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Kmiecik MJ, Micheletti S, Coker D, Heilbron K, Shi J, Stagaman K, Filshtein Sonmez T, Fontanillas P, Shringarpure S, Wetzel M, Rowbotham HM, Cannon P, Shelton JF, Hinds DA, Tung JY, Holmes MV, Aslibekyan S, Norcliffe-Kaufmann L. Genetic analysis and natural history of Parkinson's disease due to the LRRK2 G2019S variant. Brain 2024; 147:1996-2008. [PMID: 38804604 PMCID: PMC11146432 DOI: 10.1093/brain/awae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 05/29/2024] Open
Abstract
The LRRK2 G2019S variant is the most common cause of monogenic Parkinson's disease (PD); however, questions remain regarding the penetrance, clinical phenotype and natural history of carriers. We performed a 3.5-year prospective longitudinal online study in a large number of 1286 genotyped LRRK2 G2019S carriers and 109 154 controls, with and without PD, recruited from the 23andMe Research Cohort. We collected self-reported motor and non-motor symptoms every 6 months, as well as demographics, family histories and environmental risk factors. Incident cases of PD (phenoconverters) were identified at follow-up. We determined lifetime risk of PD using accelerated failure time modelling and explored the impact of polygenic risk on penetrance. We also computed the genetic ancestry of all LRRK2 G2019S carriers in the 23andMe database and identified regions of the world where carrier frequencies are highest. We observed that despite a 1 year longer disease duration (P = 0.016), LRRK2 G2019S carriers with PD had similar burden of motor symptoms, yet significantly fewer non-motor symptoms including cognitive difficulties, REM sleep behaviour disorder (RBD) and hyposmia (all P-values ≤ 0.0002). The cumulative incidence of PD in G2019S carriers by age 80 was 49%. G2019S carriers had a 10-fold risk of developing PD versus non-carriers. This rose to a 27-fold risk in G2019S carriers with a PD polygenic risk score in the top 25% versus non-carriers in the bottom 25%. In addition to identifying ancient founding events in people of North African and Ashkenazi descent, our genetic ancestry analyses infer that the G2019S variant was later introduced to Spanish colonial territories in the Americas. Our results suggest LRRK2 G2019S PD appears to be a slowly progressive predominantly motor subtype of PD with a lower prevalence of hyposmia, RBD and cognitive impairment. This suggests that the current prodromal criteria, which are based on idiopathic PD, may lack sensitivity to detect the early phases of LRRK2 PD in G2019S carriers. We show that polygenic burden may contribute to the development of PD in the LRRK2 G2019S carrier population. Collectively, the results should help support screening programmes and candidate enrichment strategies for upcoming trials of LRRK2 inhibitors in early-stage disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Paul Cannon
- 23andMe, Inc., Research, Sunnyvale, CA 94086, USA
| | | | | | - Joyce Y Tung
- 23andMe, Inc., Research, Sunnyvale, CA 94086, USA
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2
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Song J, Ramírez MC, Okano JT, Service SK, de la Hoz J, Díaz-Zuluaga AM, Upegui CV, Gallago C, Arias A, Sánchez AV, Teshiba T, Sabatti C, Gur RC, Bearden CE, Escobar JI, Reus VI, Jaramillo CL, Freimer NB, Olde Loohuis LM, Blower S. Geospatial investigations in Colombia reveal variations in the distribution of mood and psychotic disorders. COMMUNICATIONS MEDICINE 2024; 4:26. [PMID: 38383761 PMCID: PMC10881503 DOI: 10.1038/s43856-024-00441-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Geographical variations in mood and psychotic disorders have been found in upper-income countries. We looked for geographic variation in these disorders in Colombia, a middle-income country. We analyzed electronic health records from the Clínica San Juan de Dios Manizales (CSJDM), which provides comprehensive mental healthcare for the one million inhabitants of Caldas. METHODS We constructed a friction surface map of Caldas and used it to calculate the travel-time to the CSJDM for 16,295 patients who had received an initial diagnosis of mood or psychotic disorder. Using a zero-inflated negative binomial regression model, we determined the relationship between travel-time and incidence, stratified by disease severity. We employed spatial scan statistics to look for patient clusters. RESULTS We show that travel-times (for driving) to the CSJDM are less than 1 h for ~50% of the population and more than 4 h for ~10%. We find a distance-decay relationship for outpatients, but not for inpatients: for every hour increase in travel-time, the number of expected outpatient cases decreases by 20% (RR = 0.80, 95% confidence interval [0.71, 0.89], p = 5.67E-05). We find nine clusters/hotspots of inpatients. CONCLUSIONS Our results reveal inequities in access to healthcare: many individuals requiring only outpatient treatment may live too far from the CSJDM to access healthcare. Targeting of resources to comprehensively identify severely ill individuals living in the observed hotspots could further address treatment inequities and enable investigations to determine factors generating these hotspots.
