1
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Fu H, Shi G. Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms-A Study of Admixed Populations in the 1000 Genomes Project. Genes (Basel) 2024; 15:1099. [PMID: 39202458 PMCID: PMC11353365 DOI: 10.3390/genes15081099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we proposed a new LAI method based on population-specific single-nucleotide polymorphisms (SNPs) and applied it in the analysis of admixed populations in the 1000 Genomes Project (1KGP). Based on population-specific SNPs in a sliding window, we computed local ancestry information vectors, which are moment estimators of local ancestral proportions, for two haplotypes of an admixed individual and inferred the local ancestral origins. Then we used African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) populations from the 1KGP and indigenous American (AMR) populations from the Human Genome Diversity Project (HGDP) as reference populations and conducted the proposed LAI analysis on African American populations and American populations in the 1KGP. The results were compared with those obtained by RFMix, G-Nomix and FLARE. We demonstrated that the existence of alleles in a chromosomal region that are specific to a particular reference population and the absence of alleles specific to the other reference populations provide reasonable evidence for determining the ancestral origin of the region. Contemporary AFR, AMR and EUR populations approximate ancestral populations of the admixed populations well, and the results from RFMix, G-Nomix and FLARE largely agree with those from the Ancestral Spectrum Analyzer (ASA), in which the proposed method was implemented. When admixtures are ancient and contemporary reference populations do not satisfactorily approximate ancestral populations, the performances of RFMix, G-Nomix and FLARE deteriorate with increased error rates and fragmented chromosomal segments. In contrast, our method provides fair results.
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Affiliation(s)
| | - Gang Shi
- School of Telecommunications Engineering, Xidian University, 2 South Taibai Road, Xi’an 710071, China;
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2
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Obayemi JE, Callans L, Nair N, Gao H, Gandla D, Loza BL, Gao S, Mohebnasab M, Trofe-Clark J, Jacobson P, Keating B. Assessing the Utility of a Genotype-Guided Tacrolimus Equation in African American Kidney Transplant Recipients: A Single Institution Retrospective Study. J Clin Pharmacol 2024; 64:944-952. [PMID: 38766706 DOI: 10.1002/jcph.2461] [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: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 05/22/2024]
Abstract
Tacrolimus metabolism is heavily influenced by the CYP3A5 genotype, which varies widely among African Americans (AA). We aimed to assess the performance of a published genotype-informed tacrolimus dosing model in an independent set of adult AA kidney transplant (KTx) recipients. CYP3A5 genotypes were obtained for all AA KTx recipients (n = 232) from 2010 to 2019 who met inclusion criteria at a single transplant center in Philadelphia, Pennsylvania, USA. Medical record data were used to calculate predicted tacrolimus clearance using the published AA KTx dosing equation and two modified iterations. Observed and model-predicted trough levels were compared at 3 days, 3 months, and 6 months post-transplant. The mean prediction error at day 3 post-transplant was 3.05 ng/mL, indicating that the model tended to overpredict the tacrolimus trough. This bias improved over time to 1.36 and 0.78 ng/mL at 3 and 6 months post-transplant, respectively. Mean absolute prediction error-a marker of model precision-improved with time to 2.33 ng/mL at 6 months. Limiting genotype data in the model decreased bias and improved precision. The bias and precision of the published model improved over time and were comparable to studies in previous cohorts. The overprediction observed by the published model may represent overfitting to the initial cohort, possibly limiting generalizability.
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Affiliation(s)
- Joy E Obayemi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Lauren Callans
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhil Nair
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui Gao
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Divya Gandla
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Bao-Li Loza
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Gao
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Maedeh Mohebnasab
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Trofe-Clark
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pamala Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Brendan Keating
- Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Surgery, New York University, New York, NY, USA
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3
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Stoneman HR, Price A, Trout NS, Lamont R, Tifour S, Pozdeyev N, Crooks K, Lin M, Rafaels N, Gignoux CR, Marker KM, Hendricks AE. Characterizing substructure via mixture modeling in large-scale genetic summary statistics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577805. [PMID: 38766180 PMCID: PMC11100604 DOI: 10.1101/2024.01.29.577805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic summary data are broadly accessible and highly useful including for risk prediction, causal inference, fine mapping, and incorporation of external controls. However, collapsing individual-level data into groups masks intra- and inter-sample heterogeneity, leading to confounding, reduced power, and bias. Ultimately, unaccounted substructure limits summary data usability, especially for understudied or admixed populations. Here, we present Summix2, a comprehensive set of methods and software based on a computationally efficient mixture model to estimate and adjust for substructure in genetic summary data. In extensive simulations and application to public data, Summix2 characterizes finer-scale population structure, identifies ascertainment bias, and identifies potential regions of selection due to local substructure deviation. Summix2 increases the robust use of diverse publicly available summary data resulting in improved and more equitable research.
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Affiliation(s)
- Hayley R Stoneman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Adelle Price
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikole Scribner Trout
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Riley Lamont
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Souha Tifour
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Nikita Pozdeyev
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Meng Lin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher R Gignoux
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Katie M Marker
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Audrey E Hendricks
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
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4
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Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [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: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
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Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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5
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Hammami MB, Verceles JA, Goldfinger M, Shah N, Sica RA, Mantzaris I, Kornblum N, Konopleva M, Shastri A, Shapiro LC, Feldman EJ, Gritsman K, Verma A, Cooper DL. Improving Unrelated Donor Equity: Assessing Mismatched Donor Opportunities with Real-World Data in a Minority-Predominant Cohort. Transplant Cell Ther 2024; 30:544.e1-544.e8. [PMID: 38417677 DOI: 10.1016/j.jtct.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Recent advances in graft-versus-host disease (GVHD) prophylaxis including post-transplant cyclophosphamide (PTCy) and abatacept have significantly improved outcomes following HLA-mismatched allogenic hematopoietic stem cell transplantation (allo-HSCT) and have tremendous potential for reducing racial disparities in donor availability. A recent small study employing bone marrow as the source of stem cells showed similar outcomes after 5/8 versus 7/8 matches and is currently being tested in a larger study using peripheral blood stem cells. In this study, we examine real-world alternative donor HSCT options for a minority-predominant cohort in the Bronx, NY, focusing on the availability of lesser-matched (5/8 to 7/8) donors. Records of patients who underwent HLA typing at Montefiore Medical Center (2019 to 2022) were reviewed. The National Marrow Donor Program registry was queried to evaluate the availability of donors with at least 99% likelihood of HLA match at various levels (5/8, 6/8, 7/8, 8/8). Two hundred forty-one patients were included, 70% were non-White. Although the availability of ≥7/8 donors was less common in non-White patients, 100% of patients from each group had at least one or more 5/8 and 6/8 HLA-matched donors and more than 80% of these patients had >100 potential 5/8 and 6/8 HLA-matched donors. There was no statistical difference by race or ethnicity in the mean number of donors at 5/8 and 6/8 HLA-match levels. We demonstrate through real-world data that patients from diverse ethnic and racial backgrounds have access to 5/8 and 6/8 HLA-matched donors for allo-HSCT, potentially eliminating disparities in donor availability and allowing prioritization of other donor selection characteristics such as donor age, sex, ABO, and B leader matching. Further work is needed to study whether the use of mismatched donors offers a more potent graft-versus malignancy effect and optimal GVHD prophylaxis.
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Affiliation(s)
- M Bakri Hammami
- Department of Medicine, Jacobi Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Jhannine Alyssa Verceles
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Mendel Goldfinger
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Nishi Shah
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - R Alejandro Sica
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Ioannis Mantzaris
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Noah Kornblum
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Marina Konopleva
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Aditi Shastri
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Lauren C Shapiro
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Eric J Feldman
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Kira Gritsman
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Amit Verma
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Dennis L Cooper
- Department of Hematology-Oncology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York.
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6
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Grinde KE, Browning BL, Reiner AP, Thornton TA, Browning SR. Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587682. [PMID: 38617337 PMCID: PMC11014513 DOI: 10.1101/2024.04.02.587682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
Principal component analysis (PCA) is widely used to control for population structure in genome-wide association studies (GWAS). Top principal components (PCs) typically reflect population structure, but challenges arise in deciding how many PCs are needed and ensuring that PCs do not capture other artifacts such as regions with atypical linkage disequilibrium (LD). In response to the latter, many groups suggest performing LD pruning or excluding known high LD regions prior to PCA. However, these suggestions are not universally implemented and the implications for GWAS are not fully understood, especially in the context of admixed populations. In this paper, we investigate the impact of pre-processing and the number of PCs included in GWAS models in African American samples from the Women's Women's Health Initiative SNP Health Association Resource and two Trans-Omics for Precision Medicine Whole Genome Sequencing Project contributing studies (Jackson Heart Study and Genetic Epidemiology of Chronic Obstructive Pulmonary Disease Study). In all three samples, we find the first PC is highly correlated with genome-wide ancestry whereas later PCs often capture local genomic features. The pattern of which, and how many, genetic variants are highly correlated with individual PCs differs from what has been observed in prior studies focused on European populations and leads to distinct downstream consequences: adjusting for such PCs yields biased effect size estimates and elevated rates of spurious associations due to the phenomenon of collider bias. Excluding high LD regions identified in previous studies does not resolve these issues. LD pruning proves more effective, but the optimal choice of thresholds varies across datasets. Altogether, our work highlights unique issues that arise when using PCA to control for ancestral heterogeneity in admixed populations and demonstrates the importance of careful pre-processing and diagnostics to ensure that PCs capturing multiple local genomic features are not included in GWAS models.
