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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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2
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Caro-Consuegra R, Nieves-Colón MA, Rawls E, Rubin-de-Celis V, Lizárraga B, Vidaurre T, Sandoval K, Fejerman L, Stone AC, Moreno-Estrada A, Bosch E. Uncovering signals of positive selection in Peruvian populations from three ecological regions. Mol Biol Evol 2022; 39:6647595. [PMID: 35860855 PMCID: PMC9356722 DOI: 10.1093/molbev/msac158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/12/2022] Open
Abstract
Perú hosts extremely diverse ecosystems which can be broadly classified into three major ecoregions: the Pacific desert coast, the Andean highlands, and the Amazon rainforest. Since its initial peopling approximately 12,000 years ago, the populations inhabiting such ecoregions might have differentially adapted to their contrasting environmental pressures. Previous studies have described several candidate genes underlying adaptation to hypobaric hypoxia among Andean highlanders. However, the adaptive genetic diversity of coastal and rainforest populations has been less studied. Here, we gathered genome-wide SNP-array data from 286 Peruvians living across the three ecoregions and analysed signals of recent positive selection through population differentiation and haplotype-based selection scans. Among highland populations, we identify candidate genes related to cardiovascular function (TLL1, DUSP27, TBX5, PLXNA4, SGCD), to the Hypoxia-Inducible Factor pathway (TGFA, APIP), to skin pigmentation (MITF), as well as to glucose (GLIS3) and glycogen metabolism (PPP1R3C, GANC). In contrast, most signatures of adaptation in coastal and rainforest populations comprise candidate genes related to the immune system (including SIGLEC8, TRIM21, CD44 and ICAM1 in the coast; CBLB and PRDM1 in rainforest and the BRD2- HLA-DOA- HLA-DPA1 region in both), possibly as a result of strong pathogen-driven selection. This study identifies candidate genes related to human adaptation to the diverse environments of South America.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Verónica Rubin-de-Celis
- Laboratorio de Genómica Molecular Evolutiva, Instituto de Ciencia y Tecnología, Universidad Ricardo Palma, Lima, Perú
| | - Beatriz Lizárraga
- Emeritus Professor, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Elena Bosch
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
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3
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Bastard P, Hsiao KC, Zhang Q, Choin J, Best E, Chen J, Gervais A, Bizien L, Materna M, Harmant C, Roux M, Hawley NL, Weeks DE, McGarvey ST, Sandoval K, Barberena-Jonas C, Quinto-Cortés CD, Hagelberg E, Mentzer AJ, Robson K, Coulibaly B, Seeleuthner Y, Bigio B, Li Z, Uzé G, Pellegrini S, Lorenzo L, Sbihi Z, Latour S, Besnard M, Adam de Beaumais T, Jacqz Aigrain E, Béziat V, Deka R, Esera Tulifau L, Viali S, Reupena MS, Naseri T, McNaughton P, Sarkozy V, Peake J, Blincoe A, Primhak S, Stables S, Gibson K, Woon ST, Drake KM, Hill AV, Chan CY, King R, Ameratunga R, Teiti I, Aubry M, Cao-Lormeau VM, Tangye SG, Zhang SY, Jouanguy E, Gray P, Abel L, Moreno-Estrada A, Minster RL, Quintana-Murci L, Wood AC, Casanova JL. A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes. J Exp Med 2022; 219:213170. [PMID: 35442418 PMCID: PMC9026234 DOI: 10.1084/jem.20220028] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
Globally, autosomal recessive IFNAR1 deficiency is a rare inborn error of immunity underlying susceptibility to live attenuated vaccine and wild-type viruses. We report seven children from five unrelated kindreds of western Polynesian ancestry who suffered from severe viral diseases. All the patients are homozygous for the same nonsense IFNAR1 variant (p.Glu386*). This allele encodes a truncated protein that is absent from the cell surface and is loss-of-function. The fibroblasts of the patients do not respond to type I IFNs (IFN-α2, IFN-ω, or IFN-β). Remarkably, this IFNAR1 variant has a minor allele frequency >1% in Samoa and is also observed in the Cook, Society, Marquesas, and Austral islands, as well as Fiji, whereas it is extremely rare or absent in the other populations tested, including those of the Pacific region. Inherited IFNAR1 deficiency should be considered in individuals of Polynesian ancestry with severe viral illnesses.