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Affiliation(s)
- Janet Song
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Justin T Okano
- Center for Biomedical Modeling, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Juan de la Hoz
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ana M Díaz-Zuluaga
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Cristian Gallago
- Department of Mental Health and Human Behavior, University of Caldas, Manizales, Colombia
| | - Alejandro Arias
- Department of Psychiatry, University of Antioquía, Medellín, Colombia
| | | | - Terri Teshiba
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Ruben C Gur
- Department of Psychiatry, University of Pennsylvania School of Medicine and the Penn-CHOP Lifespan Brain Institute, Philadelphia, PA, USA
| | - Carrie E Bearden
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Javier I Escobar
- Department of Psychiatry, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Victor I Reus
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | | | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Sally Blower
- Center for Biomedical Modeling, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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3
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Swinford NA, Prall SP, Gopalan S, Williams CM, Sheehama J, Scelza BA, Henn BM. Increased homozygosity due to endogamy results in fitness consequences in a human population. Proc Natl Acad Sci U S A 2023; 120:e2309552120. [PMID: 37847737 PMCID: PMC10614605 DOI: 10.1073/pnas.2309552120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Recessive alleles have been shown to directly affect both human Mendelian disease phenotypes and complex traits. Pedigree studies also suggest that consanguinity results in increased childhood mortality and adverse health phenotypes, presumably through penetrance of recessive mutations. Here, we test whether the accumulation of homozygous, recessive alleles decreases reproductive success in a human population. We address this question among the Namibian Himba, an endogamous agro-pastoralist population, who until very recently practiced natural fertility. Using a sample of 681 individuals, we show that Himba exhibit elevated levels of "inbreeding," calculated as the fraction of the genome in runs of homozygosity (FROH). Many individuals contain multiple long segments of ROH in their genomes, indicating that their parents had high kinship coefficients. However, we do not find evidence that this is explained by first-cousin consanguinity, despite a reported social preference for cross-cousin marriages. Rather, we show that elevated haplotype sharing in the Himba is due to a bottleneck, likely in the past 60 generations. We test whether increased recessive mutation load results in observed fitness consequences by assessing the effect of FROH on completed fertility in a cohort of postreproductive women (n = 69). We find that higher FROH is significantly associated with lower fertility. Our data suggest a multilocus genetic effect on fitness driven by the expression of deleterious recessive alleles, especially those in long ROH. However, these effects are not the result of consanguinity but rather elevated background identity by descent.
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Affiliation(s)
- N. A. Swinford
- Department of Anthropology, University of California Davis, Davis, CA95616
| | - S. P. Prall
- Department of Anthropology, University of Missouri, Columbia, MO65211
| | - S. Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - C. M. Williams
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
| | - J. Sheehama
- Department of Human, Biological and Translational Medical Sciences, School of Medicine University of Namibia, Oshakati10005, Namibia
| | - B. A. Scelza
- Department of Anthropology, University of California Los Angeles, Los Angeles, CA90095
| | - B. M. Henn
- Department of Anthropology, University of California Davis, Davis, CA95616
- Center for Population Biology, University of California Davis, Davis, CA95616
- Genome Center, University of California Davis, Davis, CA95616
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4
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Salazar-Tortosa DF, Huang YF, Enard D. Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression. Genome Biol Evol 2023; 15:evad170. [PMID: 37713622 PMCID: PMC10563788 DOI: 10.1093/gbe/evad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
How much genome differences between species reflect neutral or adaptive evolution is a central question in evolutionary genomics. In humans and other mammals, the presence of adaptive versus neutral genomic evolution has proven particularly difficult to quantify. The difficulty notably stems from the highly heterogeneous organization of mammalian genomes at multiple levels (functional sequence density, recombination, etc.) which complicates the interpretation and distinction of adaptive versus neutral evolution signals. In this study, we introduce mixture density regressions (MDRs) for the study of the determinants of recent adaptation in the human genome. MDRs provide a flexible regression model based on multiple Gaussian distributions. We use MDRs to model the association between recent selection signals and multiple genomic factors likely to affect the occurrence/detection of positive selection, if the latter was present in the first place to generate these associations. We find that an MDR model with two Gaussian distributions provides an excellent fit to the genome-wide distribution of a common sweep summary statistic (integrated haplotype score), with one of the two distributions likely enriched in positive selection. We further find several factors associated with signals of recent adaptation, including the recombination rate, the density of regulatory elements in immune cells, GC content, gene expression in immune cells, the density of mammal-wide conserved elements, and the distance to the nearest virus-interacting gene. These results support the presence of strong positive selection in recent human evolution and highlight MDRs as a powerful tool to make sense of signals of recent genomic adaptation.
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Affiliation(s)
- Diego F Salazar-Tortosa
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Department of Ecology, University of Granada, Granada, Spain
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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5
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Kosik KS. Search Strategies for Alzheimer Protector Genes. Ann Neurol 2023; 94:613-617. [PMID: 37574772 DOI: 10.1002/ana.26764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/05/2023] [Indexed: 08/15/2023]
Abstract
Large families with autosomal dominant mutations leading to Alzheimer's disease and related conditions can show putative protective gene variants; however, no systematic search strategy exists to find these genes. Described here are the unique demographic circumstances and genetic setting in which the discovery of protective variants is likely. The identification of these genes may reveal pathways with therapeutic implications. ANN NEUROL 2023;94:613-617.
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Affiliation(s)
- Kenneth S Kosik
- The Neuroscience Research Institute and The Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
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6
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Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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7
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Cochran JN, Acosta-Uribe J, Esposito BT, Madrigal L, Aguillón D, Giraldo MM, Taylor JW, Bradley J, Fulton-Howard B, Andrews SJ, Acosta-Baena N, Alzate D, Garcia GP, Piedrahita F, Lopez HE, Anderson AG, Rodriguez-Nunez I, Roberts K, Dominantly Inherited Alzheimer Network, Absher D, Myers RM, Beecham GW, Reitz C, Rizzardi LF, Fernandez MV, Goate AM, Cruchaga C, Renton AE, Lopera F, Kosik KS. Genetic associations with age at dementia onset in the PSEN1 E280A Colombian kindred. Alzheimers Dement 2023; 19:3835-3847. [PMID: 36951251 PMCID: PMC10514237 DOI: 10.1002/alz.13021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/24/2023]
Abstract
INTRODUCTION Genetic associations with Alzheimer's disease (AD) age at onset (AAO) could reveal genetic variants with therapeutic applications. We present a large Colombian kindred with autosomal dominant AD (ADAD) as a unique opportunity to discover AAO genetic associations. METHODS A genetic association study was conducted to examine ADAD AAO in 340 individuals with the PSEN1 E280A mutation via TOPMed array imputation. Replication was assessed in two ADAD cohorts, one sporadic early-onset AD study and four late-onset AD studies. RESULTS 13 variants had p<1×10-7 or p<1×10-5 with replication including three independent loci with candidate associations with clusterin including near CLU. Other suggestive associations were identified in or near HS3ST1, HSPG2, ACE, LRP1B, TSPAN10, and TSPAN14. DISCUSSION Variants with suggestive associations with AAO were associated with biological processes including clusterin, heparin sulfate, and amyloid processing. The detection of these effects in the presence of a strong mutation for ADAD reinforces their potentially impactful role.