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Affiliation(s)
- Kelsey E. Grinde
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, 55105, USA
| | - Brian L. Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Alexander P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, 98195, USA
| | - Timothy A. Thornton
- Regeneron Genetics Center, Tarrytown, New York, 10591, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
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7
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McNamee M, Anderson LC, Borry P, Camporesi S, Derman W, Holm S, Knox TR, Leuridan B, Loland S, Lopez Frias FJ, Lorusso L, Malcolm D, McArdle D, Partridge B, Schramme T, Weed M. Sport-related concussion research agenda beyond medical science: culture, ethics, science, policy. JOURNAL OF MEDICAL ETHICS 2024:jme-2022-108812. [PMID: 36868564 DOI: 10.1136/jme-2022-108812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The Concussion in Sport Group guidelines have successfully brought the attention of brain injuries to the global medical and sport research communities, and has significantly impacted brain injury-related practices and rules of international sport. Despite being the global repository of state-of-the-art science, diagnostic tools and guides to clinical practice, the ensuing consensus statements remain the object of ethical and sociocultural criticism. The purpose of this paper is to bring to bear a broad range of multidisciplinary challenges to the processes and products of sport-related concussion movement. We identify lacunae in scientific research and clinical guidance in relation to age, disability, gender and race. We also identify, through multidisciplinary and interdisciplinary analysis, a range of ethical problems resulting from conflicts of interest, processes of attributing expertise in sport-related concussion, unjustifiably narrow methodological control and insufficient athlete engagement in research and policy development. We argue that the sport and exercise medicine community need to augment the existing research and practice foci to understand these problems more holistically and, in turn, provide guidance and recommendations that help sport clinicians better care for brain-injured athletes.
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Affiliation(s)
- Mike McNamee
- Department of Movement Sciences, KU Leuven, Leuven, Belgium
- School of Sport and Exercise Sciences, Swansea University, Swansea, UK
| | | | - Pascal Borry
- Department of Public Health and Primary Care, Leuven, Leuven, Belgium
| | - Silvia Camporesi
- Global Health & Social Medicine, King's College London, London, UK
- Department of Political Sciences, University of Vienna, Wien, Austria
| | - Wayne Derman
- Institute of Sport & Exercise Medicine, Dept of Exercise, Sport & Lifestyle Medicine, Facuty of Medicine & Health Science, Stellenbosch University, Stellenbosch, South Africa
- IOC Research Center, Stellenbosch, South Africa
| | - Soren Holm
- Centre for Social Ethics and Policy, University of Manchester, Manchester, UK
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
| | | | - Bert Leuridan
- Centre for Philosophical Psychology, University of Antwerp, Antwerpen, Belgium
| | - Sigmund Loland
- Department of Sport and Social Sciences, Norwegian School of Sports Sciences, Oslo, Norway
| | | | - Ludovica Lorusso
- Departament de Psicologia Social, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Dominic Malcolm
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | | | - Brad Partridge
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Thomas Schramme
- Department of Philosophy, University of Liverpool Faculty of Humanities and Social Sciences, Liverpool, UK
| | - Mike Weed
- Centre for Sport, Physical Education & Activity Research (spear), Canterbury Christ Church University, Canterbury, UK
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8
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Astore C, Sharma S, Nagpal S, Cutler DJ, Rioux JD, Cho JH, McGovern DPB, Brant SR, Kugathasan S, Jordan IK, Gibson G. The role of admixture in the rare variant contribution to inflammatory bowel disease. Genome Med 2023; 15:97. [PMID: 37968638 PMCID: PMC10647102 DOI: 10.1186/s13073-023-01244-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/10/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Identification of rare variants involved in complex, polygenic diseases like Crohn's disease (CD) has accelerated with the introduction of whole exome/genome sequencing association studies. Rare variants can be used in both diagnostic and therapeutic assessments; however, since they are likely to be restricted to specific ancestry groups, their contributions to risk assessment need to be evaluated outside the discovery population. Prior studies implied that the three known rare variants in NOD2 are absent in West African and Asian populations and only contribute in African Americans via admixture. METHODS Whole genome sequencing (WGS) data from 3418 African American individuals, 1774 inflammatory bowel disease (IBD) cases, and 1644 controls were used to assess odds ratios and allele frequencies (AF), as well as haplotype-specific ancestral origins of European-derived CD variants discovered in a large exome-wide association study. Local and global ancestry was performed to assess the contribution of admixture to IBD contrasting European and African American cohorts. RESULTS Twenty-five rare variants associated with CD in European discovery cohorts are typically five-fold lower frequency in African Americans. Correspondingly, where comparisons could be made, the rare variants were found to have a predicted four-fold reduced burden for IBD in African Americans, when compared to European individuals. Almost all of the rare CD European variants were found on European haplotypes in the African American cohort, implying that they contribute to disease risk in African Americans primarily due to recent admixture. In addition, proportion of European ancestry correlates the number of rare CD European variants each African American individual carry, as well as their polygenic risk of disease. Similar findings were observed for 23 mutations affecting 10 other common complex diseases for which the rare variants were discovered in European cohorts. CONCLUSIONS European-derived Crohn's disease rare variants are even more rare in African Americans and contribute to disease risk mainly due to admixture, which needs to be accounted for when performing cross-ancestry genetic assessments.
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Affiliation(s)
- Courtney Astore
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Shivam Sharma
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Sini Nagpal
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, QC, H1Y3N1, Canada
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dermot P B McGovern
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08554, USA
- Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, 21287, USA
| | - Steven R Brant
- Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - I King Jordan
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Greg Gibson
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA.
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9
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Cai R, Browning BL, Browning SR. Identity-by-descent-based estimation of the X chromosome effective population size with application to sex-specific demographic history. G3 (BETHESDA, MD.) 2023; 13:jkad165. [PMID: 37497617 PMCID: PMC10542559 DOI: 10.1093/g3journal/jkad165] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
The effective size of a population (Ne) in the recent past can be estimated through analysis of identity-by-descent (IBD) segments. Several methods have been developed for estimating Ne from autosomal IBD segments, but no such effort has been made with X chromosome IBD segments. In this work, we propose a method to estimate the X chromosome effective population size from X chromosome IBD segments. We show how to use the estimated autosome Ne and X chromosome Ne to estimate the female and male effective population sizes. We demonstrate the accuracy of our autosome and X chromosome Ne estimation with simulated data. We find that the estimated female and male effective population sizes generally reflect the simulated sex-specific effective population sizes across the past 100 generations but that short-term differences between the estimated sex-specific Ne across tens of generations may not reliably indicate true sex-specific differences. We analyzed the effective size of populations represented by samples of sequenced UK White British and UK Indian individuals from the UK Biobank.
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Affiliation(s)
- Ruoyi Cai
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
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10
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Hansen Wheat C, Larsson L, Berner P, Temrin H. Commentary by Gácsi et al. (2023) highlights general misconceptions within the field of dog domestication and dog-wolf comparisons. Ecol Evol 2023; 13:e10466. [PMID: 37736276 PMCID: PMC10509154 DOI: 10.1002/ece3.10466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
| | - Linn Larsson
- Department of ZoologyStockholm UniversityStockholmSweden
| | | | - Hans Temrin
- Department of ZoologyStockholm UniversityStockholmSweden
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11
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Ray NR, Ayodele T, Jean-Francois M, Baez P, Fernandez V, Bradley J, Crane PK, Dalgard CL, Kuzma A, Nicaretta H, Sims R, Williams J, Cuccaro ML, Pericak-Vance MA, Mayeux R, Wang LS, Schellenberg GD, Cruchaga C, Beecham GW, Reitz C. The Early-Onset Alzheimer's Disease Whole-Genome Sequencing Project: Study design and methodology. Alzheimers Dement 2023; 19:4187-4195. [PMID: 37390458 PMCID: PMC10527497 DOI: 10.1002/alz.13370] [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: 02/07/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations, resulting in a lack of understanding of its molecular etiology. METHODS Whole-genome sequencing and harmonization of clinical, neuropathological, and biomarker data of over 5000 EOAD cases of diverse ancestries. RESULTS A publicly available genomics resource for EOAD with extensive harmonized phenotypes. Primary analysis will (1) identify novel EOAD risk loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. DISCUSSION This novel resource complements over 50,000 control and late-onset AD samples generated through the Alzheimer's Disease Sequencing Project (ADSP). The harmonized EOAD/ADSP joint call will be available through upcoming ADSP data releases and will allow for additional analyses across the full onset range. HIGHLIGHTS Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations. This results in a significant lack of understanding of the molecular etiology of this devastating form of the disease. The Early-Onset Alzheimer's Disease Whole-genome Sequencing Project is a collaborative initiative to generate a large-scale genomics resource for early-onset Alzheimer's disease with extensive harmonized phenotype data. Primary analyses are designed to (1) identify novel EOAD risk and protective loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. The harmonized genomic and phenotypic data from this initiative will be available through NIAGADS.