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Affiliation(s)
- Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Kuang-Chih Hsiao
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Murdoch Children’s Research Institute, Melbourne, Australia
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Jeremy Choin
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Chair of Human Genomics and Evolution, Collège de France, Paris, France
- Paris Cité University, Paris, France
| | - Emma Best
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Christine Harmant
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Maguelonne Roux
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nicola L. Hawley
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, CT
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
| | - Daniel E. Weeks
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Stephen T. McGarvey
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
- Department of Anthropology, Brown University, Providence, RI
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Boubacar Coulibaly
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Zhi Li
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1224, Paris, France
| | - Gilles Uzé
- Institute for Regenerative Medicine and Biotherapy, Université Montpellier, INSERM, CNRS, Montpellier, France
| | - Sandra Pellegrini
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1224, Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Zineb Sbihi
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sylvain Latour
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Marianne Besnard
- Department of Neonatology, Centre Hospitalier de Polynésie Française, Papeete, French Polynesia
| | - Tiphaine Adam de Beaumais
- Precision Cancer Medicine Team, Institut Gustave Roussy, Villejuif, France
- Pharmacology - Pharmacogenetic Department, Hopital Saint-Louis, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Evelyne Jacqz Aigrain
- Paris Cité University, Paris, France
- Pharmacology - Pharmacogenetic Department, Hopital Saint-Louis, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH
| | | | | | | | - Take Naseri
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
- Ministry of Health, Apia, Samoa
| | - Peter McNaughton
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Queensland Children’s Hospital and University of Queensland, Brisbane, Queensland, Australia
| | - Vanessa Sarkozy
- Tumbatin Developmental Services, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Jane Peake
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Queensland Children’s Hospital and University of Queensland, Brisbane, Queensland, Australia
| | - Annaliesse Blincoe
- Starship Child Health, Auckland, New Zealand
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
| | - Sarah Primhak
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Simon Stables
- Department of Forensic Pathology, Auckland City Hospital, Auckland, New Zealand
| | - Kate Gibson
- Clinical Geneticist, South Island Hub, Genetic Health Service, Christchurch, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Kylie Marie Drake
- Molecular Pathology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Adrian V.S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cheng-Yee Chan
- Chemical Pathology and Genetics, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Richard King
- Chemical Pathology and Genetics, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Rohan Ameratunga
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
- Department of Clinical Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Iotefa Teiti
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Maite Aubry
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Van-Mai Cao-Lormeau
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Stuart G. Tangye
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent’s Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Paul Gray
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan L. Minster
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Lluis Quintana-Murci
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Chair of Human Genomics and Evolution, Collège de France, Paris, France
| | - Andrew C. Wood
- Starship Child Health, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique – Hôpitaux de Paris, Paris, France
- Howard Hughes Medical Institute, New York, NY
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4
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Nieves-Colón MA, Badillo Rivera KM, Sandoval K, Villanueva Dávalos V, Enriquez Lencinas LE, Mendoza-Revilla J, Adhikari K, González-Buenfil R, Chen JW, Zhang ET, Sockell A, Ortiz-Tello P, Hurtado GM, Condori Salas R, Cebrecos R, Manzaneda Choque JC, Manzaneda Choque FP, Yábar Pilco GP, Rawls E, Eng C, Huntsman S, Burchard E, Ruiz-Linares A, González-José R, Bedoya G, Rothhammer F, Bortolini MC, Poletti G, Gallo C, Bustamante CD, Baker JC, Gignoux CR, Wojcik GL, Moreno-Estrada A. Clotting factor genes are associated with preeclampsia in high-altitude pregnant women in the Peruvian Andes. Am J Hum Genet 2022; 109:1117-1139. [PMID: 35588731 PMCID: PMC9247825 DOI: 10.1016/j.ajhg.2022.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 06/26/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Preeclampsia is a multi-organ complication of pregnancy characterized by sudden hypertension and proteinuria that is among the leading causes of preterm delivery and maternal morbidity and mortality worldwide. The heterogeneity of preeclampsia poses a challenge for understanding its etiology and molecular basis. Intriguingly, risk for the condition increases in high-altitude regions such as the Peruvian Andes. To investigate the genetic basis of preeclampsia in a population living at high altitude, we characterized genome-wide variation in a cohort of preeclamptic and healthy Andean families (n = 883) from Puno, Peru, a city located above 3,800 meters of altitude. Our study collected genomic DNA and medical records from case-control trios and duos in local hospital settings. We generated genotype data for 439,314 SNPs, determined global ancestry patterns, and mapped associations between genetic variants and preeclampsia phenotypes. A transmission disequilibrium test (TDT) revealed variants near genes of biological importance for placental and blood vessel function. The top candidate region was found on chromosome 13 of the fetal genome and contains clotting factor genes PROZ, F7, and F10. These findings provide supporting evidence that common genetic variants within coagulation genes play an important role in preeclampsia. A selection scan revealed a potential adaptive signal around the ADAM12 locus on chromosome 10, implicated in pregnancy disorders. Our discovery of an association in a functional pathway relevant to pregnancy physiology in an understudied population of Native American origin demonstrates the increased power of family-based study design and underscores the importance of conducting genetic research in diverse populations.
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Affiliation(s)
- Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA; Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | | | | | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK
| | - Ram González-Buenfil
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | - Jessica W Chen
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Elisa T Zhang
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Gloria Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ramiro Condori Salas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ricardo Cebrecos
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | | | | | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Celeste Eng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Scott Huntsman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Esteban Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK; Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico-CONICET y Programa Nacional de Referencia y Biobanco Genómico de la Población Argentina (PoblAr), Ministerio de Ciencia, Tecnología e Innovación, Puerto Madryn, Chubut, Argentina
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquía, Medellin, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación Universidad de Tarapacá, Tarapacá, Chile; Programa de Genética Humana, ICBM Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carlos D Bustamante
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Genevieve L Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México.