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Affiliation(s)
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute, University of California, Santa Barbara, California, and Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, California, USA
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Bianca T Esposito
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucia Madrigal
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Margarita M Giraldo
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Jared W Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Joseph Bradley
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Brian Fulton-Howard
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shea J Andrews
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Natalia Acosta-Baena
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Gloria P Garcia
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Hugo E Lopez
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | | | | | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Christiane Reitz
- Department of Epidemiology, Sergievsky Center, Taub Institute for Research on the Aging Brain, Columbia University, New York, New York, USA
| | | | | | - Alison M Goate
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cruchaga
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alan E Renton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia. School of Medicine. Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Kenneth S Kosik
- Neuroscience Research Institute, University of California, Santa Barbara, California, and Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, California, USA
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8
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Gómez-Álzate AM, Hidalgo-López C, García-Valencia J, Martínez-Zamora M, Aguirre-Acevedo DC, Cuartas-Arias M, Arcos-Burgos M, Valencia-Evhecerry J, Lopez-Jaramillo C, Palacio-Ortiz JD. Psychopathological Risk in Siblings of Subjects with Attention-Deficit/Hyperactivity Disorder: A cross-Sectional Study. REVISTA COLOMBIANA DE PSIQUIATRIA (ENGLISH ED.) 2023; 52:193-200. [PMID: 37923415 DOI: 10.1016/j.rcpeng.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 11/07/2023]
Abstract
OBJECTIVE We aim to determine the prevalence of mental disorders in siblings of children with attention deficit hyperactivity disorder (ADHD), and to determine how psychosocial adversity factors relate to this psychopathology, in a low-middle income country (Colombia). METHODS We evaluated subjects with ADHD diagnosed according to the DSM-5 criteria, one of their parents and one of their siblings (ages 8-19). We used the ADHD rating scale and a set of instruments to assess the presence of mental disorders as well as psychosocial adversity. RESULTS We evaluated 74 trios formed by the index case with ADHD, one sibling and one of the parents. We found that 24.3% of the participating siblings also met the criteria for ADHD and another 24.3% for other psychiatric disorders. The risk of these siblings having ADHD increased further when one of the parents reported a history of ADHD. We also found that 28.3% of the families faced high levels of psychosocial adversity as per their scores in the Rutter Adversity Index. CONCLUSIONS Siblings of subjects with ADHD showed a significant risk for ADHD and other mental disorders. That risk increased if a parent reported a history of ADHD and also when two or more psychosocial adversity factors were present. This study supports the importance of early detection in efforts to decrease the risk for other siblings.
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Affiliation(s)
- Alejandra María Gómez-Álzate
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Catalina Hidalgo-López
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Jenny García-Valencia
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Marta Martínez-Zamora
- Departamento de Psicología, Universidad CES, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Daniel Camilo Aguirre-Acevedo
- Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Mauricio Cuartas-Arias
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Mauricio Arcos-Burgos
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Johanna Valencia-Evhecerry
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Carlos Lopez-Jaramillo
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia
| | - Juan David Palacio-Ortiz
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Departamento de Psicología, Escuela de Humanidades de la Universidad EAFIT, Medellín, Colombia.
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9
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Cardoso-dos-Santos AC, Reales G, Schuler-Faccini L. Clusters of rare disorders and congenital anomalies in South America. Rev Panam Salud Publica 2023; 47:e98. [PMID: 37363626 PMCID: PMC10289474 DOI: 10.26633/rpsp.2023.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/21/2023] [Indexed: 06/28/2023] Open
Abstract
Objective To map geographic clusters of rare disorders and congenital anomalies reported in South America. Methods Qualitative systematic review conducted in Medline/PubMed, Lilacs, and Scielo electronic databases to identify studies meeting eligibility criteria. The strategy resulted in 1 672 unique articles, from which 164 were selected for full reading by a pair of reviewers. Results Fifty-five articles reported at least one cluster of genetic disorders or congenital anomalies in South American territory. From these papers, 122 clusters were identified, of which half (61) were related to autosomal recessive disorders. Sixty-five (53.3%) of the clusters were located in Brazil. Conclusions The results of the review reinforce that rare diseases and congenital anomalies can occur in a non-random way in space, which is discussed in the perspective of the complex history of formation, social organization, and genetic structure of the South American population. Mapping clusters in population medical genetics can be an important public health tool, given that such places concentrate cases of rare diseases that frequently require multiprofessional, specialized care. Therefore, these results can support important agendas in public health related to rare diseases and congenital anomalies, such as health promotion and surveillance.
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Affiliation(s)
- Augusto César Cardoso-dos-Santos
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional (INaGeMP)Porto Alegre, RSBrazilInstituto Nacional de Ciência e Tecnologia de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Universidade Federal do Rio Grande do SulPorto Alegre, RSBrazilUniversidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lavinia Schuler-Faccini
- Universidade Federal do Rio Grande do SulPorto Alegre, RSBrazilUniversidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Garcia OA, Arslanian K, Whorf D, Thariath S, Shriver M, Li JZ, Bigham AW. The Legacy of Infectious Disease Exposure on the Genomic Diversity of Indigenous Southern Mexicans. Genome Biol Evol 2023; 15:7023365. [PMID: 36726304 PMCID: PMC10016042 DOI: 10.1093/gbe/evad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/19/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
To characterize host risk factors for infectious disease in Mesoamerican populations, we interrogated 857,481 SNPs assayed using the Affymetrix 6.0 genotyping array for signatures of natural selection in immune response genes. We applied three statistical tests to identify signatures of natural selection: locus-specific branch length (LSBL), the cross-population extended haplotype homozygosity (XP-EHH), and the integrated haplotype score (iHS). Each of the haplotype tests (XP-EHH and iHS) were paired with LSBL and significance was determined at the 1% level. For the paired analyses, we identified 95 statistically significant windows for XP-EHH/LSBL and 63 statistically significant windows for iHS/LSBL. Among our top immune response loci, we found evidence of recent directional selection associated with the major histocompatibility complex (MHC) and the peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling pathway. These findings illustrate that Mesoamerican populations' immunity has been shaped by exposure to infectious disease. As targets of selection, these variants are likely to encode phenotypes that manifest themselves physiologically and therefore may contribute to population-level variation in immune response. Our results shed light on past selective events influencing the host response to modern diseases, both pathogenic infection as well as autoimmune disorders.