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Affiliation(s)
- Nicholas R. Ray
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Temitope Ayodele
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Penelope Baez
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Victoria Fernandez
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Joseph Bradley
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Paul K. Crane
- Division of General Internal Medicine, University of
Washington, Seattle, WA 98195, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics,
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Uniformed Services University
of the Health Sciences, Bethesda, MD 20814, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Heather Nicaretta
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Julie Williams
- UK Dementia Research Institute, Cardiff University,
Cardiff CF10 3AT, UK
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Gary W. Beecham
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
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12
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Moorjani P, Hellenthal G. Methods for Assessing Population Relationships and History Using Genomic Data. Annu Rev Genomics Hum Genet 2023; 24:305-332. [PMID: 37220313 PMCID: PMC11040641 DOI: 10.1146/annurev-genom-111422-025117] [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] [Indexed: 05/25/2023]
Abstract
Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.
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Affiliation(s)
- Priya Moorjani
- Department of Molecular and Cell Biology and Center for Computational Biology, University of California, Berkeley, California, USA;
| | - Garrett Hellenthal
- UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom;
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13
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Chen S, Sarasua SM, Davis NJ, DeLuca JM, Thielke SM, Yu CE. Weight Loss Is a Strong Predictor of Memory Disorder Independent of Genetic Influences. Genes (Basel) 2023; 14:1563. [PMID: 37628615 PMCID: PMC10454755 DOI: 10.3390/genes14081563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Past studies identified a link between weight loss and dementia, but lacked consistent conclusions. We sought to establish this link by examining the weight change profiles before and after dementia diagnosis. METHODS Using data from the Health and Retirement Study (1996-2020), we examined 13,123 participants. We conducted a nested case-control analysis to assess differences in biennial weight change profile while controlling for BMI, longevity polygenic risk scores, and APOE gene variants. RESULTS Participants with a memory disorder lost weight (-0.63%) biennially, whereas those without a diagnosis did not (+0.013%, p-value < 0.0001). Our case-control study shows a significant difference (p-value < 0.01) in pre-dementia % weight changes between the cases (-0.29%) and controls (0.19%), but not in post-dementia weight changes. The weight loss group have the highest risk (OR = 2.01; p-value < 0.0001) of developing a memory disorder compared to the stable weight and weight gain groups. The observations hold true after adjusting for BMI, longevity polygenic risk scores, and APOE variant in a multivariable model. CONCLUSIONS We observe that weight loss in dementia is a physiological process independent of genetic factors associated with BMI and longevity. Pre-dementia weight loss may be an important prognostic criterion to assess a person's risk of developing a memory disorder.
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Affiliation(s)
- Sunny Chen
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, Seattle, WA 98108, USA;
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (S.M.S.); (N.J.D.); (J.M.D.)
| | - Sara M. Sarasua
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (S.M.S.); (N.J.D.); (J.M.D.)
| | - Nicole J. Davis
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (S.M.S.); (N.J.D.); (J.M.D.)
| | - Jane M. DeLuca
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (S.M.S.); (N.J.D.); (J.M.D.)
| | - Stephen M. Thielke
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA;
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, Seattle, WA 98108, USA;
- Department of Medicine, Division of Gerontology and Geriatric Medicine, University of Washington, Seattle, WA 98195, USA
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14
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Simon SS, Brucki SMD, Fonseca LM, Becker J, Cappi C, Marques AH, Heyn PC, Gonçalves PD, Martins SS, Busatto G, Bertola L, Suemoto CK, Nitrini R, Caramelli P, Yassuda MS, Miotto EC, Grinberg LT, Arce Renteria M, Alegria M, Stern Y, Rivera‐Mindt M. The (in)visible Brazilians: A perspective review on the need for brain health and dementia research with Brazilian immigrants in the United States. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12425. [PMID: 37744309 PMCID: PMC10517444 DOI: 10.1002/trc2.12425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/26/2023]
Abstract
Introduction The Brazilian population in the United States (U.S.), a Latinx subgroup, is rapidly growing and aging but remains underrepresented in U.S. health research. In addition to group-specific genetic and environmental risks, Brazilian immigrants and their offspring in the U.S. likely have cumulative risks for health inequities.It is estimated that 71% of Brazilian immigrants in the U.S. are undocumented, which may limit healthcare access/utilization. Furthermore, mental health is reported as a health priority by Brazilian immigrants in the U.S., and there is a lack of research on Alzheimer's disease and related dementia (AD/ADRD) in this population. Methods We reviewed the scientific literature using traditional (e.g., PubMed) sources and databases generated by U.S. and Brazilian governments, as well as international organizations, and press articles. Results This perspective review lists recommendations for researchers, health providers, and policymakers to promote greater inclusion of U.S. Brazilian populations in health research and care. The review identifies research areas in need of attention to address health inequities and promote mental/brain health in Brazilian immigrants and their offspring living in the U.S. These research areas are: 1) epidemiological studies to map the prevalence and incidence of mental/brain health conditions; 2) research on aging and AD/ADRD risk factors among Brazilian populations in the U.S.; and 3) the need for greater representation of U.S-residing Brazilian population in other relevant research areas involving genetics, neuropathology, and clinical trials. Conclusions The recommendation and research efforts proposed should help to pave the way for the development of community-engagement research and to promote mental/brain health education, improvement of mental/brain health and AD/ADRD services, and the development of culturally-informed intervention to the U.S.-residing Brazilian communities. HIGHLIGHTS The Brazilian population in the United States is growing but is underrepresented in U.S. health research.Approximately 71% of Brazilian immigrants in the United States are undocumented, with an increased risk for health inequities.Mental health is reported as a central health priority by Brazilian immigrants in the United States.There is a lack of research on Alzheimer's disease and other dementias (ADRD) in Brazilian immigrants in the United States.Epidemiological research is needed to map the prevalence/incidence of mental health conditions and ADRD risk factors among Brazilian immigrants in the United States.