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5
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Keolu Fox
- Department of Anthropology, University of California San Diego, La Jolla, CA, USA
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abdul Salam M Sofro
- Department of Biochemistry, Faculty of Medicine, Yayasan Rumah Sakit Islam (YARSI) University, Cempaka Putih, Jakarta, Indonesia
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Translational Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
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6
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Ávila-Arcos MC, McManus KF, Sandoval K, Rodríguez-Rodríguez JE, Villa-Islas V, Martin AR, Luisi P, Peñaloza-Espinosa RI, Eng C, Huntsman S, Burchard EG, Gignoux CR, Bustamante CD, Moreno-Estrada A. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes. Mol Biol Evol 2021; 37:994-1006. [PMID: 31848607 PMCID: PMC7086176 DOI: 10.1093/molbev/msz282] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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] [Indexed: 12/27/2022] Open
Abstract
Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Kimberly F McManus
- Department of Biology, Stanford University, Stanford, CA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | | | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Pierre Luisi
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina.,Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosenda I Peñaloza-Espinosa
- Division of Biological and Health Sciences, Department of Biological Systems, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Celeste Eng
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Esteban G Burchard
- Department Bioengineering & Therapeutic Sciences and Medicine, University of California San Francisco, San Francisco, CA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), UGA, CINVESTAV, Irapuato, Guanajuato 36821, Mexico
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7
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Bravo-Lopez M, Villa-Islas V, Rocha Arriaga C, Villaseñor-Altamirano AB, Guzmán-Solís A, Sandoval-Velasco M, Wesp JK, Alcantara K, López-Corral A, Gómez-Valdés J, Mejía E, Herrera A, Meraz-Moreno A, Moreno-Cabrera MDLL, Moreno-Estrada A, Nieves-Colón MA, Olvera J, Pérez-Pérez J, Iversen KH, Rasmussen S, Sandoval K, Zepeda G, Ávila-Arcos MC. Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190580. [PMID: 33012233 PMCID: PMC7702795 DOI: 10.1098/rstb.2019.0580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Carolina Rocha Arriaga
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Ana B. Villaseñor-Altamirano
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Axel Guzmán-Solís
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Julie K. Wesp
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC 27695, USA
| | - Keitlyn Alcantara
- Department of Anthropology, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Aurelio López-Corral
- Department of Archeology, National Institute of Anthropology and History, Tlaxcala, 90000, Mexico
| | | | - Elizabeth Mejía
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | - Alberto Herrera
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Maria A. Nieves-Colón
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Joel Olvera
- Graduate Program of Physical Anthropology, National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Julia Pérez-Pérez
- National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Katrine Højholt Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Gabriela Zepeda
- National Institute of Anthropology and History, Guanajuato, 36250, Mexico
| | - María C. Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
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8
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Verdugo RA, Di Genova A, Herrera L, Moraga M, Acuña M, Berríos S, Llop E, Valenzuela CY, Bustamante ML, Digman D, Symon A, Asenjo S, López P, Blanco A, Suazo J, Barozet E, Caba F, Villalón M, Alvarado S, Cáceres D, Salgado K, Portales P, Moreno-Estrada A, Gignoux CR, Sandoval K, Bustamante CD, Eng C, Huntsman S, Burchard EG, Loira N, Maass A, Cifuentes L. Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components. Biol Res 2020; 53:15. [PMID: 32299502 PMCID: PMC7161194 DOI: 10.1186/s40659-020-00284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 12/26/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Background Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. Results A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country’s average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. Conclusions We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.
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Affiliation(s)
- Ricardo A Verdugo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alex Di Genova
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Mónica Acuña
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Berríos
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Elena Llop
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Carlos Y Valenzuela
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - M Leonor Bustamante
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.,Departamento de Psiquiatría, y Salud Mental Norte, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Dayhana Digman
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Adriana Symon
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Soledad Asenjo
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Pamela López
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alejandro Blanco
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - José Suazo
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Emmanuelle Barozet
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Chile, Centro de Estudios de Conflicto y Cohesión, Social, Santiago, Chile
| | - Fresia Caba
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Marcelo Villalón
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Sergio Alvarado
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Dante Cáceres
- Instituto de Salud Poblacional "Escuela de Salud Pública", Universidad de Chile, Santiago, Chile
| | - Katherine Salgado
- Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Pilar Portales
- Corporación Municipal de Desarrollo Social, Iquique, Chile
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, 36821, Mexico
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Nicolás Loira
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Alejandro Maass
- Mathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile.,Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Lucía Cifuentes
- Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.
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9
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Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, Highland HM, Patel YM, Sorokin EP, Avery CL, Belbin GM, Bien SA, Cheng I, Cullina S, Hodonsky CJ, Hu Y, Huckins LM, Jeff J, Justice AE, Kocarnik JM, Lim U, Lin BM, Lu Y, Nelson SC, Park SSL, Poisner H, Preuss MH, Richard MA, Schurmann C, Setiawan VW, Sockell A, Vahi K, Verbanck M, Vishnu A, Walker RW, Young KL, Zubair N, Acuña-Alonso V, Ambite JL, Barnes KC, Boerwinkle E, Bottinger EP, Bustamante CD, Caberto C, Canizales-Quinteros S, Conomos MP, Deelman E, Do R, Doheny K, Fernández-Rhodes L, Fornage M, Hailu B, Heiss G, Henn BM, Hindorff LA, Jackson RD, Laurie CA, Laurie CC, Li Y, Lin DY, Moreno-Estrada A, Nadkarni G, Norman PJ, Pooler LC, Reiner AP, Romm J, Sabatti C, Sandoval K, Sheng X, Stahl EA, Stram DO, Thornton TA, Wassel CL, Wilkens LR, Winkler CA, Yoneyama S, Buyske S, Haiman CA, Kooperberg C, Le Marchand L, Loos RJF, Matise TC, North KE, Peters U, Kenny EE, Carlson CS. Genetic analyses of diverse populations improves discovery for complex traits. Nature 2019; 570:514-518. [PMID: 31217584 DOI: 10.1038/s41586-019-1310-4] [Citation(s) in RCA: 518] [Impact Index Per Article: 103.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.