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Affiliation(s)
- Obed A Garcia
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan.,Department of Biomedical Data Science, Stanford University, Stanford, California
| | | | - Daniel Whorf
- College of Medicine, University of Illinois, Peoria, Illinois
| | - Serena Thariath
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee
| | - Mark Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, California
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11
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Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose. Mol Biol Evol 2023; 40:7024794. [PMID: 36729989 PMCID: PMC9927576 DOI: 10.1093/molbev/msad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
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Affiliation(s)
| | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Sarah R Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Rolf O Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Leah M Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
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12
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Swinford N, Gallagher B, Sheehama J, Lin M, Prall S, Scelza B, Henn BM. Examination of runs of homozygosity in relation to height in an endogamous Namibian population. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:207-215. [PMID: 36790690 PMCID: PMC9937629 DOI: 10.1002/ajpa.24660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Height is a complex, highly heritable polygenic trait subject to both genetic composition and environmental influences. Recent studies suggest that a large proportion of height heritability is determined by the cumulative effect of many low allele frequency variants across the genome. Previous research has also identified an inverse relationship between height and runs of homozygosity (ROH); however, this has yet to be examined within African populations. We aim to identify this association within the Himba, an endogamous Namibian population who are recently bottlenecked, resulting in elevated haplotype sharing and increased homozygosity. MATERIALS AND METHODS Here, we calculate the fraction of the genome composed of long runs of homozygosity (FROH) in a sample of 245 adults and use mixed effects models to assess its effect on height. RESULTS We find that Himba adults exhibit increased homozygosity. However, in contrast to previous studies in other populations, we do not find a significant effect of FROH on height within the Himba. We further estimated heritability of height, noting both an enrichment of distant relatives and greater developmental homogeneity across households; we find that h g 2 = 0.59 (SE ± 0.146), comparable to estimates reported in Europeans. DISCUSSION Our results may be due to other environmental variables we were not able to include, measurement error, or low statistical power, but may also imply that phenotypic expression resulting from increased homozygosity may vary from population to population.
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Affiliation(s)
- Natalie Swinford
- Department of Anthropology, University of California, Davis, USA
| | - Brenna Gallagher
- Department of Anthropology, University of California, Davis, USA
| | | | - Meng Lin
- University of Colorado, Anschutz Medical Campus, Aurora, USA
| | | | | | - Brenna M. Henn
- Department of Anthropology, University of California, Davis, USA,UC Davis Genome Center, University of California, Davis, USA
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13
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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 GENES|GENOMES|GENETICS 2022; 12:6647844. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University , Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV) , Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University , Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester , Leicester LE1 7RH, UK
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14
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Hurtado C, Rojas-Gualdrón DF, Urrego R, Cashman K, Vásquez-Trespalacios EM, Díaz-Coronado JC, Rojas M, Jenks S, Vásquez G, Sanz I. Altered B cell phenotype and CD27+ memory B cells are associated with clinical features and environmental exposure in Colombian systemic lupus erythematosus patients. Front Med (Lausanne) 2022; 9:950452. [PMID: 36148466 PMCID: PMC9485945 DOI: 10.3389/fmed.2022.950452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
Background B lymphocytes are dysregulated in Systemic Lupus Erythematosus (SLE) including the expansion of extrafollicular B cells in patients with SLE of African American ancestry, which is associated with disease activity and nephritis. The population of Colombia has a mixture of European, Native American, and African ancestry. It is not known if Colombian patients have the same B cell distributions described previously and if they are associated with disease activity, clinical manifestations, and environmental exposures. Objective To characterize B cell phenotype in a group of Colombian Systemic Lupus Erythematosus patients with mixed ancestry and determine possible associations with disease activity, clinical manifestations, the DNA methylation status of the IFI44L gene and environmental exposures. Materials and methods Forty SLE patients and 17 healthy controls were recruited. Cryopreserved peripheral B lymphocytes were analyzed by multiparameter flow cytometry, and the DNA methylation status of the gene IFI44L was evaluated in resting Naive B cells (rNAV). Results Extrafollicular active Naive (aNAV) and Double Negative type 2, DN2 (CD27− IgD− CD21− CD11c+) B cells were expanded in severe active patients and were associated with nephritis. Patients had hypomethylation of the IFI44L gene in rNAV cells. Regarding environmental exposure, patients occupationally exposed to organic solvents had increased memory CD27+ cells (SWM). Conclusion aNAV and DN2 extrafollicular cells showed significant clinical associations in Colombian SLE patients, suggesting a relevant role in the disease’s pathophysiology. Hypomethylation of the IFI44L gene in resting Naive B cells suggests that epigenetic changes are established at exceedingly early stages of B cell ontogeny. Also, an alteration in SWM memory cells was observed for the first time in patients exposed to organic solvents. This opens different clinical and basic research possibilities to corroborate these findings and deepen the knowledge of the relationship between environmental exposure and SLE.