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Affiliation(s)
- Sharon Sanz Simon
- Cognitive Neuroscience DivisionDepartment of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
- Old Age Research Group, Department of PsychiatryUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
| | | | - Luciana Mascarenhas Fonseca
- Old Age Research Group, Department of PsychiatryUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
- Department of Community and Behavioral HealthElson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Jacqueline Becker
- Division of General Internal MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Carolina Cappi
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Seaver Autism Center for Research and TreatmentIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of PsychiatryClinics HospitalUniversity of São PauloSchool of MedicineSão PauloSão PauloBrazil
| | - Andrea Horvath Marques
- Elliott School International AffairsThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Patricia C. Heyn
- Center for Optimal AgingDepartment of Physical TherapyMarymount UniversityArlingtonVirginiaUSA
| | - Priscila Dib Gonçalves
- Department of EpidemiologyColumbia University Mailman School of Public HealthNew YorkNew YorkUSA
| | - Silvia S. Martins
- Department of EpidemiologyColumbia University Mailman School of Public HealthNew YorkNew YorkUSA
| | - Geraldo Busatto
- Laboratory of Psychiatric Neuroimaging (LIM‐21)Department of PsychiatryUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
| | - Laiss Bertola
- Department of PsychiatryEscola Paulista de Medicina, Universidade Federal de São PauloSão PauloBrazil
| | - Claudia Kimie Suemoto
- Division of GeriatricsDepartment of Clinical MedicineUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
| | - Ricardo Nitrini
- Old Age Research Group, Department of PsychiatryUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
| | - Paulo Caramelli
- Behavioral and Cognitive Neurology Research GroupFaculdade de MedicinaUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrazil
| | - Monica Sanches Yassuda
- Department of NeurologyUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
- Gerontology, School of Arts, Sciences, and HumanitiesUniversity of São PauloSão PauloSão PauloBrazil
| | - Eliane Correa Miotto
- Old Age Research Group, Department of PsychiatryUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
| | - Lea Tenenholz Grinberg
- Memory and Aging CenterDepartment of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Department of PathologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- LIM‐22Department of PathologyUniversity of São Paulo Medical SchoolSão PauloSão PauloBrazil
- Global Brain Health InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Miguel Arce Renteria
- Cognitive Neuroscience DivisionDepartment of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Margarita Alegria
- Disparities Research UnitDepartment of MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
- Department of PsychiatryHarvard Medical SchoolBostonMassachusettsUSA
| | - Yaakov Stern
- Cognitive Neuroscience DivisionDepartment of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of NeurologyColumbia UniversityVagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Monica Rivera‐Mindt
- Department of PsychologyFordham UniversityNew YorkNew YorkUSA
- Department of NeurologyIcahn School of MedicineNew YorkNew YorkUSA
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15
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Matalon DR, Zepeda-Mendoza CJ, Aarabi M, Brown K, Fullerton SM, Kaur S, Quintero-Rivera F, Vatta M. Clinical, technical, and environmental biases influencing equitable access to clinical genetics/genomics testing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100812. [PMID: 37058144 DOI: 10.1016/j.gim.2023.100812] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 04/15/2023] Open
Affiliation(s)
- Dena R Matalon
- Division of Medical Genetics, Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, CA
| | - Cinthya J Zepeda-Mendoza
- Divisions of Hematopathology and Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Stephanie M Fullerton
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA
| | - Shagun Kaur
- Department of Child Health, Phoenix Children's Hospital, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
| | - Fabiola Quintero-Rivera
- Division of Genetic and Genomic Medicine, Departments of Pathology, Laboratory Medicine, and Pediatrics, University of California Irvine, Irvine, CA
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16
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Reitz C, Pericak-Vance MA, Foroud T, Mayeux R. A global view of the genetic basis of Alzheimer disease. Nat Rev Neurol 2023; 19:261-277. [PMID: 37024647 PMCID: PMC10686263 DOI: 10.1038/s41582-023-00789-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
The risk of Alzheimer disease (AD) increases with age, family history and informative genetic variants. Sadly, there is still no cure or means of prevention. As in other complex diseases, uncovering genetic causes of AD could identify underlying pathological mechanisms and lead to potential treatments. Rare, autosomal dominant forms of AD occur in middle age as a result of highly penetrant genetic mutations, but the most common form of AD occurs later in life. Large-scale, genome-wide analyses indicate that 70 or more genes or loci contribute to AD. One of the major factors limiting progress is that most genetic data have been obtained from non-Hispanic white individuals in Europe and North America, preventing the development of personalized approaches to AD in individuals of other ethnicities. Fortunately, emerging genetic data from other regions - including Africa, Asia, India and South America - are now providing information on the disease from a broader range of ethnicities. Here, we summarize the current knowledge on AD genetics in populations across the world. We predominantly focus on replicated genetic discoveries but also include studies in ethnic groups where replication might not be feasible. We attempt to identify gaps that need to be addressed to achieve a complete picture of the genetic and molecular factors that drive AD in individuals across the globe.
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Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Columbia University, New York, NY, USA.
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17
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Daniels RJ, D'Amato ME, Lesaoana M, Kasu M, Ehlers K, Chauke PA, Lecheko P, Challis S, Rockett K, Montinaro F, González-Santos M, Capelli C. Genetic heritage of the Baphuthi highlights an over-ethnicized notion of "Bushman" in the Maloti-Drakensberg, southern Africa. Am J Hum Genet 2023; 110:880-894. [PMID: 37105174 PMCID: PMC10183465 DOI: 10.1016/j.ajhg.2023.03.018] [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: 05/25/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi.
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Affiliation(s)
- Ryan Joseph Daniels
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa.
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa
| | - Mpasi Lesaoana
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa; Lesotho Mounted Police Service, Technical Support Services, Maseru 100, Lesotho
| | - Mohaimin Kasu
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Cape Town 7535, South Africa
| | - Karen Ehlers
- Department of Genetics, University of the Free State, Bloemfontein 9300, South Africa
| | - Paballo Abel Chauke
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Puseletso Lecheko
- Rock Art Research Institute, School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Sam Challis
- Rock Art Research Institute, School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Kirk Rockett
- Wellcome Centre for Human Genomics, Oxford, OX3 7BN Oxfordshire, UK
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, 70124 Bari, Italy
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ Oxfordshire, UK; Dipartimento delle Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, 43121 Parma, Italy.
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18
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Wegmann D, Eckel R. Human evolution: When admixture met selection. Curr Biol 2023; 33:R259-R261. [PMID: 37040705 DOI: 10.1016/j.cub.2023.02.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.
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Affiliation(s)
- Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland.
| | - Raphael Eckel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
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19
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Pfennig A, Petersen LN, Kachambwa P, Lachance J. Evolutionary Genetics and Admixture in African Populations. Genome Biol Evol 2023; 15:evad054. [PMID: 36987563 PMCID: PMC10118306 DOI: 10.1093/gbe/evad054] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.
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Affiliation(s)
- Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | | | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
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20
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Hamid I, Korunes KL, Schrider DR, Goldberg A. Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes. Mol Biol Evol 2023; 40:msad074. [PMID: 36947126 PMCID: PMC10116606 DOI: 10.1093/molbev/msad074] [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: 09/04/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023] Open
Abstract
Gene flow between previously differentiated populations during the founding of an admixed or hybrid population has the potential to introduce adaptive alleles into the new population. If the adaptive allele is common in one source population, but not the other, then as the adaptive allele rises in frequency in the admixed population, genetic ancestry from the source containing the adaptive allele will increase nearby as well. Patterns of genetic ancestry have therefore been used to identify post-admixture positive selection in humans and other animals, including examples in immunity, metabolism, and animal coloration. A common method identifies regions of the genome that have local ancestry "outliers" compared with the distribution across the rest of the genome, considering each locus independently. However, we lack theoretical models for expected distributions of ancestry under various demographic scenarios, resulting in potential false positives and false negatives. Further, ancestry patterns between distant sites are often not independent. As a result, current methods tend to infer wide genomic regions containing many genes as under selection, limiting biological interpretation. Instead, we develop a deep learning object detection method applied to images generated from local ancestry-painted genomes. This approach preserves information from the surrounding genomic context and avoids potential pitfalls of user-defined summary statistics. We find the method is robust to a variety of demographic misspecifications using simulated data. Applied to human genotype data from Cabo Verde, we localize a known adaptive locus to a single narrow region compared with multiple or long windows obtained using two other ancestry-based methods.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC
| | | | - Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC
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21
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Černý V, Priehodová E, Fortes-Lima C. A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism. Genes (Basel) 2023; 14:genes14030758. [PMID: 36981029 PMCID: PMC10048103 DOI: 10.3390/genes14030758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/26/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
This review focuses on the Sahel/Savannah belt, a large region of Africa where two alternative subsistence systems (pastoralism and agriculture), nowadays, interact. It is a long-standing question whether the pastoralists became isolated here from other populations after cattle began to spread into Africa (~8 thousand years ago, kya) or, rather, began to merge with other populations, such as agropastoralists, after the domestication of sorghum and pearl millet (~5 kya) and with the subsequent spread of agriculture. If we look at lactase persistence, a trait closely associated with pastoral lifestyle, we see that its variants in current pastoralists distinguish them from their farmer neighbours. Most other (mostly neutral) genetic polymorphisms do not, however, indicate such clear differentiation between these groups; they suggest a common origin and/or an extensive gene flow. Genetic affinity and ecological symbiosis between the two subsistence systems can help us better understand the population history of this African region. In this review, we show that genomic datasets of modern Sahel/Savannah belt populations properly collected in local populations can complement the still insufficient archaeological research of this region, especially when dealing with the prehistory of mobile populations with perishable material culture and therefore precarious archaeological visibility.
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Affiliation(s)
- Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Letenská 1, 118 01 Prague, Czech Republic
| | - Edita Priehodová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Letenská 1, 118 01 Prague, Czech Republic
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
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22
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Stinson J, McCall C, Dobbs RW, Mistry N, Rosenberg A, Nettey OS, Sharma P, Dixon M, Sweis J, Macias V, Sharifi R, Kittles RA, Kajdacsy-Balla A, Murphy AB. Vitamin D and genetic ancestry are associated with apoptosis rates in benign and malignant prostatic epithelium. Prostate 2023; 83:352-363. [PMID: 36479698 PMCID: PMC9870946 DOI: 10.1002/pros.24467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/18/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE Vitamin D metabolites may be protective against prostate cancer (PCa). We conducted a cross-sectional analysis to evaluate associations between in vivo vitamin D status, genetic ancestry, and degree of apoptosis using prostatic epithelial terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. EXPERIMENTAL DESIGN Benign and tumor epithelial punch biopsies of participants with clinically localized PCa underwent indirect TUNEL staining. Serum levels of 25 hydroxyvitamin D [25(OH)D] and 1,25 dihydroxyvitamin D were assessed immediately before radical prostatectomy; levels of prostatic 25(OH)D were obtained from the specimen once the prostate was extracted. Ancestry informative markers were used to estimate the percentage of genetic West African, Native American, and European ancestry. RESULTS One hundred twenty-one newly diagnosed men, age 40-79, were enrolled between 2013 and 2018. Serum 25(OH)D correlated positively with both tumor (ρ = 0.17, p = 0.03), and benign (ρ = 0.16, p = 0.04) prostatic epithelial TUNEL staining. Similarly, prostatic 25(OH)D correlated positively with both tumor (ρ = 0.31, p < 0.001) and benign (ρ = 0.20, p = 0.03) epithelial TUNEL staining. Only Native American ancestry was positively correlated with tumor (ρ = 0.22, p = 0.05) and benign (ρ = 0.27, p = 0.02) TUNEL staining. In multivariate regression models, increasing quartiles of prostatic 25(OH)D (β = 0.25, p = 0.04) and Native American ancestry (β = 0.327, p = 0.004) were independently associated with tumor TUNEL staining. CONCLUSIONS Physiologic serum and prostatic 25(OH)D levels and Native American ancestry are positively associated with the degree of apoptosis in tumor and benign prostatic epithelium in clinically localized PCa. Vitamin D may have secondary chemoprevention benefits in preventing PCa progression in localized disease.