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Affiliation(s)
- Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine K Nishimura
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey Haessler
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher R Gignoux
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.,Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yesha M Patel
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gillian M Belbin
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie A Bien
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sinead Cullina
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yao Hu
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Janina Jeff
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan M Kocarnik
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Bridget M Lin
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yingchang Lu
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sung-Shim L Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hannah Poisner
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael H Preuss
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa A Richard
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Hasso-Plattner-Institute for Digital Engineering, Digital Health Center, Potsdam, Germany.,Hasso-Plattner-Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Veronica W Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Sockell
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karan Vahi
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Marie Verbanck
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abhishek Vishnu
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan W Walker
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Niha Zubair
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Jose Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Hasso-Plattner-Institute for Digital Engineering, Digital Health Center, Potsdam, Germany.,Hasso-Plattner-Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Christian Caberto
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ewa Deelman
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Fernández-Rhodes
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Benyam Hailu
- NIH National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brenna M Henn
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | | | - Rebecca D Jackson
- Center for Clinical and Translational Science, Ohio State Medical Center, Columbus, OH, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Yuqing Li
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Cancer Prevention Institute of California, Fremont, CA, USA
| | - Dan-Yu Lin
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul J Norman
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Loreall C Pooler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jane Romm
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), Irapuato, Mexico
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eli A Stahl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Cheryl A Winkler
- Basic Science Program, Frederick National Laboratory, Frederick, MD, USA
| | - Sachi Yoneyama
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, New Brunswick, NJ, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charles Kooperberg
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ulrike Peters
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eimear E Kenny
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Christopher S Carlson
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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10
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Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol 2019; 143:957-969. [PMID: 30201514 PMCID: PMC6927816 DOI: 10.1016/j.jaci.2016.08.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 10/13/2015] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Asthma is a common but complex disease with racial/ethnic differences in prevalence, morbidity, and response to therapies. OBJECTIVE We sought to perform an analysis of genetic ancestry to identify new loci that contribute to asthma susceptibility. METHODS We leveraged the mixed ancestry of 3902 Latinos and performed an admixture mapping meta-analysis for asthma susceptibility. We replicated associations in an independent study of 3774 Latinos, performed targeted sequencing for fine mapping, and tested for disease correlations with gene expression in the whole blood of more than 500 subjects from 3 racial/ethnic groups. RESULTS We identified a genome-wide significant admixture mapping peak at 18q21 in Latinos (P = 6.8 × 10-6), where Native American ancestry was associated with increased risk of asthma (odds ratio [OR], 1.20; 95% CI, 1.07-1.34; P = .002) and European ancestry was associated with protection (OR, 0.86; 95% CI, 0.77-0.96; P = .008). Our findings were replicated in an independent childhood asthma study in Latinos (P = 5.3 × 10-3, combined P = 2.6 × 10-7). Fine mapping of 18q21 in 1978 Latinos identified a significant association with multiple variants 5' of SMAD family member 2 (SMAD2) in Mexicans, whereas a single rare variant in the same window was the top association in Puerto Ricans. Low versus high SMAD2 blood expression was correlated with case status (13.4% lower expression; OR, 3.93; 95% CI, 2.12-7.28; P < .001). In addition, lower expression of SMAD2 was associated with more frequent exacerbations among Puerto Ricans with asthma. CONCLUSION Ancestry at 18q21 was significantly associated with asthma in Latinos and implicated multiple ancestry-informative noncoding variants upstream of SMAD2 with asthma susceptibility. Furthermore, decreased SMAD2 expression in blood was strongly associated with increased asthma risk and increased exacerbations.
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Affiliation(s)
- Christopher R Gignoux
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif.
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Lawrence H Uricchio
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Joshua Galanter
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Elizabeth A Nguyen
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | | | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Meghan McGarry
- Department of Pediatrics, University of California, San Francisco, San Francisco, Calif
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Molecular Genetics Epidemiology Section, Frederick National Laboratory for Cancer Research, Frederick, Md
| | - Max A Seibold
- Integrated Center for Genes, Environment, and Health, Department of Pediatrics, Division of Pulmonary and Critical Care Medicine, National Jewish Health, Denver, Colo
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - David V Conti
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Pedro Avila
- Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, Lehman College, City University of New York, Bronx, NY
| | | | - Shannon Thyne
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Bonnie R Joubert
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Isabelle Romieu
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Albert M Levin
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - Juan-Jose Sienra-Monge
- Departmento de Alergia e Inmunologia, Clinica Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | | | - Weiniu Gan
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, Bethesda, Md
| | - Benjamin A Raby
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Eugene Bleecker
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | - Deborah A Meyers
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | | | - W James Gauderman
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Frank Gilliland
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | | | - Dan L Nicolae
- Physical Sciences Division, Department of Statistics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tenn
| | - Kathleen Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Ryan D Hernandez
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
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11
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Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin ML, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon JM, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat Commun 2018; 9:5388. [PMID: 30568240 PMCID: PMC6300600 DOI: 10.1038/s41467-018-07748-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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: 02/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.
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Affiliation(s)
- Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Jorge Gómez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Paola Everardo Martínez
- Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia
| | - René Vásquez
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia
| | - Elena Llop
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru
| | | | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Karla Sandoval
- National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico
| | - Rosenda I Peñaloza-Espinosa
- Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Claudio Bravi
- Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Verónica Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Carlos Resende
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Leonor Gusmão
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil
| | - Antonio Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France
| | - Pedro Moral
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France.
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12
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Spear ML, Hu D, Pino-Yanes M, Huntsman S, Eng C, Levin AM, Ortega VE, White MJ, McGarry ME, Thakur N, Galanter J, Mak ACY, Oh SS, Ampleford E, Peters SP, Davis A, Kumar R, Farber HJ, Meade K, Avila PC, Serebrisky D, Lenoir MA, Brigino-Buenaventura E, Cintron WR, Thyne SM, Rodriguez-Santana JR, Ford JG, Chapela R, Estrada AM, Sandoval K, Seibold MA, Winkler CA, Bleecker ER, Myers DA, Williams LK, Hernandez RD, Torgerson DG, Burchard EG. A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma. Pharmacogenomics J 2018; 19:249-259. [PMID: 30206298 PMCID: PMC6414286 DOI: 10.1038/s41397-018-0042-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 06/08/2018] [Accepted: 06/19/2018] [Indexed: 01/15/2023]
Abstract
Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the U.S1, 2. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma3. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1,830 Latinos (Total=2,779). Lastly, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p=7.69×10−9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958, and rs7081864, p≤5×10−8). Our results failed to replicate in three additional populations of 416 Latinos and 1,615 African Americans. Our findings indicate that both population specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups.
