The genetics of Mexico recapitulates Native American substructure and affects biomedical traits
Andrés Moreno-Estrada,Christopher R. Gignoux,Juan Carlos Fernández-López,Fouad Zakharia,Martin Sikora,Alejandra V. Contreras,Victor Acuña-Alonzo,Karla Sandoval,Celeste Eng,Sandra Romero-Hidalgo,Patricia Ortiz-Tello,Victoria Robles,Eimear E. Kenny,Ismael Nuño-Arana,Rodrigo Barquera-Lozano,Gastón Macín-Pérez,Julio Granados-Arriola,Scott Huntsman,Joshua Galanter,Marc Via,Jean G. Ford,Rocio Chapela,William Rodriguez-Cintron,J.R. Rodriguez-Santana,Isabelle Romieu,Juan José Luis Sienra-Monge,Blanca E. del Rio Navarro,Stephanie J. London,Andres Ruiz-Linares,Rodrigo García-Herrera,Karol Estrada,Alfredo Hidalgo-Miranda,Gerardo Jimenez-Sanchez,Alessandra Carnevale,Xavier Soberón,Samuel Canizales-Quinteros,Héctor Rangel-Villalobos,Irma Silva-Zolezzi,Esteban G. Burchard,Carlos Bustamante +39 more
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TLDR
Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country, and two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function.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.read more
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Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations
Alicia R. Martin,Christopher R. Gignoux,Raymond K. Walters,Genevieve L. Wojcik,Benjamin M. Neale,Benjamin M. Neale,Simon Gravel,Mark J. Daly,Mark J. Daly,Carlos Bustamante,Eimear E. Kenny +10 more
TL;DR: It is demonstrated that scores inferred from European GWASs are biased by genetic drift in other populations even when choosing the same causal variants and that biases in any direction are possible and unpredictable.
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The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States
Katarzyna Bryc,Eric Durand,J. Michael Macpherson,David Reich,David Reich,David Reich,Joanna L. Mountain +6 more
TL;DR: The authors studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and showed that the legacy of these historical interactions is visible in the genetic lineage of present-day Americans.
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Genomic evidence for the Pleistocene and recent population history of Native Americans
Maanasa Raghavan,Matthias Steinrücken,Matthias Steinrücken,Kelley Harris,Stephan Schiffels,Simon Rasmussen,Michael DeGiorgio,Anders Albrechtsen,Cristina Valdiosera,Cristina Valdiosera,María C. Ávila-Arcos,María C. Ávila-Arcos,Anna-Sapfo Malaspinas,Anders Eriksson,Anders Eriksson,Ida Moltke,Mait Metspalu,Mait Metspalu,Julian R. Homburger,Jeffrey D. Wall,Omar E. Cornejo,J. Víctor Moreno-Mayar,Thorfinn Sand Korneliussen,Tracey Pierre,Morten Rasmussen,Morten Rasmussen,Paula F. Campos,Paula F. Campos,Peter de Barros Damgaard,Morten E. Allentoft,John Lindo,Ene Metspalu,Ene Metspalu,Ricardo Rodríguez-Varela,Josefina Mansilla,Celeste Henrickson,Andaine Seguin-Orlando,Helena Malmström,Thomas W. Stafford,Thomas W. Stafford,Suyash Shringarpure,Andrés Moreno-Estrada,Monika Karmin,Monika Karmin,Kristiina Tambets,Anders Bergström,Yali Xue,Vera Warmuth,Andrew D. Friend,Joy S. Singarayer,Paul J. Valdes,Francois Balloux,Ilán Leboreiro,Jose Luis Vera,Héctor Rangel-Villalobos,Davide Pettener,Donata Luiselli,Loren G. Davis,Evelyne Heyer,Christoph P. E. Zollikofer,Marcia S. Ponce de León,Colin Smith,Vaughan Grimes,Vaughan Grimes,Kelly-Anne Pike,Michael Deal,Benjamin T. Fuller,Bernardo Arriaza,Vivien G. Standen,Maria F. Luz,Francois Ricaut,Niede Guidon,Ludmila P. Osipova,Ludmila P. Osipova,Mikhail Voevoda,Mikhail Voevoda,Olga L. Posukh,Olga L. Posukh,Oleg Balanovsky,Maria Lavryashina,Yuri Bogunov,Elza Khusnutdinova,Elza Khusnutdinova,Marina Gubina,Elena Balanovska,Sardana A. Fedorova,Sergey Litvinov,Sergey Litvinov,Boris Malyarchuk,Miroslava Derenko,M. J. Mosher,David Archer,Jerome S. Cybulski,Jerome S. Cybulski,Barbara Petzelt,Joycelynn Mitchell,Rosita Worl,Paul Norman,Peter Parham,Brian M. Kemp,Toomas Kivisild,Toomas Kivisild,Chris Tyler-Smith,Manjinder S. Sandhu,Manjinder S. Sandhu,Michael H. Crawford,Richard Villems,Richard Villems,David Glenn Smith,Michael R. Waters,Ted Goebel,John R. Johnson,Ripan S. Malhi,Mattias Jakobsson,David J. Meltzer,David J. Meltzer,Andrea Manica,Richard Durbin,Carlos Bustamante,Yun S. Song,Rasmus Nielsen,Eske Willerslev +121 more
TL;DR: The results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders.
"The Genetic Ancestry of African Americans, Latinos, and European Americans Across the United States" data files
TL;DR: It is shown that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US, which informs the understanding of the relationship between racial and ethnic identities and genetic ancestry.
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Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
Kevin Galinsky,Kevin Galinsky,Gaurav Bhatia,Po-Ru Loh,Po-Ru Loh,Stoyan Georgiev,Sayan Mukherjee,Nick Patterson,Alkes L. Price,Alkes L. Price +9 more
TL;DR: The FastPCA software is developed, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude.
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Journal ArticleDOI
Ancestral Components of Admixed Genomes in a Mexican Cohort
Nicholas A. Johnson,Marc Coram,Mark D. Shriver,Isabelle Romieu,Gregory S. Barsh,Stephanie J. London,Hua Tang +6 more
TL;DR: The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.
Journal ArticleDOI
Genetic ancestry and risk of breast cancer among U.S. Latinas.
Laura Fejerman,Esther M. John,Esther M. John,Scott Huntsman,Kenny Beckman,Shweta Choudhry,Eliseo J. Pérez-Stable,Esteban G. Burchard,Elad Ziv +8 more
TL;DR: Higher European ancestry was associated with increased breast cancer risk, and the association was attenuated but remained statistically significant when known risk factors and place of birth were adjusted for.
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