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Affiliation(s)
- James Stinson
- Division of Urology, Cook County Health and Hospitals System, Chicago IL
| | - Cordero McCall
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Ryan W. Dobbs
- Division of Urology, Cook County Health and Hospitals System, Chicago IL
| | - Neil Mistry
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Adrian Rosenberg
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Oluwarotimi S. Nettey
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Pooja Sharma
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Michael Dixon
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Jamila Sweis
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Virgilia Macias
- Department of Pathology, University of Illinois at Chicago School of Medicine, Chicago IL
| | | | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Cancer Center, Duarte CA
| | - Andre Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago School of Medicine, Chicago IL
| | - Adam B. Murphy
- Division of Urology, Cook County Health and Hospitals System, Chicago IL
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago IL
- Section of Urology, Jesse Brown VA Medical Center, Chicago IL
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23
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Micheletti SJ, Ancona Esselmann SG, Bryc K, Mountain JL. Response to Pfenning and Lachance. Am J Hum Genet 2023; 110:368-369. [PMID: 36736294 PMCID: PMC9943716 DOI: 10.1016/j.ajhg.2022.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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24
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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25
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Samtal C, El Jaddaoui I, Hamdi S, Bouguenouch L, Ouldim K, Nejjari C, Ghazal H, Bekkari H. Review of prostate cancer genomic studies in Africa. Front Genet 2022; 13:911101. [PMID: 36303548 PMCID: PMC9593051 DOI: 10.3389/fgene.2022.911101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/28/2022] [Indexed: 09/07/2024] Open
Abstract
Prostate cancer (PCa) is the second most commonly diagnosed in men worldwide and one of the most frequent cancers in men in Africa. The heterogeneity of this cancer fosters the need to identify potential genetic risk factors/biomarkers. Omics variations may significantly contribute to early diagnosis and personalized treatment. However, there are few genomic studies of this disease in African populations. This review sheds light on the status of genomics research on PCa in Africa and outlines the common variants identified thus far. The allele frequencies of the most significant SNPs in Afro-native, Afro-descendants, and European populations were compared. We advocate how these few but promising data will aid in understanding, better diagnosing, and precisely treating this cancer and the need for further collaborative research on the genomics of PCa in the African continent.
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Affiliation(s)
- Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz–Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Islam El Jaddaoui
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Salsabil Hamdi
- Laboratory of Environmental Health, Institut Pasteur Maroc, Casablanca, Morocco
| | - Laila Bouguenouch
- Faculty of Medicine, Pharmacy and Dentistry‒Sidi Mohammed Ben Abdellah University, University Hospital Hassan II, Fez, Morocco
| | - Karim Ouldim
- Faculty of Medicine, Pharmacy and Dentistry‒Sidi Mohammed Ben Abdellah University, University Hospital Hassan II, Fez, Morocco
| | - Chakib Nejjari
- Department of Medicine, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- School of Medicine and Pharmacy, Fes, Morocco
| | - Hassan Ghazal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz–Sidi Mohammed Ben Abdellah University, Fez, Morocco
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences, Casablanca, Morocco
- National Center for Scientific and Technical Research, Rabat, Morocco
| | - Hicham Bekkari
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz–Sidi Mohammed Ben Abdellah University, Fez, Morocco
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26
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Oill AMT, Handley C, Howell EK, Stone AC, Mathew S, Wilson MA. Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 178:488-503. [PMID: 36790743 PMCID: PMC9949739 DOI: 10.1002/ajpa.24521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/04/2022] [Accepted: 02/21/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES The aim of this study was to characterize the genetic relationships within and among four neighboring ethnolinguistic groups in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. MATERIALS AND METHODS We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. RESULTS Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. DISCUSSION Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.
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Affiliation(s)
- Angela M. Taravella Oill
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA
| | - Carla Handley
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA
| | - Emma K. Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA,Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| | - Sarah Mathew
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287 USA,Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA,Co-corresponding authors
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287 USA,Co-corresponding authors
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27
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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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/24/2022] [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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28
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Asiimwe IG, Pirmohamed M. Ethnic Diversity and Warfarin Pharmacogenomics. Front Pharmacol 2022; 13:866058. [PMID: 35444556 PMCID: PMC9014219 DOI: 10.3389/fphar.2022.866058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
Warfarin has remained the most commonly prescribed vitamin K oral anticoagulant worldwide since its approval in 1954. Dosing challenges including having a narrow therapeutic window and a wide interpatient variability in dosing requirements have contributed to making it the most studied drug in terms of genotype-phenotype relationships. However, most of these studies have been conducted in Whites or Asians which means the current pharmacogenomics evidence-base does not reflect ethnic diversity. Due to differences in minor allele frequencies of key genetic variants, studies conducted in Whites/Asians may not be applicable to underrepresented populations such as Blacks, Hispanics/Latinos, American Indians/Alaska Natives and Native Hawaiians/other Pacific Islanders. This may exacerbate health inequalities when Whites/Asians have better anticoagulation profiles due to the existence of validated pharmacogenomic dosing algorithms which fail to perform similarly in the underrepresented populations. To examine the extent to which individual races/ethnicities are represented in the existing body of pharmacogenomic evidence, we review evidence pertaining to published pharmacogenomic dosing algorithms, including clinical utility studies, cost-effectiveness studies and clinical implementation guidelines that have been published in the warfarin field.
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Affiliation(s)
- Innocent G Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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29
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Shen H, Feldman MW. Diversity and its causes: Lewontin on racism, biological determinism and the adaptationist programme. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200417. [PMID: 35430891 PMCID: PMC9014190 DOI: 10.1098/rstb.2020.0417] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lewontin's 1972 paper (RC Lewontin, 1972 The apportionment of human diversity, in Evolutionary biology, vol. 6 (eds T Dobzhansky, MK Hecht, WC Steere), pp. 381–398) can be viewed as one foray in his battle against biological determinism. Our paper shows where Lewontin, The apportionment of human diversity, fits in the debate over human classification that it stimulated. We outline three assumptions inherent in the biological deterministic view of human phenotypic diversity and show how the 1972 paper, as well as Lewontin's papers in 1970 and 1974 on the problems with the heritability statistic and his 1979 criticism of naive pan-selectionism, invalidate these assumptions. These papers were crucial components of his campaign against biological determinism and the racism with which it was associated. In the current climate of widespread racism and the rise of sociogenomics, it is important to revisit Lewontin's writings and to disseminate the messages they contain. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Hao Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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30
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Barton JC, Wiener HW, Acton RT. Estimates of West African Ancestry in African Americans Using Alleles of Iron-Related Genes HJV, SLC40A1, and TFR2. Genet Test Mol Biomarkers 2022; 26:96-102. [PMID: 35225679 DOI: 10.1089/gtmb.2021.0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Few studies have estimated African ancestry of African Americans (AA). In sub-Saharan West African (WA) Blacks, some nonancestral alleles of iron-related genes HJV, SLC40A1, and TFR2 are common, whereas in European Americans (EA) the same alleles are rare. These alleles have not been used to estimate WA Black ancestry in AA. Methods: We estimated WA Black ancestry in AA (M) using published HJV c.929C>G (rs7540883), SLC40A1 c.744G>T (rs11568350), and TFR2 c.713C>T (rs34242818) allele frequencies in WA Blacks, AA, and EA. We computed standard error (SE) and one-sided 95% confidence intervals (CI) for each M. Results: The combined representation of WA Blacks from The Gambia and Nigeria was 79-89%. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in WA Blacks were 0.1025 [95% CI: 0.0835-0.1253] (n = 405), 0.0517 [0.0469-0.0569] (n = 3839), and 0.1432 [0.1202-0.1697] (n = 405), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in AA were 0.0718 [0.0648-0.0797] (n = 2352), 0.0557 [0.0506-0.0613] (n = 3590), and 0.1224 [0.1132-0.1322] (n = 2352), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in 4449 EA were 0.0002 [0-0.0009], 0.0003 [0.0001-0.0010], and 0.0004 [0.0001-0.0012], respectively. M (SE [one-sided 95% CI]) for HJV, SLC40A1, and TFR2 alleles was 0.7006 (0.0818 [0.5402-1.0000]), 1.0000 (0.0752 [0.9306-1.0000]), and 0.8546 (0.0810 [0.6959-1.0000]), respectively. Mean of these M is 0.8777 (87.8%). Conclusions: The mean proportional WA Black ancestry in AA of 87.8% using HJV c.929C>G, SLC40A1 c.744G>T, and TFR2 c.713C>T allele frequencies is consistent with that of previous studies that used other autosomal markers and methods.