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Affiliation(s)
- Carolina Hurtado
- School of Medicine, Universidad CES, Medellín, Colombia
- School of Graduate Studies, Universidad CES, Medellín, Colombia
| | | | - Rodrigo Urrego
- Group INCA-CES, School of Veterinary Medicine and Zootechnic, Universidad CES, Medellín, Colombia
| | - Kevin Cashman
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA, United States
| | | | - Juan Camilo Díaz-Coronado
- School of Medicine, Universidad CES, Medellín, Colombia
- Group of Clinical Information, Artmedica IPS, Medellín, Colombia
| | - Mauricio Rojas
- Grupo de Inmunología Celular e Inmunogenética, Universidad de Antioquia, Medellín, Colombia
- Unidad de Citometría de Flujo, Universidad de Antioquia, Medellín, Colombia
| | - Scott Jenks
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Gloria Vásquez
- Grupo de Inmunología Celular e Inmunogenética, Universidad de Antioquia, Medellín, Colombia
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA, United States
- *Correspondence: Ignacio Sanz,
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15
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da Cruz PRS, Ananina G, Secolin R, Gil-da-Silva-Lopes VL, Lima CSP, de França PHC, Donatti A, Lourenço GJ, de Araujo TK, Simioni M, Lopes-Cendes I, Costa FF, de Melo MB. Demographic history differences between Hispanics and Brazilians imprint haplotype features. G3 GENES|GENOMES|GENETICS 2022; 12:6576632. [PMID: 35511163 PMCID: PMC9258545 DOI: 10.1093/g3journal/jkac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022]
Abstract
Admixture is known to greatly impact the genetic landscape of a population and, while genetic variation underlying human phenotypes has been shown to differ among populations, studies on admixed subjects are still scarce. Latin American populations are the result of complex demographic history, such as 2 or 3-way admixing events, bottlenecks and/or expansions, and adaptive events unique to the American continent. To explore the impact of these events on the genetic structure of Latino populations, we evaluated the following haplotype features: linkage disequilibrium, shared identity by descent segments, runs of homozygosity, and extended haplotype homozygosity (integrated haplotype score) in Latinos represented in the 1000 Genome Project along with array data from 171 Brazilians sampled in the South and Southeast regions of Brazil. We found that linkage disequilibrium decay relates to the amount of American and African ancestry. The extent of identity by descent sharing positively correlates with historical effective population sizes, which we found to be steady or growing, except for Puerto Ricans and Colombians. Long runs of homozygosity, a particular instance of autozygosity, was only enriched in Peruvians and Native Americans. We used simulations to account for random sampling and linkage disequilibrium to filter positive selection indexes and found 244 unique markers under selection, 26 of which are common to 2 or more populations. Some markers exhibiting positive selection signals had estimated time to the most recent common ancestor consistent with human adaptation to the American continent. In conclusion, Latino populations present highly divergent haplotype characteristics that impact genetic architecture and underlie complex phenotypes.
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Affiliation(s)
- Pedro Rodrigues Sousa da Cruz
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Galina Ananina
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
| | - Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Carmen Silvia Passos Lima
- Clinical Oncology Service, Department of Internal Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | | | - Amanda Donatti
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Tânia Kawasaki de Araujo
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Milena Simioni
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP , Campinas, SP 13083-887, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN) , Campinas, SP 13083-887, Brazil
| | - Fernando Ferreira Costa
- Hematology and Hemotherapy Center, University of Campinas—UNICAMP, Campinas, SP, 13083-878 , Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas—UNICAMP , Campinas, SP 13083-875, Brazil
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16
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Ariano B, Mattiangeli V, Breslin EM, Parkinson EW, McLaughlin TR, Thompson JE, Power RK, Stock JT, Mercieca-Spiteri B, Stoddart S, Malone C, Gopalakrishnan S, Cassidy LM, Bradley DG. Ancient Maltese genomes and the genetic geography of Neolithic Europe. Curr Biol 2022; 32:2668-2680.e6. [PMID: 35588742 PMCID: PMC9245899 DOI: 10.1016/j.cub.2022.04.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.
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Affiliation(s)
- Bruno Ariano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eóin W Parkinson
- Department of Classics and Archaeology, University of Malta, Msida 2080, Malta
| | - T Rowan McLaughlin
- Department of Scientific Research, The British Museum, Great Russell Street, London WC1B 3DG, UK
| | - Jess E Thompson
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronika K Power
- Department of History and Archaeology, Macquarie University, 25B Wally's Walk, Sydney, NSW, Australia
| | - Jay T Stock
- Department of Anthropology, Western University, 1151 Richmond St, London, ON N6G 2V4, Canada
| | | | - Simon Stoddart
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Caroline Malone
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, UK
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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Gopalan S, Smith SP, Korunes K, Hamid I, Ramachandran S, Goldberg A. Human genetic admixture through the lens of population genomics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200410. [PMID: 35430881 PMCID: PMC9014191 DOI: 10.1098/rstb.2020.0410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Katharine Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
- Data Science Initiative, Brown University, Providence, RI 02912, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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18
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Gómez-Álzate AM, Hidalgo-López C, García-Valencia J, Martínez-Zamora M, Aguirre-Acevedo DC, Cuartas-Arias M, Arcos-Burgos M, Valencia-Evhecerry J, Lopez-Jaramillo C, Palacio-Ortiz JD. Psychopathological Risk in Siblings of Subjects with Attention-Deficit/Hyperactivity Disorder: A cross-Sectional Study. REVISTA COLOMBIANA DE PSIQUIATRIA (ENGLISH ED.) 2021; 52:S0034-7450(21)00077-9. [PMID: 34147265 DOI: 10.1016/j.rcp.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/20/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVE We aim to determine the prevalence of mental disorders in siblings of children with attention deficit hyperactivity disorder (ADHD), and to determine how psychosocial adversity factors relate to this psychopathology, in a low-middle income country (Colombia). METHODS We evaluated subjects with ADHD diagnosed according to the DSM-5 criteria, one of their parents and one of their siblings (ages 8-19). We used the ADHD rating scale and a set of instruments to assess the presence of mental disorders as well as psychosocial adversity. RESULTS We evaluated 74 trios formed by the index case with ADHD, one sibling and one of the parents. We found that 24.3% of the participating siblings also met the criteria for ADHD and another 24.3% for other psychiatric disorders. The risk of these siblings having ADHD increased further when one of the parents reported a history of ADHD. We also found that 28.3% of the families faced high levels of psychosocial adversity as per their scores in the Rutter Adversity Index. CONCLUSIONS Siblings of subjects with ADHD showed a significant risk for ADHD and other mental disorders. That risk increased if a parent reported a history of ADHD and also when two or more psychosocial adversity factors were present. This study supports the importance of early detection in efforts to decrease the risk for other siblings.
