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Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FUR, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. Nat Commun 2023; 14:3377. [PMID: 37291107 PMCID: PMC10250394 DOI: 10.1038/s41467-023-38766-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
- Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - J Fah Sathirapongsasuti
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
| | - Ravi Gupta
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Asif Rasheed
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Radha Venkatesan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Saurabh Belsare
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Ramesh Menon
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Sameer Phalke
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - John Fang
- Thermo Fisher Scientific, Santa Clara, CA, 95051, USA
| | - Deepak Tanneeru
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - Akshi Bassi
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | | | | | - Zameer Ul-Asar
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Imran Saleem
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Unzila Ishtiaq
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Areej Fatima
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | | | | | | | | | | | - Anjum Jalal
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Philippe Frossard
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Qixin Bei
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA
| | | | - Priya B V
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | | | - Minxian Wang
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amit V Khera
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
| | - B R Lakshmi
- MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Aliya Naheed
- Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh
| | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | | | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Uday B Muthane
- Parkinson and Ageing Research Foundation, Bengaluru, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Prashanth L Kukkle
- All India Institute of Medical Sciences, Rishikesh, India
- Manipal Hospital, Miller Road, Bengaluru, India
- Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India
| | - Somasekar Seshagiri
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arkasubhra Ghosh
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | - V Mohan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Danish Saleheen
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
- Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA
| | - Eric W Stawiski
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
- Caribou Biosciences, Berkeley, CA, 94710, USA
| | - Andrew S Peterson
- MedGenome Inc., Foster City, CA, 94404, USA.
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
- Broadwing Bio, South San Francisco, CA, 94080, USA.
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2
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Niarchou M, Gustavson DE, Sathirapongsasuti JF, Anglada-Tort M, Eising E, Bell E, McArthur E, Straub P, McAuley JD, Capra JA, Ullén F, Creanza N, Mosing MA, Hinds DA, Davis LK, Jacoby N, Gordon RL. Genome-wide association study of musical beat synchronization demonstrates high polygenicity. Nat Hum Behav 2022; 6:1292-1309. [PMID: 35710621 PMCID: PMC9489530 DOI: 10.1038/s41562-022-01359-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2022] [Indexed: 02/02/2023]
Abstract
Moving in synchrony to the beat is a fundamental component of musicality. Here we conducted a genome-wide association study to identify common genetic variants associated with beat synchronization in 606,825 individuals. Beat synchronization exhibited a highly polygenic architecture, with 69 loci reaching genome-wide significance (P < 5 × 10-8) and single-nucleotide-polymorphism-based heritability (on the liability scale) of 13%-16%. Heritability was enriched for genes expressed in brain tissues and for fetal and adult brain-specific gene regulatory elements, underscoring the role of central-nervous-system-expressed genes linked to the genetic basis of the trait. We performed validations of the self-report phenotype (through separate experiments) and of the genome-wide association study (polygenic scores for beat synchronization were associated with patients algorithmically classified as musicians in medical records of a separate biobank). Genetic correlations with breathing function, motor function, processing speed and chronotype suggest shared genetic architecture with beat synchronization and provide avenues for new phenotypic and genetic explorations.