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Affiliation(s)
- James C Barton
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Southern Iron Disorders Center, Birmingham, Alabama, USA
| | - Howard W Wiener
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ronald T Acton
- Southern Iron Disorders Center, Birmingham, Alabama, USA.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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31
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Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent. Genes (Basel) 2022; 13:genes13020220. [PMID: 35205264 PMCID: PMC8871784 DOI: 10.3390/genes13020220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
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Shahian DM, Badhwar V, O'Brien SM, Habib RH, Han J, McDonald DE, Antman MS, Higgins RSD, Preventza O, Estrera AL, Calhoon JH, Grondin SC, Cooke DT. Social Risk Factors in Society of Thoracic Surgeons Risk Models Part 1: Concepts, Indicator Variables, and Controversies. Ann Thorac Surg 2022; 113:1703-1717. [PMID: 34998732 DOI: 10.1016/j.athoracsur.2021.11.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/01/2022]
Affiliation(s)
- David M Shahian
- Division of Cardiac Surgery, Department of Surgery, and Center for Quality and Safety, Massachusetts General Hospital and Harvard Medical School, Boston, MA.
| | - Vinay Badhwar
- Department of Cardiovascular and Thoracic Surgery, West Virginia University, Morgantown WV
| | | | | | - Jane Han
- Society of Thoracic Surgeons, Chicago, IL
| | | | | | - Robert S D Higgins
- Johns Hopkins University School of Medicine and Johns Hopkins Hospital, Baltimore, MD
| | - Ourania Preventza
- Baylor College of Medicine, Texas Heart Institute, Baylor St. Luke's Medical Center, Houston, TX
| | - Anthony L Estrera
- McGovern Medical School at UTHealth; Memorial Hermann Heart and Vascular Institute; Houston, TX
| | - John H Calhoon
- Department of Cardiothoracic Surgery, University of Texas Health Science Center at San Antonio
| | - Sean C Grondin
- Cumming School of Medicine, University of Calgary, and Foothills Medical Centre, Calgary, Alberta, Canada
| | - David T Cooke
- Division of General Thoracic Surgery, UC Davis Health, Sacramento, CA
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Noren Hooten N, Pacheco NL, Smith JT, Evans MK. The accelerated aging phenotype: The role of race and social determinants of health on aging. Ageing Res Rev 2022; 73:101536. [PMID: 34883202 PMCID: PMC10862389 DOI: 10.1016/j.arr.2021.101536] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
Abstract
The pursuit to discover the fundamental biology and mechanisms of aging within the context of the physical and social environment is critical to designing interventions to prevent and treat its complex phenotypes. Aging research is critically linked to understanding health disparities because these inequities shape minority aging, which may proceed on a different trajectory than the overall population. Health disparities are characteristically seen in commonly occurring age-associated diseases such as cardiovascular and cerebrovascular disease as well as diabetes mellitus and cancer. The early appearance and increased severity of age-associated disease among African American and low socioeconomic status (SES) individuals suggests that the factors contributing to the emergence of health disparities may also induce a phenotype of 'premature aging' or 'accelerated aging' or 'weathering'. In marginalized and low SES populations with high rates of early onset age-associated disease the interaction of biologic, psychosocial, socioeconomic and environmental factors may result in a phenotype of accelerated aging biologically similar to premature aging syndromes with increased susceptibility to oxidative stress, premature accumulation of oxidative DNA damage, defects in DNA repair and higher levels of biomarkers of oxidative stress and inflammation. Health disparities, therefore, may be the end product of this complex interaction in populations at high risk. This review will examine the factors that drive both health disparities and the accelerated aging phenotype that ultimately contributes to premature mortality.
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Affiliation(s)
- Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jessica T Smith
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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Kinesin Family Member C1 (KIFC1/HSET): A Potential Actionable Biomarker of Early Stage Breast Tumorigenesis and Progression of High-Risk Lesions. J Pers Med 2021; 11:jpm11121361. [PMID: 34945833 PMCID: PMC8708236 DOI: 10.3390/jpm11121361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
The enigma of why some premalignant or pre-invasive breast lesions transform and progress while others do not remains poorly understood. Currently, no radiologic or molecular biomarkers exist in the clinic that can successfully risk-stratify high-risk lesions for malignant transformation or tumor progression as well as serve as a minimally cytotoxic actionable target for at-risk subpopulations. Breast carcinogenesis involves a series of key molecular deregulatory events that prompt normal cells to bypass tumor-suppressive senescence barriers. Kinesin family member C1 (KIFC1/HSET), which confers survival of cancer cells burdened with extra centrosomes, has been observed in premalignant and pre-invasive lesions, and its expression has been shown to correlate with increasing neoplastic progression. Additionally, KIFC1 has been associated with aggressive breast tumor molecular subtypes, such as basal-like and triple-negative breast cancers. However, the role of KIFC1 in malignant transformation and its potential as a predictive biomarker of neoplastic progression remain elusive. Herein, we review compelling evidence suggesting the involvement of KIFC1 in enabling pre-neoplastic cells to bypass senescence barriers necessary to become immortalized and malignant. We also discuss evidence inferring that KIFC1 levels may be higher in premalignant lesions with a greater inclination to transform and acquire aggressive tumor intrinsic subtypes. Collectively, this evidence provides a strong impetus for further investigation into KIFC1 as a potential risk-stratifying biomarker and minimally cytotoxic actionable target for high-risk patient subpopulations.
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Christian LM, Cole SW, McDade T, Pachankis JE, Morgan E, Strahm AM, Kamp Dush CM. A biopsychosocial framework for understanding sexual and gender minority health: A call for action. Neurosci Biobehav Rev 2021; 129:107-116. [PMID: 34097981 PMCID: PMC8429206 DOI: 10.1016/j.neubiorev.2021.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 12/29/2022]
Abstract
The number of US adults identifying as lesbian, gay, bisexual, transgender, or a different sexual identity has doubled since 2008, and about 40 % of the sexual and gender minority population identify as people of color. Minority stress theory posits that sexual and gender minorities are at particular risk for stress via stigma and discrimination at the structural, interpersonal, and individual levels. This stress, in turn, elevates the risk of adverse health outcomes across several domains. However, there remains a conspicuously limited amount of research on the psychoneuroimmunology of stress among sexual and gender minorities. We developed the Biopsychosocial Minority Stress Framework which posits that sexual minority status leads to unique experiences of minority stress which results in adverse health behavioral factors, elevated psychological distress and sleep disturbance, and immune dysregulation. Moderators in the model include both individual differences and intersectional identities. There is a crucial need to understand the biological-psychological axis of stress among the increasingly visible sexual and gender minority population to increase their health, longevity, and quality of life.
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Affiliation(s)
- Lisa M Christian
- Department of Psychiatry & Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; The Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| | - Steve W Cole
- Department of Psychiatry & Biobehavioral Sciences and Medicine, UCLA School of Medicine, Los Angeles, CA, USA
| | - Thomas McDade
- Department of Anthropology, Northwestern University, Evanston, IL, USA; Institute for Policy Research, Northwestern University, Evanston, IL, USA; Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - John E Pachankis
- Yale School of Public Health, New Haven, CT, USA; Center for Interdisciplinary Research on AIDS, Yale School of Public Health, New Haven, CT, USA
| | - Ethan Morgan
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Anna M Strahm
- Department of Psychiatry & Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; The Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Claire M Kamp Dush
- Minnesota Population Center, University of Minnesota, Minneapolis, MN, USA; Department of Sociology, University of Minnesota, Minneapolis, MN, USA
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Shi G, Kuang Q. Ancestral Spectrum Analysis With Population-Specific Variants. Front Genet 2021; 12:724638. [PMID: 34646302 PMCID: PMC8503515 DOI: 10.3389/fgene.2021.724638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
With the advance of sequencing technology, an increasing number of populations have been sequenced to study the histories of worldwide populations, including their divergence, admixtures, migration, and effective sizes. The variants detected in sequencing studies are largely rare and mostly population specific. Population-specific variants are often recent mutations and are informative for revealing substructures and admixtures in populations; however, computational methods and tools to analyze them are still lacking. In this work, we propose using reference populations and single nucleotide polymorphisms (SNPs) specific to the reference populations. Ancestral information, the best linear unbiased estimator (BLUE) of the ancestral proportion, is proposed, which can be used to infer ancestral proportions in recently admixed target populations and measure the extent to which reference populations serve as good proxies for the admixing sources. Based on the same panel of SNPs, the ancestral information is comparable across samples from different studies and is not affected by genetic outliers, related samples, or the sample sizes of the admixed target populations. In addition, ancestral spectrum is useful for detecting genetic outliers or exploring co-ancestry between study samples and the reference populations. The methods are implemented in a program, Ancestral Spectrum Analyzer (ASA), and are applied in analyzing high-coverage sequencing data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP). In the analyses of American populations from the 1000 Genomes Project, we demonstrate that recent admixtures can be dissected from ancient admixtures by comparing ancestral spectra with and without indigenous Americans being included in the reference populations.