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Affiliation(s)
- Alejandra María Gómez-Álzate
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Catalina Hidalgo-López
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Jenny García-Valencia
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia
| | | | | | - Mauricio Cuartas-Arias
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Mauricio Arcos-Burgos
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Johanna Valencia-Evhecerry
- Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Carlos Lopez-Jaramillo
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Palacio-Ortiz
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Antioquia. Hospital Universitario San Vicente de Paúl, Medellín, Colombia; Grupo de investigación en psiquiatría (GIPSI), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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19
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Peng Q, Ehlers CL. Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population. Mol Psychiatry 2021; 26:2200-2211. [PMID: 33398086 PMCID: PMC8254832 DOI: 10.1038/s41380-020-00989-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 11/20/2022]
Abstract
Runs of homozygosity (ROH) arise when an individual inherits two copies of the same haplotype segment. While ROH are ubiquitous across human populations, Native populations-with shared parental ancestry arising from isolation and endogamy-can carry a substantial enrichment for ROH. We have been investigating genetic and environmental risk factors for alcohol use disorders (AUD) in a group of American Indians (AI) who have higher rates of AUD than the general U. S. population. Here we explore whether ROH might be associated with incidence and severity of AUD in this admixed AI population (n = 742) that live on geographically contiguous reservations, using low-coverage whole genome sequences. We have found that the genomic regions in the ROH that were identified in this population had significantly elevated American Indian heritage compared with the rest of the genome. Increased ROH abundance and ROH burden are likely risk factors for AUD severity in this AI population, especially in those diagnosed with severe and moderate AUD. The association between ROH and AUD was mostly driven by ROH of moderate lengths between 1 and 2 Mb. An ROH island on chromosome 1p32.3 and a rare ROH pool on chromosome 3p12.3 were found to be significantly associated with AUD severity. They contain genes involved in lipid metabolism, oxidative stress and inflammatory responses; and OSBPL9 was found to reside on the consensus part of the ROH island. These data demonstrate that ROH are associated with risk for AUD severity in this AI population.
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Affiliation(s)
- Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Cindy L Ehlers
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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20
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Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, Torre D, Moscati A, Wojcik GL, Shemirani R, Beckmann ND, Cohain A, Sorokin EP, Park DS, Ambite JL, Ellis S, Auton A, Bottinger EP, Cho JH, Loos RJF, Abul-Husn NS, Zaitlen NA, Gignoux CR, Kenny EE. Toward a fine-scale population health monitoring system. Cell 2021; 184:2068-2083.e11. [PMID: 33861964 DOI: 10.1016/j.cell.2021.03.034] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/18/2020] [Accepted: 03/12/2021] [Indexed: 12/22/2022]
Abstract
Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations. Here, we propose a framework for repurposing data from electronic health records (EHRs) in concert with genomic data to explore the demographic ties that can impact disease burdens. Using data from a diverse biobank in New York City, we identified 17 communities sharing recent genetic ancestry. We observed 1,177 health outcomes that were statistically associated with a specific group and demonstrated significant differences in the segregation of genetic variants contributing to Mendelian diseases. We also demonstrated that fine-scale population structure can impact the prediction of complex disease risk within groups. This work reinforces the utility of linking genomic data to EHRs and provides a framework toward fine-scale monitoring of population health.
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Affiliation(s)
- Gillian M Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephane Wenric
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arden Moscati
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ruhollah Shemirani
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariella Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Danny S Park
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jose-Luis Ambite
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Steve Ellis
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Erwin P Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Judy H Cho
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J F Loos
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90033, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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21
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Abstract
Dogs and humans have coexisted together for thousands of years, but it was not until the Victorian Era that humans practiced selective breeding to produce the modern standards we see today. Strong artificial selection during the breed formation period has simplified the genetic architecture of complex traits and caused an enrichment of identity-by-descent (IBD) segments in the dog genome. This study demonstrates the value of IBD segments and utilizes them to infer the recent demography of canids, predict case-control status for complex traits, locate regions of the genome potentially linked to inbreeding depression, and to identify understudied breeds where there is potential to discover new disease-associated variants. Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.
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Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland. Hum Genet 2021; 140:1011-1029. [PMID: 33710394 PMCID: PMC8197721 DOI: 10.1007/s00439-021-02268-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.
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23
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Identification of Variants (rs11571707, rs144848, and rs11571769) in the BRCA2 Gene Associated with Hereditary Breast Cancer in Indigenous Populations of the Brazilian Amazon. Genes (Basel) 2021; 12:genes12020142. [PMID: 33499154 PMCID: PMC7911168 DOI: 10.3390/genes12020142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/09/2022] Open
Abstract
Estimates show that 5–10% of breast cancer cases are hereditary, caused by genetic variants in autosomal dominant genes; of these, 16% are due to germline mutations in the BRCA1 and BRCA2 genes. The comprehension of the mutation profile of these genes in the Brazilian population, particularly in Amazonian Amerindian groups, is scarce. We investigated fifteen polymorphisms in the BRCA1 and BRCA2 genes in Amazonian Amerindians and compared the results with the findings of global populations publicly available in the 1000 Genomes Project database. Our study shows that three variants (rs11571769, rs144848, and rs11571707) of the BRCA2 gene, commonly associated with hereditary breast cancer, had a significantly higher allele frequency in the Amazonian Amerindian individuals in comparison with the African, American, European, and Asian groups analyzed. These data outline the singular genetic profiles of the indigenous population from the Brazilian Amazon region. The knowledge about BRCA1 and BRCA2 variants is critical to establish public policies for hereditary breast cancer screening in Amerindian groups and populations admixed with them, such as the Brazilian population.
