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This document contians Supplementary Figures S1 – S10 and S19 – S28 for a manuscript titled ’Pathophysiologic inferences from 243 genetic loci for depression and risk prediction of recurrence and comorbid psychiatric disorders', submitted to Nature Medicine.

This document contians Supplementary Figures S1 – S10, S14 - S17 and S23 – S28 for a manuscript titled ’Pathophysiologic inferences from 243 genetic loci for depression and risk prediction of recurrence and comorbid psychiatric disorders', submitted to Nature Medicine.

Rare coding variation has historically provided the most direct connections between gene function and disease pathogenesis. By meta-analyzing the whole-exomes of 24,248 cases and 97,322 controls, we implicate ultra-rare coding variants (URVs) in ten genes as conferring substantial risk for schizophrenia (odds ratios 3 – 50, P < 2.14 × 10(−6)), and 32 genes at a FDR < 5%. These genes have the greatest expression in central nervous system neurons and have diverse molecular functions that include the formation, structure, and function of the synapse. The associations of NMDA receptor subunit GRIN2A and AMPA receptor subunit GRIA3 provide support for the dysfunction of the glutamatergic system as a mechanistic hypothesis in the pathogenesis of schizophrenia. We observe an overlap of rare variant risk between schizophrenia, autism spectrum disorders (ASD)(1), epilepsy and severe neurodevelopmental disorders (DD/ID)(2), though in some shared genes different mutation types are implicated. Most genes described here however are not implicated in neurodevelopment and we demonstrate that genes prioritized from common variant analyses of schizophrenia are enriched in rare variant risk(3), suggesting that common and rare genetic risk factors at least partially converge on the same underlying pathogenic biological processes. Even after excluding significantly associated genes, schizophrenia cases still carry a substantial excess of URVs, implying that more risk genes await discovery using this approach.

Bipolar disorder is a heritable mental illness with complex etiology. We performed a genome-wide association study of 41,917 bipolar disorder cases and 371,549 controls of European ancestry, which identified 64 associated genomic loci. Bipolar disorder risk alleles were enriched in genes in synaptic signaling pathways and brain-expressed genes, particularly those with high specificity of expression in neurons of the prefrontal cortex and hippocampus. Significant signal enrichment was found in genes encoding targets of antipsychotics, calcium channel blockers, antiepileptics and anesthetics. Integrating expression quantitative trait locus data implicated 15 genes robustly linked to bipolar disorder via gene expression, encoding druggable targets such as HTR6, MCHR1, DCLK3 and FURIN. Analyses of bipolar disorder subtypes indicated high but imperfect genetic correlation between bipolar disorder type I and II and identified additional associated loci. Together, these results advance our understanding of the biological etiology of bipolar disorder, identify novel therapeutic leads and prioritize genes for functional follow-up studies.

Hair cortisol concentration (HCC) is a promising measure of long-term hypothalamus-pituitary-adrenal (HPA) axis activity. Previous research has suggested an association between HCC and psychological variables, and initial studies of inter-individual variance in HCC have implicated genetic factors. However, whether HCC and psychological variables share genetic risk factors remains unclear. The aims of the present twin study were to: (i) assess the heritability of HCC; (ii) estimate the phenotypic and genetic correlation between HPA axis activity and the psychological variables perceived stress, depressive symptoms, and neuroticism; using formal genetic twin models and molecular genetic methods, i.e. polygenic risk scores (PRS). HCC was measured in 671 adolescents and young adults. These included 115 monozygotic and 183 dizygotic twin-pairs. For 432 subjects PRS scores for plasma cortisol, major depression, and neuroticism were calculated using data from large genome wide association studies. The twin model revealed a heritability for HCC of 72%. No significant phenotypic or genetic correlation was found between HCC and the three psychological variables of interest. PRS did not explain variance in HCC. The present data suggest that HCC is highly heritable. However, the data do not support a strong biological link between HCC and any of the investigated psychological variables. Consortia CORtisolNETwork (CORNET) Consortium Jennifer L. Bolton21 Caroline Hayward23 Nese Direk24,25 Anna Anderson21 Jennifer Huffman23 James F. Wilson26 Harry Campbell26 Igor Rudan26 Alan Wright23 Nicholas Hastie23 Sarah H. Wild26 Fleur P. Velders24 Albert Hofman24 Andre G. Uitterlinden24,27 Jari Lahti28 Katri Räikkönen28 Eero Kajantie29 