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Affiliation(s)
- Maria Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Daniel E. Gustavson
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - Manuel Anglada-Tort
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Else Eising
- grid.419550.c0000 0004 0501 3839Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Eamonn Bell
- grid.21729.3f0000000419368729Department of Music, Columbia University, New York, NY USA ,grid.8250.f0000 0000 8700 0572Department of Computer Science, Durham University, Durham, UK
| | - Evonne McArthur
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Peter Straub
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - J. Devin McAuley
- grid.17088.360000 0001 2150 1785Department of Psychology, Michigan State University, East Lansing, MI USA
| | - John A. Capra
- grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Epidemiology & Biostatistics, University of California, San Francisco, CA USA
| | - Fredrik Ullén
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Nicole Creanza
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN USA
| | - Miriam A. Mosing
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany ,grid.1008.90000 0001 2179 088XMelbourne School of Psychological Sciences, University of Melbourne, Melbourne, Victoria Australia
| | - David A. Hinds
- grid.420283.f0000 0004 0626 085823andMe, Inc, Sunnyvale, CA USA
| | - Lea K. Davis
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN USA
| | - Nori Jacoby
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Reyna L. Gordon
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Otolaryngology—Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Psychology, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN USA
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3
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Suryamohan K, Diwanji D, Stawiski EW, Gupta R, Miersch S, Liu J, Chen C, Jiang YP, Fellouse FA, Sathirapongsasuti JF, Albers PK, Deepak T, Saberianfar R, Ratan A, Washburn G, Mis M, Santhosh D, Somasekar S, Hiranjith GH, Vargas D, Mohan S, Phalke S, Kuriakose B, Antony A, Ustav M, Schuster SC, Sidhu S, Junutula JR, Jura N, Seshagiri S. Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. Commun Biol 2021; 4:475. [PMID: 33846513 PMCID: PMC8041869 DOI: 10.1038/s42003-021-02030-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [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: 11/06/2020] [Accepted: 03/23/2021] [Indexed: 01/07/2023] Open
Abstract
COVID-19 is a respiratory illness caused by a novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10-15-fold higher affinity compared to SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter host susceptibility to SARS-CoV-2 by affecting this interaction. We analyzed over 290,000 samples representing >400 population groups from public genomic datasets and identified multiple ACE2 protein-altering variants. Using reported structural data, we identified natural ACE2 variants that could potentially affect virus-host interaction and thereby alter host susceptibility. These include variants S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P and H378R that were predicted to increase susceptibility, while variants K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L and D509Y were predicted to be protective variants that show decreased binding to S-protein. Using biochemical assays, we confirmed that K31R and E37K had decreased affinity, and K26R and T92I variants showed increased affinity for S-protein when compared to wildtype ACE2. Consistent with this, soluble ACE2 K26R and T92I were more effective in blocking entry of S-protein pseudotyped virus suggesting that ACE2 variants can modulate susceptibility to SARS-CoV-2.
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Affiliation(s)
- Kushal Suryamohan
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Eric W Stawiski
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Ravi Gupta
- MedGenome Labs Ltd., Bangalore, Karnataka, India
| | - Shane Miersch
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jiang Liu
- ModMab Therapeutics, Foster City, CA, USA
| | - Chao Chen
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Frederic A Fellouse
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Reza Saberianfar
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gavin Washburn
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Monika Mis
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | | | | | - G H Hiranjith
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Sangeetha Mohan
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Sameer Phalke
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | | | - Aju Antony
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Mart Ustav
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sachdev Sidhu
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Somasekar Seshagiri
- ModMab Therapeutics, Foster City, CA, USA.
- SciGenom Research Foundation, Bangalore, Karnataka, India.
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4
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Ganna A, Verweij KJH, Nivard MG, Maier R, Wedow R, Busch AS, Abdellaoui A, Guo S, Sathirapongsasuti JF, Lichtenstein P, Lundström S, Långström N, Auton A, Harris KM, Beecham GW, Martin ER, Sanders AR, Perry JRB, Neale BM, Zietsch BP. Response to Comment on "Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior". Science 2021; 371:eaba5693. [PMID: 33766859 DOI: 10.1126/science.aba5693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/15/2020] [Accepted: 03/09/2021] [Indexed: 11/02/2022]
Abstract
Hamer et al argue that the variable "ever versus never had a same-sex partner" does not capture the complexity of human sexuality. We agree and said so in our paper. But Hamer et al neglect to mention that we also reported follow-up analyses showing substantial overlap of the genetic influences on our main variable and on more nuanced measures of sexual behavior, attraction, and identity.