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Affiliation(s)
- Gang Shi
- State Key Laboratory of Integrated Services Networks, Xidian University, Xi’an, China
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Lang CCV, Renert-Yuval Y, Del Duca E, Pavel AB, Wu J, Zhang N, Dubin C, Obi A, Chowdhoury M, Kim M, Estrada YD, Krueger JG, Kaderbhai H, Semango G, Schmid-Grendelmeier P, Brüggen MC, Masenga JE, Guttman-Yassky E. Immune and barrier characterization of atopic dermatitis skin phenotype in Tanzanian patients. Ann Allergy Asthma Immunol 2021; 127:334-341. [PMID: 33975024 PMCID: PMC11344219 DOI: 10.1016/j.anai.2021.04.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is a common disease, with particularly high prevalence found in Africa. It is increasingly recognized that patients with AD of different ethnic backgrounds have unique molecular signatures in the skin, potentially accounting for treatment response variations. Nevertheless, the skin profile of patients with AD from Africa is unknown, hindering development of new treatments targeted to this patient population. OBJECTIVE To characterize the skin profile of patients with AD from Africa. METHODS Gene expression studies, including RNA sequencing (using threshold of fold change of >2 and false discovery rate of <0.05) and real-time polymerase chain reaction, were performed on skin biopsies of Tanzanian patients with moderate-to-severe AD and controls. RESULTS Tanzanian AD skin presented robust up-regulations of multiple key mediators of both T helper 2 (TH2) (interleukin 13 [IL-13], IL-10, IL-4R, CCL13,CCL17,CCL18,CCL26) and TH22 (IL22, S100As) pathways. Markers related to TH17 and IL-23 (IL-17A, IL-23A, IL-12, PI3, DEFB4B) and TH1 (interferon gamma, CXCL9,CXCL10,CXCL11) were also significantly overexpressed in AD tissues (FDR<.05), albeit to a lesser extent. IL-36 isoforms revealed substantial up-regulations in African skin. The barrier fingerprint of Tanzanian AD revealed no suppression of hallmark epidermal barrier differentiation genes, such as filaggrin, loricrin, and periplakin, with robust attenuation of lipid metabolism genes (ie, AWAT1). CONCLUSION The skin phenotype of Tanzanian patients with AD is consistent with that of African Americans, exhibiting dominant TH2 and TH22 skewing, minimal dysregulation of terminal differentiation, and even broader attenuation of lipid metabolism-related products. These data highlight the unique characteristic of AD in Black individuals and the need to develop unique treatments targeting patients with AD from these underrepresented populations.
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Affiliation(s)
- Claudia C V Lang
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Dermatology, University Hospital Zürich, Zürich, Switzerland
| | - Yael Renert-Yuval
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York
| | - Ester Del Duca
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Dermatology, University of Magna Graecia, Catanzaro, Italy
| | - Ana B Pavel
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Biomedical Engineering, University of Mississippi, Oxford, Mississippi
| | - Jianni Wu
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ning Zhang
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celina Dubin
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ashley Obi
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mashkura Chowdhoury
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Madeline Kim
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yeriel D Estrada
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York
| | - Hashim Kaderbhai
- Department of Dermatology, M.P. Shah Hospital, Nairobi, Kenya; Department of Dermatology, Regional Dermatology Training Center, Moshi, Tanzania
| | - George Semango
- Department of Dermatology, Regional Dermatology Training Center, Moshi, Tanzania
| | | | - Marie-Charlotte Brüggen
- Department of Dermatology, University Hospital Zürich, Zürich, Switzerland; Hochgebirgsklinik Davos, Davos, Switzerland
| | - John E Masenga
- Department of Dermatology, Regional Dermatology Training Center, Moshi, Tanzania
| | - Emma Guttman-Yassky
- Laboratory of Inflammatory Skin Diseases, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York.
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Millogo M, Soubeiga ST, Bazie BVJT, Zohoncon TM, Ouattara AK, Yonli AT, Simpore J. Disputed paternity presumption in Burkina Faso: determination of the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays. J Genet Eng Biotechnol 2021; 19:130. [PMID: 34459998 PMCID: PMC8405726 DOI: 10.1186/s43141-021-00221-3] [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: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 12/04/2022]
Abstract
BACKGROUND In resource-limited countries, ABO, HLA, MNS, Kells, and hemoglobin electrophoresis are classic tests for the resolution of paternity disputes due to their affordable cost. The limitations of these tests in cases of disputed paternity require the use of Short Tandem Repeats (STR) for their certification. This study aimed to determine the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays in Burkina Faso, West Africa. RESULTS Of the fourteen trios studied, the ABO-rhesus/hemoglobin electrophoresis analysis revealed ten probable inclusion cases, three exclusion cases, and one undetermined paternity. DNA STR analysis found five inclusions of paternity out of the ten probable inclusions with ABO-rhesus/hemoglobin electrophoresis assay versus nine exclusions of paternity. CONCLUSION This study showed that the implementation of the analysis of short tandem repeat is required to resolve increasing disputed filiation cases in Burkina Faso.
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Affiliation(s)
- Missa Millogo
- Direction of Scientific and Technical Police, Ouagadougou, Burkina Faso
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
| | - Serge Theophile Soubeiga
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso.
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso.
- Research Institute of Health Sciences (IRSS)), P.O. 03. BOX 7192, Ouagadougou, Ouaga 03, Burkina Faso.
| | - Bapio Valerie Jean Telesphore Bazie
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso
- Research Institute of Applied and Technical Sciences (IRSAT)), P.O. 03 BOX 7047, Ouagadougou, Ouaga 03, Burkina Faso
| | - Theodora Mahoukede Zohoncon
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso
- University of Saint Thomas d'Aquin (USTA)), P.O. 06 BOX 10212, Ouagadougou, Ouaga 06, Burkina Faso
| | - Abdoul Karim Ouattara
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso
| | - Albert Theophane Yonli
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LABIOGENE) of University Joseph Ki-Zerbo, P.O. 03 BOX, 7021 Ouaga 03, Ouagadougou, Burkina Faso
- Biomolecular Research Centre Pietro Annigoni (CERBA)), P.O. 01 BOX 364, Ouagadougou, Ouaga 01, Burkina Faso
- University of Saint Thomas d'Aquin (USTA)), P.O. 06 BOX 10212, Ouagadougou, Ouaga 06, Burkina Faso
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Wamai RG, Hirsch JL, Van Damme W, Alnwick D, Bailey RC, Hodgins S, Alam U, Anyona M. What Could Explain the Lower COVID-19 Burden in Africa despite Considerable Circulation of the SARS-CoV-2 Virus? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8638. [PMID: 34444386 PMCID: PMC8391172 DOI: 10.3390/ijerph18168638] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 01/12/2023]
Abstract
The differential spread and impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing Coronavirus Disease 2019 (COVID-19), across regions is a major focus for researchers and policy makers. Africa has attracted tremendous attention, due to predictions of catastrophic impacts that have not yet materialized. Early in the pandemic, the seemingly low African case count was largely attributed to low testing and case reporting. However, there is reason to consider that many African countries attenuated the spread and impacts early on. Factors explaining low spread include early government community-wide actions, population distribution, social contacts, and ecology of human habitation. While recent data from seroprevalence studies posit more extensive circulation of the virus, continuing low COVID-19 burden may be explained by the demographic pyramid, prevalence of pre-existing conditions, trained immunity, genetics, and broader sociocultural dynamics. Though all these prongs contribute to the observed profile of COVID-19 in Africa, some provide stronger evidence than others. This review is important to expand what is known about the differential impacts of pandemics, enhancing scientific understanding and gearing appropriate public health responses. Furthermore, it highlights potential lessons to draw from Africa for global health on assumptions regarding deadly viral pandemics, given its long experience with infectious diseases.