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Affiliation(s)
- Melissa L Spear
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Victor E Ortega
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Marquitta J White
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Meghan E McGarry
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Galanter
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elizabeth Ampleford
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Stephen P Peters
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Adam Davis
- UCSF Benioff Children's Hospital Oakland, Center for Community Health and Engagement, Oakland, CA, USA
| | - Rajesh Kumar
- Ann & Robert H. Lurie Children's Hospital of Chicago, Pediatrics, Chicago, IL, USA
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Kelley Meade
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Pedro C Avila
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, NY, USA.,Albert Einstein College of Medicine, Pediatrics, Bronx, NY, USA
| | | | | | | | - Shannon M Thyne
- Department of Pediatrics, David Geffen School of Medicine at ULCA, Olive View-UCLA Medical Center, Sylmar, CA, USA
| | | | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Andrés Moreno Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, USA
| | | | - Deborah A Myers
- Department of Medicine, The University of Arizona, Tucson, AZ, USA
| | - L Keoki Williams
- Center for Health Policy and Health Services Research,, Henry Ford Health System, Detroit, MI, USA.,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. .,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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13
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Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med 2018; 197:1552-1564. [PMID: 29509491 PMCID: PMC6006403 DOI: 10.1164/rccm.201712-2529oc] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [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: 12/15/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
RATIONALE Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. OBJECTIVES To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. METHODS We performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. MEASUREMENTS AND MAIN RESULTS We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P < 3.53 × 10-7) and suggestive (P < 7.06 × 10-6) loci near genes previously associated with lung capacity (DNAH5), immunity (NFKB1 and PLCB1), and β-adrenergic signaling (ADAMTS3 and COX18). Functional analyses of the BDR-associated SNP in NFKB1 revealed potential regulatory function in bronchial smooth muscle cells. The SNP is also an expression quantitative trait locus for a neighboring gene, SLC39A8. The lack of other asthma study populations with BDR and whole-genome sequencing data on minority children makes it impossible to perform replication of our rare variant associations. Minority underrepresentation also poses significant challenges to identify age-matched and population-matched cohorts of sufficient sample size for replication of our common variant findings. CONCLUSIONS The lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. Our study expands the understanding of pharmacogenetic analyses in racially/ethnically diverse populations and advances the foundation for precision medicine in at-risk and understudied minority populations.
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Affiliation(s)
| | | | | | | | | | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N. S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | - Ann Chen Wu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Precision Medicine Translational Research (PRoMoTeR) Center, Department of Population Medicine, Harvard Medical School and Pilgrim Health Care Institute, Boston, Massachusetts
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics and
| | | | | | | | | | | | | | | | | | | | | | - Pui-Yan Kwok
- Cardiovascular Research Institute
- Institute for Human Genetics, and
| | | | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | - Patrick M. Sleiman
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York
| | | | - Harold J. Farber
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas
| | - Kelley Meade
- Children’s Hospital and Research Center, Oakland, California
| | | | - Pedro C. Avila
- Department of Medicine, Northwestern University, Chicago, Illinois
| | | | - Shannon M. Thyne
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | | | - Cheryl A. Winkler
- Basic Science Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Rajesh Kumar
- Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - L. Keoki Williams
- Department of Internal Medicine, and
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics, and
| | | | - Max A. Seibold
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado; and
| | - Robert B. Darnell
- New York Genome Center, New York, New York
- Laboratory of Molecular Neuro-Oncology and
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York
| | | | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences
- Cardiovascular Research Institute
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California
| | - on behalf of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Department of Medicine
- Department of Bioengineering and Therapeutic Sciences
- Department of Pediatrics
- Cardiovascular Research Institute
- Institute for Human Genetics, and
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California
- Research Unit, Hospital Universitario N. S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Precision Medicine Translational Research (PRoMoTeR) Center, Department of Population Medicine, Harvard Medical School and Pilgrim Health Care Institute, Boston, Massachusetts
- Department of Biostatistics, Epidemiology and Informatics and
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- New York Genome Center, New York, New York
- Department of Public Health Sciences
- Department of Internal Medicine, and
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York
- Department of Allergy and Immunology, Kaiser Permanente Vallejo Medical Center, Vallejo, California
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas
- Children’s Hospital and Research Center, Oakland, California
- Bay Area Pediatrics, Oakland, California
- Department of Medicine, Northwestern University, Chicago, Illinois
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Veterans Caribbean Health Care System, San Juan, Puerto Rico
- Basic Science Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Centro de Neumologia Pediatrica, San Juan, Puerto Rico
- Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado; and
- Laboratory of Molecular Neuro-Oncology and
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York
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14
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Sharma A, Contreras E, Sandoval K, Nicholson L, Waalen J, Bhangoo M. 223P Sarcomatoid lung carcinoma: An uncommon and deadly entity. J Thorac Oncol 2018. [DOI: 10.1016/s1556-0864(18)30495-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O'Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol 2014; 135:1502-10. [PMID: 25488688 DOI: 10.1016/j.jaci.2014.10.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/06/2014] [Accepted: 10/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND IgE is a key mediator of allergic inflammation, and its levels are frequently increased in patients with allergic disorders. OBJECTIVE We sought to identify genetic variants associated with IgE levels in Latinos. METHODS We performed a genome-wide association study and admixture mapping of total IgE levels in 3334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1564 European Americans, and 3187 African Americans from independent studies. RESULTS We confirmed associations of 6 genes identified by means of previous genome-wide association studies and identified a novel genome-wide significant association of a polymorphism in the zinc finger protein 365 gene (ZNF365) with total IgE levels (rs200076616, P = 2.3 × 10(-8)). We next identified 4 admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) at which local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower IgE levels (P = 4.95 × 10(-8)). All but 22q13.1 were replicated in an independent sample of Latinos, and 2 of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified 6 genome-wide significant single nucleotide polymorphisms in Latinos, 2 of which replicated in European Americans. Another single nucleotide polymorphism was peak-wide significant within 14q23.2 in African Americans (rs1741099, P = 3.7 × 10(-6)) and replicated in non-African American samples (P = .011). CONCLUSION We confirmed genetic associations at 6 genes and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse multiethnic populations to uncover novel loci associated with total IgE levels.
