2
|
Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J, Barnes KC. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun 2016; 7:12522. [PMID: 27725671 PMCID: PMC5062574 DOI: 10.1038/ncomms12522] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/12/2016] [Indexed: 01/20/2023] Open
Abstract
The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.
Collapse
Affiliation(s)
- Rasika Ann Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wenqing Fu
- Department of Genomic Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shaila Musharoff
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Candelaria Vergara
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Dara G. Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Suyash S. Shringarpure
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lili Huang
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Nicholas Rafaels
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | | | - Henry Richard Johnston
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
| | - Victor E. Ortega
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Wei Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Raul Torres
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94158, USA
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Delmy-Aracely Mejia-Mejia
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
- Faculty of Medicine, Centro Medico de la Familia, San Pedro Sula 21102, Honduras
| | - Trevor Ferguson
- Tropical Medicine Research Institute, The University of the West Indies, St. Michael BB11115, Barbados
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
| | - Alan F. Scott
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden 2333ZA, The Netherlands
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
| | - Javier Marrugo
- Instituto de Investigaciones Immunologicas, Universidad de Cartagena, Cartagena 130000, Colombia
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Rajesh Kumar
- Department of Pediatrics, Northwestern University, Chicago, Illinois 60637, USA
- The Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60637, USA
| | - Pedro C. Avila
- Department of Medicine, Northwestern University, Chicago, Illinois 60637, USA
| | - L. Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados
- Queen Elizabeth Hospital, The University of the West Indies, St. Michael BB11115, Barbados
| | - Lorraine B. Ware
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Christopher Olopade
- Department of Medicine and Center for Global Health, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Ricardo Oliveira
- Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz, Salvador 40296-710, Brazil
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Dan L. Nicolae
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Department of Statistics, University of Chicago, Chicago, Illinois 60637, USA
| | - Deborah Meyers
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Alvaro Mayorga
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
| | - Jennifer Knight-Madden
- Tropical Medicine Research Institute, The University of the West Indies, St. Michael BB11115, Barbados
| | - Tina Hartert
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Nadia N. Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Marilyn G. Foreman
- Pulmonary and Critical Care Medicine, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Jean G. Ford
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
- Department of Medicine, The Brooklyn Hospital Center, Brooklyn, New York 11201, USA
| | - Mezbah U. Faruque
- National Human Genome Center, Howard University College of Medicine, Washington DC 20059, USA
| | - Georgia M. Dunston
- National Human Genome Center, Howard University College of Medicine, Washington DC 20059, USA
- Department of Microbiology, Howard University College of Medicine, Washington DC 20059, USA
| | - Luis Caraballo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena 130000, Colombia
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Eugene Bleecker
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Maria Ilma Araujo
- Immunology Service, Universidade Federal da Bahia, Salvador 401110170, Brazil
| | - Edwin Francisco Herrera-Paz
- Centro de Neumologia y Alergias, San Pedro Sula 21102, Honduras
- Faculty of Medicine, Centro Medico de la Familia, San Pedro Sula 21102, Honduras
- Facultad de Medicina, Universidad Catolica de Honduras, San Pedro Sula 21102, Honduras
| | | | | | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eimear E. Kenny
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, California 94143, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| | - Joshua Akey
- Department of Genomic Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kathleen C. Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, Maryland 21205, USA
| |
Collapse
|