Elisabeth Widen30 Aarno Palotie30,31 Johan G. Eriksson29,32,33,34,35 Marika Kaakinen36 Marjo-Riitta Järvelin36,37,38,39 Nicholas J. Timpson40 George Davey Smith40 Susan M. Ring41 David M. Evans40 Beate St Pourcain41 Toshiko Tanaka42 Yuri Milaneschi42,43 Stefania Bandinelli44 Luigi Ferrucci42 Pim van der Harst45,46,47 Judith GM Rosmalen48 Stephen JL Bakker49 Niek Verweij45 Robin PF Dullaart49 Anubha Mahajan50 Cecilia M. Lindgren50 Andrew Morris50 Lars Lind51 Erik Ingelsson51 Laura N. Anderson52 Craig E. Pennell53 Stephen J. Lye52 Stephen G. Matthews54 Joel Eriksson55 Dan Mellstrom55 Claes Ohlsson55 Jackie F. Price26 Mark WJ Strachan21 Rebecca M. Reynolds21 Henning Tiemeier24,56,57 Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (PGC) Stephan Ripke58,59,60 Manuel Mattheisen61,62,63 Abdel Abdellaoui64 Mark J. Adams65 Esben Agerbo66,8,67 Tracy M. Air68 Till FM Andlauer69,70 Silviu-Alin Bacanu71 Marie Bækvad-Hansen67,72 Aartjan TF Beekman43 David A. Bennett73 Klaus Berger74 Tim B. Bigdeli71,11 Jonas Bybjerg-Grauholm67,72 Enda M. Byrne5 Na Cai75 Enrique Castelao76 Toni-Kim Clarke65 Jonathan RI Coleman77 Converge Consortium78 Nick Craddock79 Udo Dannlowski80,81 Gareth Davies82 Gail Davies83 Eco. J. C. de Geus64,84 Philip De Jager85 Ian J. Deary83 Franziska Degenhardt12,13 Erin C. Dunn86,87,88 Erik A. Ehli82 Thalia C. Eley77 Valentina Escott-Price89 Tõnu Esko58,90,91,92 Hilary K. Finucane93,94 Michael Gill95 Scott D. Gordon96 Jakob Grove61,62,67,97 Lynsey S. Hall65,98 Thomas F. Hansen99,100 Christine Søholm Hansen67,72 Thomas F. Hansen101 Andrew C. Heath102 Anjali K. Henders5 Stefan Herms12,13,15 Per Hoffmann12,13,15 Georg Homuth103 Carsten Horn104 Jouke- Jan Hottenga64 David Hougaard67,72 Hailiang Huang59,86,105 Marcus Ising106 Rick Jansen43 Eric Jorgenson107 Stefan Kloiber108,109 James A Knowles110 Warren W. Kretzschmar50 Jesper Krogh111 Zoltán Kutalik112,113 Maren Lang3 Glyn Lewis114 Yihan Li50 Donald J. MacIntyre115,116 Pamela AF Madden102 Jonathan Marchine117 Hamdi Mbarek118,64 Peter McGuffin77 Divya Mehta119 Andres Metspalu92,120 Christel M. Middeldorp64 Evelin Mihailov92,121 Lili Milani92 Grant W. Montgomery122 Sara Mostafavi123,124 Niamh Mullins77 Matthias Nauck125,126 Bernard Ng124 Merete Nordentoft67,127 Dale R. Nyholt128 Michael C. O’Donovan129 Paul F. O’Reilly77 Hogni Oskarsson130 Michael J. Owen129 Sara A. Paciga131 Carsten Bøcker Pedersen66,67,8 Marianne Giørtz Pedersen66,67,8 Nancy L. Pedersen132 Michele L. Pergadia133 Roseann E. Peterson11,71 Erik Pettersson134 Wouter J. Peyrot43 David J. Porteous135 Danielle Posthuma136,137 James B. Potash138 Jorge A. Quiroz139 John P. Rice102 Brien P. Riley71 Margarita Rivera77,140 Douglas M. Ruderfer141 Saira Saeed Mirza24 Robert Schoevers142 Ling Shen107 Jianxin Shi143 Engilbert Sigurdsson144 Grant CB Sinnamon145 Johannes H. Smit43 Daniel J. Smith146 Jordan W. Smoller86 Hreinn Stephansson147 Stacy Steinberg147 Jana Strohmaier3 Katherine E. Tansey148 Alexander Teumer149 Wesley Thompson100,135,150,151,152 Pippa A. Thomson135 Thorgeir E. Thorgeirsson147 Jens Treutlein3 Maciej Trzaskowski153 Daniel Umbricht154 Sandra van der Auwera155 Gerard van Grootheest43 Albert M. van Hemert156 Alexander Viktorin132 Henry Völzke149 Yunpeng Wang67,100,151 Bradley T. Webb157 Myrna M. Weissman158,159 Jürgen Wellmann74 Gonneke Willemsen64 Hualin S. Xi160 Bernhard T. Baune68 Douglas H. R. Blackwood65 Dorret I. Boomsma64 Anders D. Børglum61,62,67 Henriette N. Buttenschøn62,67,161 Sven Cichon12,162,163,164 Enrico Domenici165 Jonathan Flint50,166 Hans J. Grabe155 Steven P. Hamilton167 Kenneth S. Kendler71 Qingqin S. Li168 Susanne Lucae106 Patrik K. Magnusson132 Andrew M. McIntosh65,83 Ole Mors67,169 Preben Bo Mortensen62,8,67 Bertram Müller-Myhsok69,70,170 Brenda WJH Penninx43 Roy H. Perlis87,171 Martin Preisig76 Catherine Schaefer107 Jordan W. Smoller87,88 Kari Stephansson147 Henning Tiemeier24,56,57 Rudolf Uher172 Thomas Werge100,150,173 Ashley R. Winslow174,175 Gerome Breen77,176 Douglas F. Levinson177 Cathryn M. Lewis77,178 Naomi R. Wray5,153 Patrick F. Sullivan134,179,180 23MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. 24Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands. 25Psychiatry, Dokuz Eylul University School Of Medicine, Izmir, TR, Turkey. 26Centre for Population Health Sciences, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH8 9AG, UK. 27Internal Medicine, Erasmus MC, Rotterdam, NL, Netherlands. 28Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland. 29National Institute for Health and Welfare, Helsinki, Finland. 30Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. 31Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland. 32Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland. 33Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland. 34Folkhalsan Research Centre, Helsinki, Finland. 35Vasa Central Hospital, Vasa, Finland. 36Institute of Health Sciences and Biocenter Oulu, University of Oulu, Oulu, Finland. 