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Affiliation(s)
- Andrea Ganna
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, 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
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, Netherlands
| | - Robert Maier
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, 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
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Sociology, Harvard University, Cambridge, MA 02138, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Sociology, University of Colorado, Boulder, CO 80309, USA
- Health and Society Program and Population Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309, USA
| | - Alexander S Busch
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, Copenhagen, Denmark
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | | | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Lundström
- Centre for Ethics, Law and Mental Health, University of Gothenburg, Gothenburg, Sweden
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adam Auton
- 23andMe Inc., Mountain View, CA 94041, USA
| | - Kathleen Mullan Harris
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Sociology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, 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
| | - Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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5
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Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AM. Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest 2020; 130:6189. [PMID: 33136096 DOI: 10.1172/jci143863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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6
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Ganna A, Verweij KJH, Nivard MG, Maier R, Wedow R, Busch AS, Abdellaoui A, Guo S, Sathirapongsasuti JF, Lichtenstein P, Lundström S, Långström N, Auton A, Harris KM, Beecham GW, Martin ER, Sanders AR, Perry JRB, Neale BM, Zietsch BP. Genome studies must account for history-Response. Science 2019; 366:1461-1462. [PMID: 31857477 DOI: 10.1126/science.aaz8941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Ganna
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, VU University, 1081 BT, Amsterdam, Netherlands
| | - Robert Maier
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Sociology, Harvard University, Cambridge, MA 02138, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Sociology, University of Colorado, Boulder, CO 80309-0483, USA.,Health and Society Program and Population Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309-0483, USA.,Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0483, USA
| | - Alexander S Busch
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK.,Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, Copenhagen, Denmark
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, Netherlands
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | | | | | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Lundström
- Centre for Ethics, Law, and Mental Health, University of Gothenburg, Gothenburg, Sweden
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Kathleen Mullan Harris
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.,Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL 60201, USA.,Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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7
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Ganna A, Verweij KJH, Nivard MG, Maier R, Wedow R, Busch AS, Abdellaoui A, Guo S, Sathirapongsasuti JF, Lichtenstein P, Lundström S, Långström N, Auton A, Harris KM, Beecham GW, Martin ER, Sanders AR, Perry JRB, Neale BM, Zietsch BP. Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior. Science 2019; 365:eaat7693. [PMID: 31467194 PMCID: PMC7082777 DOI: 10.1126/science.aat7693] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [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: 09/10/2018] [Accepted: 07/22/2019] [Indexed: 12/11/2022]
Abstract
Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual's sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.
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Affiliation(s)
- Andrea Ganna
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 5, 1105 AZ Amsterdam, Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT, Amsterdam, Netherlands
| | - Robert Maier
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Sociology, Harvard University, Cambridge, MA 02138, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Sociology, University of Colorado, Boulder, CO 80309-0483, USA
- Health and Society Program and Population Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309-0483, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0483, USA
| | - Alexander S Busch
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, Copenhagen, Denmark
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 5, 1105 AZ Amsterdam, Netherlands
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | | | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Lundström
- Centre for Ethics, Law and Mental Health, Gillberg Neuropsychiatry Centre, University of Gothenburg, Sweden
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Kathleen Mullan Harris
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - John R B Perry
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, St. Lucia, Brisbane QLD 4072, Australia.
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8
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Dudding T, Haworth S, Lind PA, Sathirapongsasuti JF, Tung JY, Mitchell R, Colodro-Conde L, Medland SE, Gordon S, Elsworth B, Paternoster L, Franks PW, Thomas SJ, Martin NG, Timpson NJ. Genome wide analysis for mouth ulcers identifies associations at immune regulatory loci. Nat Commun 2019; 10:1052. [PMID: 30837455 PMCID: PMC6400940 DOI: 10.1038/s41467-019-08923-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 10/12/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
Mouth ulcers are the most common ulcerative condition and encompass several clinical diagnoses, including recurrent aphthous stomatitis (RAS). Despite previous evidence for heritability, it is not clear which specific genetic loci are implicated in RAS. In this genome-wide association study (n = 461,106) heritability is estimated at 8.2% (95% CI: 6.4%, 9.9%). This study finds 97 variants which alter the odds of developing non-specific mouth ulcers and replicate these in an independent cohort (n = 355,744) (lead variant after meta-analysis: rs76830965, near IL12A, OR 0.72 (95% CI: 0.71, 0.73); P = 4.4e−483). Additional effect estimates from three independent cohorts with more specific phenotyping and specific study characteristics support many of these findings. In silico functional analyses provide evidence for a role of T cell regulation in the aetiology of mouth ulcers. These results provide novel insight into the pathogenesis of a common, important condition. Oral ulcerations are sores of the mucous membrane of the mouth and highly prevalent in the population. Here, in a genome-wide association study, the authors identify 97 loci associated with mouth ulcers highlighting genes involved in T cell-mediated immunity and TH1 responses.