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Affiliation(s)
- Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Christopher R Gignoux
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif; Department of Genetics, Stanford University, Palo Alto, Calif
| | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Mich
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Wash
| | - Brian J O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Wash; Molecular & Medical Genetics Department, Oregon Health and Science University, Portland, Ore
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Rasika A Mathias
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Md
| | | | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Ill
| | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California San Francisco, San Francisco General Hospital, San Francisco, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, City University of New York, Bronx, NY
| | | | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, Calif
| | - Rajesh Kumar
- Children's Memorial Hospital and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Fernando D Martinez
- Arizona Respiratory Center, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Deborah A Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, Calif
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Wash; Howard Hughes Medical Institute, Seattle, Wash
| | - Kathleen C Barnes
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, Calif
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
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16
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Pino-Yanes M, Thakur N, Gignoux CR, Galanter JM, Roth LA, Eng C, Nishimura KK, Oh SS, Vora H, Huntsman S, Nguyen EA, Hu D, Drake KA, Conti DV, Moreno-Estrada A, Sandoval K, Winkler CA, Borrell LN, Lurmann F, Islam TS, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Bibbins-Domingo K, Lenoir MA, Ford JG, Brigino-Buenaventura E, Rodriguez-Cintron W, Thyne SM, Sen S, Rodriguez-Santana JR, Bustamante CD, Williams LK, Gilliland FD, Gauderman WJ, Kumar R, Torgerson DG, Burchard EG. Genetic ancestry influences asthma susceptibility and lung function among Latinos. J Allergy Clin Immunol 2014; 135:228-35. [PMID: 25301036 DOI: 10.1016/j.jaci.2014.07.053] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Childhood asthma prevalence and morbidity varies among Latinos in the United States, with Puerto Ricans having the highest and Mexicans the lowest. OBJECTIVE To determine whether genetic ancestry is associated with the odds of asthma among Latinos, and secondarily whether genetic ancestry is associated with lung function among Latino children. METHODS We analyzed 5493 Latinos with and without asthma from 3 independent studies. For each participant, we estimated the proportion of African, European, and Native American ancestry using genome-wide data. We tested whether genetic ancestry was associated with the presence of asthma and lung function among subjects with and without asthma. Odds ratios (OR) and effect sizes were assessed for every 20% increase in each ancestry. RESULTS Native American ancestry was associated with lower odds of asthma (OR = 0.72, 95% CI: 0.66-0.78, P = 8.0 × 10(-15)), while African ancestry was associated with higher odds of asthma (OR = 1.40, 95% CI: 1.14-1.72, P = .001). These associations were robust to adjustment for covariates related to early life exposures, air pollution, and socioeconomic status. Among children with asthma, African ancestry was associated with lower lung function, including both pre- and post-bronchodilator measures of FEV1 (-77 ± 19 mL; P = 5.8 × 10(-5) and -83 ± 19 mL; P = 1.1 x 10(-5), respectively) and forced vital capacity (-100 ± 21 mL; P = 2.7 × 10(-6) and -107 ± 22 mL; P = 1.0 x 10(-6), respectively). CONCLUSION Differences in the proportions of genetic ancestry can partially explain disparities in asthma susceptibility and lung function among Latinos.
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Affiliation(s)
- Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Neeta Thakur
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | | | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Katherine K Nishimura
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Hita Vora
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Elizabeth A Nguyen
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Katherine A Drake
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, Calif
| | - David V Conti
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Basic Research Laboratory, SAIC-Frederick, Inc, Center for Cancer Research, National Cancer Institute, Frederick, Md
| | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, City University of New York, Bronx, NY
| | | | - Talat S Islam
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Ill
| | | | | | | | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | | | | | - Shannon M Thyne
- Department of Pediatrics, UCSF, San Francisco General Hospital, San Francisco, Calif
| | - Saunak Sen
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, Calif
| | | | | | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Frank D Gilliland
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - W James Gauderman
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Rajesh Kumar
- Children's Memorial Hospital and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, Calif
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17
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Moreno-Estrada A, Gignoux CR, Fernández-López JC, Zakharia F, Sikora M, Contreras AV, Acuña-Alonzo V, Sandoval K, Eng C, Romero-Hidalgo S, Ortiz-Tello P, Robles V, Kenny EE, Nuño-Arana I, Barquera-Lozano R, Macín-Pérez G, Granados-Arriola J, Huntsman S, Galanter JM, Via M, Ford JG, Chapela R, Rodriguez-Cintron W, Rodríguez-Santana JR, Romieu I, Sienra-Monge JJ, del Rio Navarro B, London SJ, Ruiz-Linares A, Garcia-Herrera R, Estrada K, Hidalgo-Miranda A, Jimenez-Sanchez G, Carnevale A, Soberón X, Canizales-Quinteros S, Rangel-Villalobos H, Silva-Zolezzi I, Burchard EG, Bustamante CD. Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 2014; 344:1280-5. [PMID: 24926019 PMCID: PMC4156478 DOI: 10.1126/science.1251688] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [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] [Indexed: 12/18/2022]
Abstract
Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.