37Department of Children and Yond People and Families, National Institute for Health and elfare, Oulu, Finland. 38Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, Imperial College London, London, UK. 39Unit of Primary Care, Oulu University Hospital, Oulu, Finland. 40MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK. 41School of Social and Community Medicine, University of Bristol, Bristol, UK. 42Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, Baltimore, MD, USA. 43Department of Psychiatry, VU University Medical Center/GGZ inGeest, Amsterdam, Netherlands. 44Geriatric Unit, ASF, Florence, Italy. 45University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, Netherlands. 46University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. 47Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, Netherlands. 48University of Groningen, University Medical Center Groningen, Interdisciplinary Center for Psychiatric Epidemiology, Groningen, Netherlands. 49University of Groningen, University Medical Center Groningen, Department of Internal Medicine, Groningen, Netherlands. 50Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. 51Department of Medical Sciences, Uppsala University, Uppsala, Sweden. 52Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. 53School of Women’s and Infant’s Health, The University of Western Australia, Crawley, Australia. 54Department of Physiology, University of Toronto, Toronto, Ontario, Canada. 55Center for Bone and Arthritis Research, Institute of Medicin, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. 56Child and Adolescent Psychiatry, Erasmus MC, Rotterdam, Netherlands. 57Psychiatry, Erasmus MC, Rotterdam, Netherlands. 58Medical and Population Genetics, Broad Institute, Cambridge, USA. 59Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA. 60Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany. 61Department of Biomedicine, Aarhus University, Aarhus, Denmark. 62iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. 63iSPYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark. 64Dept of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands. 65Division of Psychiatry, University of Edinburgh, Edinburgh, UK. 66Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark. 67iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark. 68Discipline of Psychiatry, University of Adelaide, Adelaide, Australia. 69Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany. 70Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. 71Department of Psychiatry, Virginia Commonwealth University, Richmond, USA. 72Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark. 73Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, USA. 74Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, UK. 75Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK. 76Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland. 77MRC Social Genetic and Developmental Psychiatry Centre, King’s College London, London, UK. 78University of Oxford, Oxford, UK. 79Psychological Medicine, Cardiff University, Cardiff, UK. 80Department of Psychiatry, University of Marburg, Marburg, Germany. 81Department of Psychiatry, University of Münster, Münster, Germany. 82Avera Institute for Human Genetics, Sioux Falls, USA. 83Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK. 84EMGO+ Institute, VU University Medical Center, Amsterdam, Netherlands. 85Neurology, Brigham and Women’s Hospital, Boston, USA. 86Stanley Center for Psychiatric Research, Broad Institute, Cambridge, USA. 87Department of Psychiatry, Massachusetts General Hospital, Boston, USA. 88Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, USA. 89Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK. 90Division of Endocrinology, Children’s Hospital Boston, Boston, USA. 91Department of Genetics, Harvard Medical School, Boston, USA. 92Estonian Genome Center, University of Tartu, Tartu, Estonia. 93Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA. 94Department of Mathematics, Massachusetts Institute of Technology, Cambridge, USA. 95Department of Psychiatry, Trinity College Dublin, Dublin, Ireland. 96Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia. 97Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark. 98Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK. 99Danish Headache Centre, Department of Neurology, Rigshospitalet Glostrup, Glostrup, Denmark. 100Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Roskilde, Denmark. 101iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Copenhagen, Denmark. 102Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, USA. 103Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany. 104Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. 105Department of Medicine, Harvard Medical School, Boston, USA. 106Max Planck Institute of Psychiatry, Munich, Germany. 107Division of Research, Kaiser Permanente Northern California, Oakland, USA. 108Centre for Addiction and Mental Health, Toronto, Canada. 