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Affiliation(s)
- Tom Dudding
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.,Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Simon Haworth
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.,Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Penelope A Lind
- Department of Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Queensland, Australia
| | | | | | - Joyce Y Tung
- Research, 23andMe, Inc, Mountain View, 94041, CA, USA
| | - Ruth Mitchell
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Lucía Colodro-Conde
- Department of Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Queensland, Australia
| | - Sarah E Medland
- Department of Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Queensland, Australia
| | - Scott Gordon
- Department of Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Queensland, Australia
| | - Benjamin Elsworth
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, 221 00, Sweden.,Department of Public Health & Clinical Medicine, Umeå University, Umeå, 901 87, Sweden.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, 02115, MA, USA
| | - Steven J Thomas
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Nicholas G Martin
- Department of Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Queensland, Australia
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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9
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Fejzo MS, Sazonova OV, Sathirapongsasuti JF, Hallgrímsdóttir IB, Vacic V, MacGibbon KW, Schoenberg FP, Mancuso N, Slamon DJ, Mullin PM. Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum. Nat Commun 2018; 9:1178. [PMID: 29563502 PMCID: PMC5862842 DOI: 10.1038/s41467-018-03258-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 12/20/2016] [Accepted: 01/30/2018] [Indexed: 01/01/2023] Open
Abstract
Hyperemesis gravidarum (HG), severe nausea and vomiting of pregnancy, occurs in 0.3-2% of pregnancies and is associated with maternal and fetal morbidity. The cause of HG remains unknown, but familial aggregation and results of twin studies suggest that understanding the genetic contribution is essential for comprehending the disease etiology. Here, we conduct a genome-wide association study (GWAS) for binary (HG) and ordinal (severity of nausea and vomiting) phenotypes of pregnancy complications. Two loci, chr19p13.11 and chr4q12, are genome-wide significant (p < 5 × 10-8) in both association scans and are replicated in an independent cohort. The genes implicated at these two loci are GDF15 and IGFBP7 respectively, both known to be involved in placentation, appetite, and cachexia. While proving the casual roles of GDF15 and IGFBP7 in nausea and vomiting of pregnancy requires further study, this GWAS provides insights into the genetic risk factors contributing to the disease.
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Affiliation(s)
- Marlena S Fejzo
- Division of Hematology-Oncology, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Maternal-Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | | | | | | | | | | | - Frederic P Schoenberg
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Dennis J Slamon
- Division of Hematology-Oncology, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Patrick M Mullin
- Department of Maternal-Fetal Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
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10
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Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LPC, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TFJ, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JGJ, Ikram MA, Uitterlinden AG, van Duijn CM, Daly MJ, MacArthur DG. Quantifying prion disease penetrance using large population control cohorts. Sci Transl Med 2016; 8:322ra9. [PMID: 26791950 DOI: 10.1126/scitranslmed.aad5169] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.
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Affiliation(s)
- Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA.
| | - Sonia M Vallabh
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karol Estrada
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Cory Y McLean
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Joyce Y Tung
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Linda P C Yu
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Pierluigi Gambetti
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Janis Blevins
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Shulin Zhang
- University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Yvonne Cohen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Wei Chen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Tsuyoshi Hamaguchi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Nobuo Sanjo
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hidehiro Mizusawa
- National Center Hospital, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Yosikazu Nakamura
- Department of Public Health, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Steven J Collins
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Boyd
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert G Will
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard Knight
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Claudia Ponto
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Inga Zerr
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Sabina Eigenbrod
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Miguel Calero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Jesús de Pedro-Cuesta
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Stéphane Haïk
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Jean-Louis Laplanche
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Elodie Bouaziz-Amar
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Jean-Philippe Brandel
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Sabina Capellari
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Piero Parchi
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Anna Poleggi
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anna Ladogana
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jamie L Marshall
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio 70210, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Anna Kähler
- Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA. Karolinska Institutet, Stockholm SE-171 77, Sweden
| | | | - Shaun M Purcell
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Annemieke Rozemuller
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Casper Jansen
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | | | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands. Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | | | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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Sathirapongsasuti JF. Pushing the boundaries of somatic copy-number variation detection: advances and challenges. Ann Oncol 2015; 26:11-12. [PMID: 25403588 DOI: 10.1093/annonc/mdu536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023] Open
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Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AMK. Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest 2013; 123:5212-30. [PMID: 24200693 DOI: 10.1172/jci69636] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 08/30/2013] [Indexed: 01/05/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) involves aberrant airway inflammatory responses to cigarette smoke (CS) that are associated with epithelial cell dysfunction, cilia shortening, and mucociliary clearance disruption. Exposure to CS reduced cilia length and induced autophagy in vivo and in differentiated mouse tracheal epithelial cells (MTECs). Autophagy-impaired (Becn1+/- or Map1lc3B-/-) mice and MTECs resisted CS-induced cilia shortening. Furthermore, CS increased the autophagic turnover of ciliary proteins, indicating that autophagy may regulate cilia homeostasis. We identified cytosolic deacetylase HDAC6 as a critical regulator of autophagy-mediated cilia shortening during CS exposure. Mice bearing an X chromosome deletion of Hdac6 (Hdac6-/Y) and MTECs from these mice had reduced autophagy and were protected from CS-induced cilia shortening. Autophagy-impaired Becn1-/-, Map1lc3B-/-, and Hdac6-/Y mice or mice injected with an HDAC6 inhibitor were protected from CS-induced mucociliary clearance (MCC) disruption. MCC was preserved in mice given the chemical chaperone 4-phenylbutyric acid, but was disrupted in mice lacking the transcription factor NRF2, suggesting that oxidative stress and altered proteostasis contribute to the disruption of MCC. Analysis of human COPD specimens revealed epigenetic deregulation of HDAC6 by hypomethylation and increased protein expression in the airways. We conclude that an autophagy-dependent pathway regulates cilia length during CS exposure and has potential as a therapeutic target for COPD.