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24
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Dzomba EF, Chimonyo M, Pierneef R, Muchadeyi FC. Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data. BMC Genomics 2021; 22:7. [PMID: 33407115 PMCID: PMC7788743 DOI: 10.1186/s12864-020-07314-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
Background Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. Conclusions Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07314-2.
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Affiliation(s)
- E F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - M Chimonyo
- Discipline of Animal & Poultry Science; School of Agricultural, Earth & Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - R Pierneef
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
| | - F C Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
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25
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Naseri A, Shi J, Lin X, Zhang S, Zhi D. RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID. PLoS Genet 2021; 17:e1009315. [PMID: 33476339 PMCID: PMC7853505 DOI: 10.1371/journal.pgen.1009315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/02/2021] [Accepted: 12/18/2020] [Indexed: 11/19/2022] Open
Abstract
Inference of relationships from whole-genome genetic data of a cohort is a crucial prerequisite for genome-wide association studies. Typically, relationships are inferred by computing the kinship coefficients (ϕ) and the genome-wide probability of zero IBD sharing (π0) among all pairs of individuals. Current leading methods are based on pairwise comparisons, which may not scale up to very large cohorts (e.g., sample size >1 million). Here, we propose an efficient relationship inference method, RAFFI. RAFFI leverages the efficient RaPID method to call IBD segments first, then estimate the ϕ and π0 from detected IBD segments. This inference is achieved by a data-driven approach that adjusts the estimation based on phasing quality and genotyping quality. Using simulations, we showed that RAFFI is robust against phasing/genotyping errors, admix events, and varying marker densities, and achieves higher accuracy compared to KING, the current leading method, especially for more distant relatives. When applied to the phased UK Biobank data with ~500K individuals, RAFFI is approximately 18 times faster than KING. We expect RAFFI will offer fast and accurate relatedness inference for even larger cohorts.
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Affiliation(s)
- Ardalan Naseri
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Junjie Shi
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Degui Zhi
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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26
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Riggs K, Chen HS, Rotunno M, Li B, Simonds NI, Mechanic LE, Peng B. On the application, reporting, and sharing of in silico simulations for genetic studies. Genet Epidemiol 2020; 45:131-141. [PMID: 33063887 PMCID: PMC7984380 DOI: 10.1002/gepi.22362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/31/2022]
Abstract
In silico simulations play an indispensable role in the development and application of statistical models and methods for genetic studies. Simulation tools allow for the evaluation of methods and investigation of models in a controlled manner. With the growing popularity of evolutionary models and simulation‐based statistical methods, genetic simulations have been applied to a wide variety of research disciplines such as population genetics, evolutionary genetics, genetic epidemiology, ecology, and conservation biology. In this review, we surveyed 1409 articles from five journals that publish on major application areas of genetic simulations. We identified 432 papers in which genetic simulations were used and examined the targets and applications of simulation studies and how these simulation methods and simulated data sets are reported and shared. Whereas a large proportion (30%) of the surveyed articles reported the use of genetic simulations, only 28% of these genetic simulation studies used existing simulation software, 2% used existing simulated data sets, and 19% and 12% made source code and simulated data sets publicly available, respectively. Moreover, 15% of articles provided no information on how simulation studies were performed. These findings suggest a need to encourage sharing and reuse of existing simulation software and data sets, as well as providing more information regarding the performance of simulations.
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Affiliation(s)
- Kaleigh Riggs
- Department of Statistics, Rice University, Houston, Texas, USA
| | - Huann-Sheng Chen
- Division of Cancer Control and Population Sciences, Statistical Research and Applications Branch, Surveillance Research Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, NCI, NIH, Bethesda, Maryland, USA
| | - Bing Li
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | | | - Leah E Mechanic
- Division of Cancer Control and Population Sciences, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, NCI, NIH, Bethesda, Maryland, USA
| | - Bo Peng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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27
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Boca SM, Huang L, Rosenberg NA. On the heterozygosity of an admixed population. J Math Biol 2020; 81:1217-1250. [PMID: 33034736 DOI: 10.1007/s00285-020-01531-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 08/04/2020] [Indexed: 01/18/2023]
Abstract
In this study, we consider admixed populations through their expected heterozygosity, a measure of genetic diversity. A population is termed admixed if its members possess recent ancestry from two or more separate sources. As a result of the fusion of source populations with different genetic variants, admixed populations can exhibit high levels of genetic diversity, reflecting contributions of their multiple ancestral groups. For a model of an admixed population derived from K source populations, we obtain a relationship between its heterozygosity and its proportions of admixture from the various source populations. We show that the heterozygosity of the admixed population is at least as great as that of the least heterozygous source population, and that it potentially exceeds the heterozygosities of all of the source populations. The admixture proportions that maximize the heterozygosity possible for an admixed population formed from a specified set of source populations are also obtained under specific conditions. We examine the special case of [Formula: see text] source populations in detail, characterizing the maximal admixture in terms of the heterozygosities of the two source populations and the value of [Formula: see text] between them. In this case, the heterozygosity of the admixed population exceeds the maximal heterozygosity of the source groups if the divergence between them, measured by [Formula: see text], is large enough, namely above a certain bound that is a function of the heterozygosities of the source groups. We present applications to simulated data as well as to data from human admixture scenarios, providing results useful for interpreting the properties of genetic variability in admixed populations.
