bioRxiv 076794; doi: http://dx.doi.org/10.1101/076794
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Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility
Felix Day, Deborah Thompson, Hannes Helgason, Daniel Chasman, Hilary Finucane, Patrick Sulem, Katherine Ruth, Sean Whalen, Abhishek Sarkar, Eva Albrecht, Elisabeth Altmaier, Marzyeh Amini, Caterina Barbieri, Thibaud Boutin, Archie Campbell, Ellen Demerath, Ayush Giri, Chunyan He, Jouke Hottenga, Robert Karlsson, Ivana Kolcic, Po-Ru Loh, Kathryn Lunetta, Massimo Mangino, Brumat Marco, Gerorge McMahon, Sarah Medland, Ilja Nolte, Raymond Noordam, Teresa Nutile, Lavinia Paternoster, Natalia Perjakova, Eleonora Porcu, Lynda Rose, Katharina Schraut, Ayellet Segre, Albert Smith, Lisette Stolk, Alexander Teumer, Irene Andrulis, Stefania Bandinelli, Matthias Beckmann, Javier Benitez, Sven Bergmann, Murielle Bochud, Eric Boerwinkle, Stig Bojesen, Manjeet Bolla, Judith Brand, Hiltrud Braunch, Hermann Brenner, Linda Broer, Thomas Bruning, Julie Buring, Harry Campbell, Eulalia Catamo, Stephen Chanock, Georgia Chenevix-Trench, Tanguy Corre, Fergus Couch, Diana Cousminer, Angela Cox, Laura Crisponi, Kamila Czene, George Davey-Smith, Eco de Geus, Renne de Mutsert, Immaculata De Vivo, Joe Dennis, Peter Devilee, Isabel dos-Santos-Silva, Alison Dunning, Johan Eriksson, Peter Fasching, Lindsay Fernandez-Rhodes, Luigi Ferrucci, Dieter Flesch-Janys, Lude Franke, Marike Gabrielson, Ilaria Gandin, Graham Giles, Harald Grallert, Daniel Gudbjartsson, Pascal Guenel, Per Hall, Emily Hallberg, Ute Hamann, Tamara Harris, Catharina Hartman, Gerardo Heiss, Maartje Hooning, John Hopper, Frank Hu, David Hunter, Arfan Ikram, Hae Kyung Im, Marjo-Riitta Jarvelin, Peter Joshi, David Karasik, Zoltan Kutalik, Genevieve LaChance, Diether Lambrechts, Claudia Langenberg, Lenore Launer, Joop Laven, Stefania Lenarduzzi, Jingmei Li, Penelope Lind, Sara Lindstrom, YongMei Liu, Jianan Luan, Reedik Magi, Arto Mannermaa, Hamdi Mbarek, Mark McCarthy, Christa Meisinger, Thomas Meitinger, Cristina Menni, Andres Metspalu, Kyriaki Michailidou, Lili Milani, Roger Milne, Grant Montgomery, Anna Mulligan, Mike Nalls, Pau Navarro, Heli Nevanlinna, Dale Nyholt, Albertine Oldehinkel, Tracy O'Mara, Sandosh Padmanabhan, Aarno Palotie, Nancy Pedersen, Annette Peters, Julian Peto, Paul Pharoah, Anneli Pouta, Paolo Radice, Iffat Rahman, Susan Ring, Antonietta Robino, Frits Rosendaal, Igor Rudan, Rico Rueedi, Daniela Ruggiero, Cinzia Sala, Marjanka Schmidt, Robert Scott, Mitul Shah, Rossella Sorice, Melissa Southey, Ulla Sovio, Meir Stampfer, Maristella Steri, Konstantin Strauch, Toshiko Tanaka, Emmi Tikkanen, Nicholas Timpson, Michela Traglia, Therese Truong, Jonathan Tyrer, Andre Uitterlinden, Digna Velez Edwards, Veronique Vitart, Uwe Volker, Peter Vollenweider, Qin Wang, Elisabeth Widen, Ko Willems van Dijk, Gonneke Willemsen, Robert Winqvist, Bruce Wolffenbuttel, Jing Hua Zhao, Magdalena Zoledziewska, Marek Zygmunt, Behrooz Alizadeh, Dorret Boomsma, Marina Ciullo, Francesco Cucca, Tonu Esko, Nora Franceschini, Christian Gieger, Vilmundur Gudnason, Caroline Hayward, Peter Kraft, Debbie Lawlor, Patrik Magnusson, Nicholas Martin, Dennis Mook-Kanamori, Ellen Nohr, Ozren Polasek, David Porteous, Alkes Price, Paul Ridker, Harold Snieder, Tim Spector, Doris Stockl, Daniela Toniolo, Sheila Ulivi, Jenny Visser, Henry Volzke, Nicholas Wareham, James Wilson, The LifeLines Cohort Study, The InterAct Consortium, kConFab/AOCS Investigators, Endometrial Cancer Association Consortium, Ovarian Cancer Association Consortium, PRACTICAL consortium, Amanda Spurdle, Unnur Thorsteinsdottir, Katherine Pollard, Douglas Easton, Joyce Tung, Jenny Chang-Claude, David Hinds, Anna Murray, Joanne Murabito, Kari Stefansson, Ken Ong, John Perry
bioRxiv 076794; doi: http://dx.doi.org/10.1101/076794

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