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Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 2012; 8:e1002606. [PMID: 22807668 PMCID: PMC3395616 DOI: 10.1371/journal.pcbi.1002606] [Citation(s) in RCA: 914] [Impact Index Per Article: 76.2] [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: 01/30/2012] [Accepted: 05/21/2012] [Indexed: 02/07/2023] Open
Abstract
The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome. The human body is a complex ecosystem where microbes compete, and cooperate. These interactions can support health or promote disease, e.g. in dental plaque formation. The Human Microbiome Project collected and sequenced ca. 5,000 samples from 18 different body sites, including the airways, gut, skin, oral cavity and vagina. These data allowed the first assessment of significant patterns of co-presence and exclusion among human-associated bacteria. We combined sparse regression with an ensemble of similarity measures to predict microbial relationships within and between body sites. This captured known relationships in the dental plaque, vagina, and gut, and also predicted novel interactions involving members of under-characterized phyla such as TM7. We detected relationships necessary for plaque formation and differences in community composition among dominant members of the gut and vaginal microbiomes. Most relationships were strongly niche-specific, with only a few hub microorganisms forming links across multiple body areas. We also found that phylogenetic distance had a strong impact on the interaction type: closely related microorganisms co-occurred within the same niche, whereas most exclusive relationships occurred between more distantly related microorganisms. This establishes both the specific organisms and general principles by which microbial communities associated with healthy humans are assembled and maintained.
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Affiliation(s)
- Karoline Faust
- Department of Structural Biology, VIB, Brussels, Belgium
- Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - J. Fah Sathirapongsasuti
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Jacques Izard
- Department of Molecular Genetics, Forsyth Institute, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Nicola Segata
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Dirk Gevers
- Microbial Systems and Communities, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeroen Raes
- Department of Structural Biology, VIB, Brussels, Belgium
- Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- * E-mail: (JR); (CH)
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Microbial Systems and Communities, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (JR); (CH)
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Sathirapongsasuti JF, Sathira N, Suzuki Y, Huttenhower C, Sugano S. Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing. Nucleic Acids Res 2010; 39:1967-79. [PMID: 21062826 PMCID: PMC3064809 DOI: 10.1093/nar/gkq949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [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] [Indexed: 11/13/2022] Open
Abstract
Ultraconservation, defined as perfect human-to-rodent sequence identity at least 200-bp long, is a strong indicator of evolutionary and functional importance and has been explored extensively at the genome level. However, it has not been investigated at the transcript level, where such extreme conservation might highlight loci with important post-transcriptional regulatory roles. We present 96 ultraconserved cDNA segments (UCSs), stretches of human mature mRNAs that match identically with orthologous regions in the mouse and rat genomes. UCSs can span multiple exons, a feature we leverage here to elucidate the role of ultraconservation in post-transcriptional regulation. UCS sites are implicated in functions at essentially every post-transcriptional stage: pre-mRNA splicing and degradation through alternative splicing and nonsense-mediated decay (AS-NMD), mature mRNA silencing by miRNA, fast mRNA decay rate and translational repression by upstream AUGs. We also found UCSs to exhibit resistance to formation of RNA secondary structure. These multiple layers of regulation underscore the importance of the UCS-containing genes as key global RNA processing regulators, including members of the serine/arginine-rich protein and heterogeneous nuclear ribonucleoprotein (hnRNP) families of essential splicing regulators. The discovery of UCSs shed new light on the multifaceted, fine-tuned and tight post-transcriptional regulation of gene families as conserved through the majority of the mammalian lineage.
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Affiliation(s)
- J Fah Sathirapongsasuti
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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