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Affiliation(s)
| | - Christopher R Gignoux
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
| | | | - Fouad Zakharia
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Victor Acuña-Alonzo
- Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico. Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Karla Sandoval
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Patricia Ortiz-Tello
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Victoria Robles
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E Kenny
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ismael Nuño-Arana
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, Mexico
| | | | | | - Julio Granados-Arriola
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco, CA, USA. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Marc Via
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Jean G Ford
- The Brooklyn Hospital Center, Brooklyn, NY, USA
| | - Rocío Chapela
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | | | - Jose R Rodríguez-Santana
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | | | | | | | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Karol Estrada
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | | | | | | | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico. Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Esteban Gonzalez Burchard
- Department of Medicine, University of California, San Francisco, CA, USA. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Drake KA, Torgerson DG, Gignoux CR, Galanter JM, Roth LA, Huntsman S, Eng C, Oh SS, Yee SW, Lin L, Bustamante CD, Moreno-Estrada A, Sandoval K, Davis A, Borrell LN, Farber HJ, Kumar R, Avila PC, Brigino-Buenaventura E, Chapela R, Ford JG, Lenoir MA, Lurmann F, Meade K, Serebrisky D, Thyne S, Rodríguez-Cintrón W, Sen S, Rodríguez-Santana JR, Hernandez RD, Giacomini KM, Burchard EG. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. J Allergy Clin Immunol 2014; 133:370-8. [PMID: 23992748 PMCID: PMC3938989 DOI: 10.1016/j.jaci.2013.06.043] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [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: 01/16/2013] [Revised: 05/09/2013] [Accepted: 06/18/2013] [Indexed: 01/29/2023]
Abstract
BACKGROUND The primary rescue medication to treat acute asthma exacerbation is the short-acting β₂-adrenergic receptor agonist; however, there is variation in how well a patient responds to treatment. Although these differences might be due to environmental factors, there is mounting evidence for a genetic contribution to variability in bronchodilator response (BDR). OBJECTIVE To identify genetic variation associated with bronchodilator drug response in Latino children with asthma. METHODS We performed a genome-wide association study (GWAS) for BDR in 1782 Latino children with asthma using standard linear regression, adjusting for genetic ancestry and ethnicity, and performed replication studies in an additional 531 Latinos. We also performed admixture mapping across the genome by testing for an association between local European, African, and Native American ancestry and BDR, adjusting for genomic ancestry and ethnicity. RESULTS We identified 7 genetic variants associated with BDR at a genome-wide significant threshold (P < 5 × 10(-8)), all of which had frequencies of less than 5%. Furthermore, we observed an excess of small P values driven by rare variants (frequency, <5%) and by variants in the proximity of solute carrier (SLC) genes. Admixture mapping identified 5 significant peaks; fine mapping within these peaks identified 2 rare variants in SLC22A15 as being associated with increased BDR in Mexicans. Quantitative PCR and immunohistochemistry identified SLC22A15 as being expressed in the lung and bronchial epithelial cells. CONCLUSION Our results suggest that rare variation contributes to individual differences in response to albuterol in Latinos, notably in SLC genes that include membrane transport proteins involved in the transport of endogenous metabolites and xenobiotics. Resequencing in larger, multiethnic population samples and additional functional studies are required to further understand the role of rare variation in BDR.
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Affiliation(s)
- Katherine A Drake
- Department of Medicine, University of California, San Francisco, Calif
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, Calif.
| | | | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, Calif
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Lawrence Lin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | | | | | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, Calif
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, Lehman College, City University of New York, Bronx, New York
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Rajesh Kumar
- Children's Memorial Hospital, and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | - Pedro C Avila
- Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | | | | | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York
| | - Shannon Thyne
- Department of Pediatrics, University of California, San Francisco, Calif
| | | | - Saunak Sen
- Department of Biostatistics, University of California, San Francisco, Calif
| | | | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
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19
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Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 2013; 9:e1004023. [PMID: 24385924 PMCID: PMC3873240 DOI: 10.1371/journal.pgen.1004023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [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: 05/06/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations. Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.
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Affiliation(s)
- Simon Gravel
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- * E-mail:
| | - Fouad Zakharia
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andres Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jake K. Byrnes
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Ancestry.com DNA LLC, San Francisco, California, United States of America
| | - Marina Muzzio
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE). CCT- CONICET-La Plata, Argentina and Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Eimear E. Kenny
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Center for Statistical Genetics, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Maples
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Wilfried Guiblet
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Marc Via
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | | | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | | | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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20
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Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, Sandoval K, Moreno-Estrada A, Li Y, Wang J, Gilbert MTP, Willerslev E, Greenleaf WJ, Bustamante CD. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 2013; 93:852-64. [PMID: 24568772 DOI: 10.1016/j.ajhg.2013.10.002] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [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: 08/03/2013] [Revised: 09/27/2013] [Accepted: 10/02/2013] [Indexed: 12/01/2022] Open
Abstract
Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.
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Affiliation(s)
- Meredith L Carpenter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cristina Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Department of Archaeology, Environment, and Community Planning, Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark
| | - Martin Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark
| | - Simon Gravel
- Department of Human Genetics and Génome Québec Innovation Centre, McGill University, Montréal, QC H3A 0G1, Canada
| | - Sonia Guillén
- Centro Mallqui, Calle Ugarte y Moscoso 165, San Isidro, Lima 27, Peru
| | - Georgi Nekhrizov
- Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria
| | - Krasimir Leshtakov
- Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria
| | - Diana Dimitrova
- Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria
| | - Nikola Theodossiev
- Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria
| | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Karla Sandoval
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrés Moreno-Estrada
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; Macau University of Science and Technology, Taipa, Macau 999078, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Ancient DNA Laboratory, Murdoch University, South Street, Perth, WA 6150, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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21
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Kumar R, Nguyen EA, Roth LA, Oh SS, Gignoux CR, Huntsman S, Eng C, Moreno-Estrada A, Sandoval K, Peñaloza-Espinosa RI, López-López M, Avila PC, Farber HJ, Tcheurekdjian H, Rodriguez-Cintron W, Rodriguez-Santana JR, Serebrisky D, Thyne SM, Williams LK, Winkler C, Bustamante CD, Pérez-Stable EJ, Borrell LN, Burchard EG. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: the Genes-environments and Admixture in Latino Asthmatics (GALA II) study. J Allergy Clin Immunol 2013; 132:896-905.e1. [PMID: 23684070 DOI: 10.1016/j.jaci.2013.02.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 12/05/2012] [Accepted: 02/07/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Atopy varies by ethnicity, even within Latino groups. This variation might be due to environmental, sociocultural, or genetic factors. OBJECTIVE We sought to examine risk factors for atopy within a nationwide study of US Latino children with and without asthma. METHODS Aeroallergen skin test responses were analyzed in 1830 US Latino subjects. Key determinants of atopy included country/region of origin, generation in the United States, acculturation, genetic ancestry, and site to which subjects migrated. Serial multivariate zero-inflated negative binomial regressions stratified by asthma status examined the association of each key determinant variable with the number of positive skin test responses. In addition, the independent effect of each key variable was determined by including all key variables in the final models. RESULTS In baseline analyses African ancestry was associated with 3 times (95% CI, 1.62-5.57) as many positive skin test responses in asthmatic participants and 3.26 times (95% CI, 1.02-10.39) as many positive skin test responses in control participants. Generation and recruitment site were also associated with atopy in crude models. In final models adjusted for key variables, asthmatic patients of Puerto Rican (exp[β] [95% CI], 1.31 [1.02-1.69]) and mixed (exp[β] [95% CI], 1.27 [1.03-1.56]) ethnicity had a greater probability of positive skin test responses compared with Mexican asthmatic patients. Ancestry associations were abrogated by recruitment site but not region of origin. CONCLUSIONS Puerto Rican ethnicity and mixed origin were associated with degree of atopy within US Latino children with asthma. African ancestry was not associated with degree of atopy after adjusting for recruitment site. Local environment variation, represented by site, was associated with degree of sensitization.