109Department of Psychiatry, University of Toronto, Toronto, Canada. 110Psychiatry & The Behavioral Sciences, University of Southern California, Los Angeles, USA. 111Department of Endocrinology at Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark. 112Swiss Institute of Bioinformatics, Lausanne, Switzerland. 113Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland. 114Division of Psychiatry, University College London, London, UK. 115Mental Health NHS 24, Glasgow, UK. 116Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK. 117Statistics, University of Oxford, Oxford, UK. 118EMGO+ Institute for Health and Care Research, Amsterdam, Netherlands. 119School of Psychology and Counseling, Queensland University of Technology, Brisbane, Australia. 120Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. 121Estonian Biocentre, Tartu, Estonia. 122Institute for Molecular Biology, University of Queensland, Brisbane, Australia. 123Medical Genetics, University of British Columbia, Vancouver, Canada. 124Statistics, University of British Columbia, Vancouver, Canada. 125DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Matthias Nauck, Greifswald, Germany. 126Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany. 127Mental Health Centre Copenhagen, Copenhagen Universtity Hospital, Copenhagen, Denmark. 128Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia. 129MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK. 130Humus, Reykjavik, Iceland. 131Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Groton, USA. 132Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. 133Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, USA. 134Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. 135Medical Genetics Section, CGEM, IGMM, University of Edinburgh, Edinburgh, UK. 136Complex Trait Genetics, VU University Amsterdam, Amsterdam, Netherlands. 137Clinical Genetics, VU University Medical Center, Amsterdam, Netherlands. 138Psychiatry, University of Iowa, Iowa City, USA. 139Solid GT, Boston, USA. 140Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain. 141Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA. 142Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, Netherlands. 143Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA. 144Faculty of Medicine, Department of Psychiatry, School of Health Sciences, University of Iceland, Reykjavik, Iceland. 145School of Medicine and Dentistry, James Cook University, Townsville, Australia. 146Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK. 147deCODE Genetics/Amgen, Reykjavik, Iceland. 148College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK. 149Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany. 150iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark. 151KG Jebsen Centre for Psychosis Research, Norway Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway. 152Department of Psychiatry, University of California, San Diego, San Diego, USA. 153Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia. 154Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. 155Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany. 156Department of Psychiatry, Leiden University Medical Center, Leiden, Netherlands. 157Virginia Institute of Psychiatric & Behavioral Genetics, Virginia Commonwealth University, Richmond, USA. 158Psychiatry, Columbia University College of Physicians and Surgeons, New York, USA. 159Division of Epidemiology, New York State Psychiatric Institute, New York, USA. 160Computational Sciences Center of Emphasis, Pfizer Global Research and Development, Cambridge, USA. 161Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark. 162Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany. 163Department of Biomedicine, University of Basel, Basel, CH, Switzerland. 164Division of Medical Genetics, University of Basel, Basel, CH, Switzerland. 165Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy. 166Psychiatry, University of California Los Angeles, Los Angeles, USA. 167Psychiatry, Kaiser Permanente Northern California, San Francisco, USA. 168Neuroscience Therapeutic Area, Janssen Research and Development, LLC, Titusville, USA. 169Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, Denmark. 170Institute of Translational Medicine, University of Liverpool, Liverpool, UK. 171Psychiatry, Harvard Medical School, Boston, USA. 172Psychiatry, Dalhousie University, Halifax, Canada. 173Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. 174Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Cambridge, USA. 175Orphan Disease Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA. 176NIHR BRC for Mental Health, King’s College London, London, UK. 177Psychiatry & Behavioral Sciences, Stanford University, Stanford, USA. 178Department of Medical & Molecular Genetics, King’s College London, London, UK. 179Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA. 180Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, USA.