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Affiliation(s)
- Simina M Boca
- Department of Oncology, Department of Biostatistics, Bioinformatics and Biomathematics, Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, 20007, USA.
| | - Lucy Huang
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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28
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Mas-Sandoval A, Arauna LR, Gouveia MH, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Salzano FM, Hünemeier T, Tarazona-Santos E, Bortolini MC, Comas D. Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. Genome Biol Evol 2020; 11:2593-2604. [PMID: 31328768 PMCID: PMC6756188 DOI: 10.1093/gbe/evz161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/19/2023] Open
Abstract
After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.
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Affiliation(s)
- Alex Mas-Sandoval
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil
| | | | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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29
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Dai CL, Vazifeh MM, Yeang CH, Tachet R, Wells RS, Vilar MG, Daly MJ, Ratti C, Martin AR. Population Histories of the United States Revealed through Fine-Scale Migration and Haplotype Analysis. Am J Hum Genet 2020; 106:371-388. [PMID: 32142644 PMCID: PMC7058830 DOI: 10.1016/j.ajhg.2020.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
The population of the United States is shaped by centuries of migration, isolation, growth, and admixture between ancestors of global origins. Here, we assemble a comprehensive view of recent population history by studying the ancestry and population structure of more than 32,000 individuals in the US using genetic, ancestral birth origin, and geographic data from the National Geographic Genographic Project. We identify migration routes and barriers that reflect historical demographic events. We also uncover the spatial patterns of relatedness in subpopulations through the combination of haplotype clustering, ancestral birth origin analysis, and local ancestry inference. Examples of these patterns include substantial substructure and heterogeneity in Hispanics/Latinos, isolation-by-distance in African Americans, elevated levels of relatedness and homozygosity in Asian immigrants, and fine-scale structure in European descents. Taken together, our results provide detailed insights into the genetic structure and demographic history of the diverse US population.
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Affiliation(s)
- Chengzhen L Dai
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mohammad M Vazifeh
- Senseable City Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan
| | - Remi Tachet
- Senseable City Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Miguel G Vilar
- Genographic Project, National Geographic Society, Washington, DC 20036, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Carlo Ratti
- Senseable City Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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30
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Barbieri C, Barquera R, Arias L, Sandoval JR, Acosta O, Zurita C, Aguilar-Campos A, Tito-Álvarez AM, Serrano-Osuna R, Gray RD, Mafessoni F, Heggarty P, Shimizu KK, Fujita R, Stoneking M, Pugach I, Fehren-Schmitz L. The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast. Mol Biol Evol 2019; 36:2698-2713. [PMID: 31350885 PMCID: PMC6878948 DOI: 10.1093/molbev/msz174] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.
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Affiliation(s)
- Chiara Barbieri
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José R Sandoval
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Oscar Acosta
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Camilo Zurita
- Cátedra de Inmunología, Facultad de Medicina, Universidad Central del Ecuador, Quito, Ecuador
- Zurita & Zurita Laboratorios, Unidad de Investigaciones en Biomedicina, Quito, Ecuador
| | - Abraham Aguilar-Campos
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Ana M Tito-Álvarez
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Serrano-Osuna
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paul Heggarty
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ricardo Fujita
- Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Peru
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
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31
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Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF. Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions. PLoS Genet 2019; 15:e1008480. [PMID: 31765389 PMCID: PMC6901239 DOI: 10.1371/journal.pgen.1008480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/09/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023] Open
Abstract
Human population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.
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Affiliation(s)
- Mihail Halachev
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Martin S. Taylor
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shona M. Kerr
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Lucija Klaric
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | | | - Timothy J. Aitman
- Centre for Genomic and Experimental Medicine, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - James G. Prendergast
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Carys Pugh
- Centre for Clinical Brain Sciences, Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - David C. Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
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32
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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33
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Zeevi DA, Zahdeh F, Kling Y, Carmi S, Altarescu G. Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications. J Assist Reprod Genet 2019; 36:727-739. [PMID: 30617673 PMCID: PMC6504987 DOI: 10.1007/s10815-018-1392-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/18/2018] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Pre-implantation genetic diagnosis (PGD) for molecular disorders requires the construction of parental haplotypes. Classically, haplotype resolution ("phasing") is obtained by genotyping multiple polymorphic markers in both parents and at least one additional relative. However, this process is time-consuming, and immediate family members are not always available. The recent availability of massive genomic data for many populations promises to eliminate the needs for developing family-specific assays and for recruiting additional family members. In this study, we aimed to validate population-assisted haplotype phasing for PGD. METHODS Targeted sequencing of CFTR gene variants and ~ 1700 flanking polymorphic SNPs (± 2 Mb) was performed on 54 individuals from 12 PGD families of (a) Full Ashkenazi (FA; n = 16), (b) mixed Ashkenazi (MA; n = 23 individuals with at least one Ashkenazi and one non-Ashkenazi grandparents), or (c) non-Ashkenazi (NA; n = 15) descent. Heterozygous genotype calls in each individual were phased using various whole genome reference panels and appropriate computational models. All computationally derived haplotype predictions were benchmarked against trio-based phasing. RESULTS Using the Ashkenazi reference panel, phasing of FA was highly accurate (99.4% ± 0.2% accuracy); phasing of MA was less accurate (95.4% ± 4.5% accuracy); and phasing of NA was predictably low (83.4% ± 6.6% accuracy). Strikingly, for founder mutation carriers, our haplotyping approach facilitated near perfect phasing accuracy (99.9% ± 0.1% and 98.2% ± 2.8% accuracy for W1282X and delF508 carriers, respectively). CONCLUSIONS Our results demonstrate the feasibility of replacing classical haplotype phasing with population-based phasing with uncompromised accuracy.
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Affiliation(s)
- David A Zeevi
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel.
| | - Fouad Zahdeh
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Yehuda Kling
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gheona Altarescu
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
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