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Affiliation(s)
- Rajesh Kumar
- Division of Allergy and Immunology, Children's Memorial Hospital, and the Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Ill.
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Sandoval K, Moreno-Estrada A, Mendizabal I, Underhill PA, Lopez-Valenzuela M, Peñaloza-Espinosa R, Lopez-Lopez M, Buentello-Malo L, Avelino H, Calafell F, Comas D. Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas. Am J Phys Anthropol 2012; 148:395-405. [PMID: 22576278 DOI: 10.1002/ajpa.22062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 02/29/2012] [Indexed: 12/11/2022]
Abstract
The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.
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Affiliation(s)
- Karla Sandoval
- Institut de Biologia Evolutiva, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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Sandoval K, Buentello-Malo L, Peñaloza-Espinosa R, Avelino H, Salas A, Calafell F, Comas D. Linguistic and maternal genetic diversity are not correlated in Native Mexicans. Hum Genet 2009; 126:521-31. [PMID: 19495796 PMCID: PMC2762527 DOI: 10.1007/s00439-009-0693-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [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] [Received: 02/17/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.
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Affiliation(s)
- Karla Sandoval
- Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, 08003 Barcelona, Catalonia, Spain
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Mendizabal I, Sandoval K, Berniell-Lee G, Calafell F, Salas A, Martínez-Fuentes A, Comas D. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol Biol 2008; 8:213. [PMID: 18644108 PMCID: PMC2492877 DOI: 10.1186/1471-2148-8-213] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/21/2008] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. RESULTS The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. CONCLUSION While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.
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Affiliation(s)
- Isabel Mendizabal
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karla Sandoval
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Berniell-Lee
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, and Grupo de Medicina Xenómica, Hospital Clínico Universitario, Santiago de Compostela, Galicia, Spain
| | - Antonio Martínez-Fuentes
- Departamento de Biología Animal y Humana. Facultad de Biología, Universidad de la Habana, Ciudad de la Habana, Cuba
| | - David Comas
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
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Berniell-Lee G, Sandoval K, Mendizabal I, Bosch E, Comas D. SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening. Electrophoresis 2007; 28:3201-6. [PMID: 17703471 DOI: 10.1002/elps.200700078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.
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Affiliation(s)
- Gemma Berniell-Lee
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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Evers BM, Rady PL, Sandoval K, Arany I, Tyring SK, Sanchez RL, Nealon WH, Townsend CM, Thompson JC. Gastrinomas demonstrate amplification of the HER-2/neu proto-oncogene. Ann Surg 1994; 219:596-601; discussion 602-4. [PMID: 7911296 PMCID: PMC1243202 DOI: 10.1097/00000658-199406000-00002] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE This study determined whether genomic amplification of HER-2/neu or mutations of the p53 and ras genes were present in gastrinomas. SUMMARY BACKGROUND DATA Amplification of HER-2/neu, a proto-oncogene related to the epidermal growth factor receptor, and mutation of the ras proto-oncogene and p53 tumor suppressor gene appear to play a role in the pathogenesis of some human cancers. Little is known about possible molecular alterations in gastrinomas, tumors that may be particularly virulent because of gastrin overproduction, resulting in the severe ulcer diathesis, the Zollinger-Ellison syndrome. METHODS The differential polymerase chain reaction (PCR) procedure was used to detect amplification of the HER-2/neu gene in DNA samples from the novel human gastrinoma cell line (PT) and from paraffin-embedded samples of gastrinomas. Sequencing techniques were used to determine whether mutations of the p53 or ras (Ha-ras, N-ras, Ki-ras) genes were present. RESULTS Amplification (> twofold) occurred in all gastrinoma tumor samples. Compared with normal pancreas or ileum, a 4- to 12-fold amplification of HER-2/neu was found in 3 gastrinomas, 3 to 3.3-fold in four samples and 2.1- to 2.4-fold in the remaining five tumors. A heterozygous point mutation in the p53 gene (codon 273) was found in a single sample; none of the gastrinomas contained a mutation of the ras genes. CONCLUSIONS Amplification of the HER-2/neu gene, but not alterations of either p53 or ras, may be involved in the pathogenesis of gastrinomas. The unique PT cell line will be a useful model to further elucidate the molecular mechanisms that contribute to gastrinoma formation and growth.
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Affiliation(s)
- B M Evers
- Department of Surgery, University of Texas Medical Branch, Galveston
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Riedemann P, Lanas F, Montecinos A, Inostroza J, Rodríguez J, Sandoval K. [Ventricular rate in cardiac insufficiency with atrial fibrillation, an adequate index of digitalization?]. Rev Med Chil 1988; 116:651-4. [PMID: 3256908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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