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Affiliation(s)
- Richard G. Wamai
- Department of Cultures, Societies, and Global Studies, Northeastern University, 201 Renaissance Park, 360 Huntington Ave., Boston, MA 02115, USA;
| | - Jason L. Hirsch
- Department of Cultures, Societies, and Global Studies, Northeastern University, 201 Renaissance Park, 360 Huntington Ave., Boston, MA 02115, USA;
| | - Wim Van Damme
- Department of Public Health, Institute of Tropical Medicine, B-2000 Antwerp, Belgium;
| | - David Alnwick
- DUNDEX (Deployable U.N.-Experienced Development Experts), FX68 Belturbet, Ireland;
| | - Robert C. Bailey
- School of Public Health, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Stephen Hodgins
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Uzma Alam
- Researcher Africa Institute for Health Policy Foundation, Nairobi 020, Kenya;
| | - Mamka Anyona
- T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA;
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Caldwell J, Jackson FLC. Evolutionary perspectives on African North American genetic diversity: Origins and prospects for future investigations. Evol Anthropol 2021; 30:242-252. [PMID: 34388300 DOI: 10.1002/evan.21910] [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: 05/28/2020] [Revised: 09/03/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
African-descended peoples of the Americas represent an amalgamation of West, Central, and Southeast African regional and ethnic groups with modest gene flow from specific non-African populations. Despite 16+ generations of residence in the Americas, there is a deficit of evolutionary knowledge about these populations. Focusing on Legacy African American, the African North American descendants of survivors of the transatlantic trade in enslaved Africans, we report on emic evolutionary perspectives of their self-identity gleaned from our interviews of 600 individuals collected over 2 years. Gullah-Geechee peoples of Carolina Coastal regions are a model case study due to their historical antiquity, substantial African retentions, relative geospatial isolation, and proposed progenitor status to other Legacy African American microethnic groups. We identify salient research questions for future studies that will begin to bridge the evolutionary gaps in our knowledge of these diverse peoples and the historical evidence for specific evolutionary processes.
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Affiliation(s)
- Jennifer Caldwell
- Genetics Department, Howard University, Washington, District of Columbia, USA
| | - Fatimah L C Jackson
- Biology Department, Howard University, Washington, District of Columbia, USA
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Graves JL. Human biological variation and the "normal". Am J Hum Biol 2021; 33:e23658. [PMID: 34342914 DOI: 10.1002/ajhb.23658] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 11/12/2022] Open
Abstract
Anatomically modern human being is a relatively young species (~300 000 years old) with small amounts of genetic variation contained within them. The vast majority of its existence was spent in Eastern Africa, migration out of the region began around 100 000 YBP. Sub-Saharan African populations have the greatest amount of human genetic variation. However, migration allowed populations to accumulate genomic variation associated with living in the arctic, higher altitudes, disease resistance, living on high fat or starchy foods, surviving toxic arsenic-rich environments, lactase persistence, changing skin pigmentation, gaining thicker hair, and changing height and body mass index. Understanding these aspects of human evolution forces us to reconsider our notion of the "normal." Thus, normal for our species includes having dark melanic skin, brown eyes, and brown tightly curled hair. Derived features include lighter skin (~10 000 YBP), blue eyes (~6000 YBP), and blond straight hair (~6000 YBP). Yet in reality, "normal" has no meaning for a species that inhabits such a broad geographic range. Natural selection and genetic drift have genetically differentiated human populations in ways that impact our morphological and physiological traits. The genomic differentiation is small and does not allow any unambiguous classification of human populations into biological races. Despite these now well-established facts of human variation, significant confusion associated with Eurocentric notions of the normal still persist in both the lay public and various professions such as biomedical research and clinical practice.
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Affiliation(s)
- Joseph L Graves
- Joint School of Nanosciences & Nanoengineering, North Carolina A&T State University, UNC Greensboro, Greensboro, North Carolina, USA
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Frayer ME, Payseur BA. Demographic history shapes genomic ancestry in hybrid zones. Ecol Evol 2021; 11:10290-10302. [PMID: 34367575 PMCID: PMC8328415 DOI: 10.1002/ece3.7833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.
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Affiliation(s)
- Megan E. Frayer
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
| | - Bret A. Payseur
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
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43
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Mullings L, Torres JB, Fuentes A, Gravlee CC, Roberts D, Thayer Z. The Biology of Racism. AMERICAN ANTHROPOLOGIST 2021. [DOI: 10.1111/aman.13630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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44
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Chu BB, Sobel EM, Wasiolek R, Ko S, Sinsheimer JS, Zhou H, Lange K. A fast Data-Driven method for genotype imputation, phasing, and local ancestry inference: MendelImpute.jl. Bioinformatics 2021; 37:4756-4763. [PMID: 34289008 PMCID: PMC8665755 DOI: 10.1093/bioinformatics/btab489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Current methods for genotype imputation and phasing exploit the volume of data in haplotype reference panels and rely on hidden Markov models. Existing programs all have essentially the same imputation accuracy, are computationally intensive, and generally require pre-phasing the typed markers. RESULTS We introduce a novel data-mining method for genotype imputation and phasing that substitutes highly efficient linear algebra routines for hidden Markov model calculations. This strategy, embodied in our Julia program MendelImpute.jl, avoids explicit assumptions about recombination and population structure while delivering similar prediction accuracy, better memory usage, and an order of magnitude or better run-times compared to the fastest competing method. MendelImpute operates on both dosage data and unphased genotype data and simultaneously imputes missing genotypes and phase at both the typed and untyped SNPs. Finally, MendelImpute naturally extends to global and local ancestry estimation and lends itself to new strategies for data compression and hence faster data transport and sharing. AVAILABILITY Software, documentation, and scripts to reproduce our results are available from https://github.com/OpenMendel/MendelImpute.jl. SUPPLEMENTARY INFORMATION Supplementary data are available from Bioinformatics online.
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Affiliation(s)
- Benjamin B Chu
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Eric M Sobel
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Rory Wasiolek
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Seyoon Ko
- Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, USA
| | - Janet S Sinsheimer
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, USA
| | - Hua Zhou
- Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, USA
| | - Kenneth Lange
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USA
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45
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Ongaro L, Mondal M, Flores R, Marnetto D, Molinaro L, Alarcón-Riquelme ME, Moreno-Estrada A, Mabunda N, Ventura M, Tambets K, Hellenthal G, Capelli C, Kivisild T, Metspalu M, Pagani L, Montinaro F. Continental-scale genomic analysis suggests shared post-admixture adaptation in the Americas. Hum Mol Genet 2021; 30:2123-2134. [PMID: 34196708 PMCID: PMC8561420 DOI: 10.1093/hmg/ddab177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023] Open
Abstract
American populations are one of the most interesting examples of recently admixed groups, where ancestral components from three major continental human groups (Africans, Eurasians and Native Americans) have admixed within the last 15 generations. Recently, several genetic surveys focusing on thousands of individuals shed light on the geography, chronology and relevance of these events. However, even though gene flow could drive adaptive evolution, it is unclear whether and how natural selection acted on the resulting genetic variation in the Americas. In this study, we analysed the patterns of local ancestry of genomic fragments in genome-wide data for ~ 6000 admixed individuals from 10 American countries. In doing so, we identified regions characterized by a divergent ancestry profile (DAP), in which a significant over or under ancestral representation is evident. Our results highlighted a series of genomic regions with DAPs associated with immune system response and relevant medical traits, with the longest DAP region encompassing the human leukocyte antigen locus. Furthermore, we found that DAP regions are enriched in genes linked to cancer-related traits and autoimmune diseases. Then, analysing the biological impact of these regions, we showed that natural selection could have acted preferentially towards variants located in coding and non-coding transcripts and characterized by a high deleteriousness score. Taken together, our analyses suggest that shared patterns of post admixture adaptation occurred at a continental scale in the Americas, affecting more often functional and impactful genomic variants.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, GENYO. Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica, Av de la Ilustración 114, Parque Tecnológico de la Salud (PTS), 18016, Granada, Spain
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Nedio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N°1, Província de Maputo, Maputo, 1120, Mozambique
| | - Mario Ventura
- Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Herestraat 49 - box 602, B-3000, Leuven, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, Tartu, Riia 23b, 51010, Estonia.,Department of Biology-Genetics, University of Bari, Bari, 70126, Italy
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46
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Khatri I, Berkowska MA, van den Akker EB, Teodosio C, Reinders MJT, van Dongen JJM. Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations. Genes Immun 2021; 22:172-186. [PMID: 34120151 PMCID: PMC8196923 DOI: 10.1038/s41435-021-00143-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023]
Abstract
Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be specific to human populations. The current immunogenetics resources gather the germline alleles, however, lack the population specificity of the alleles which poses limitations for disease-association studies related to immune responses in different human populations. Therefore, we systematically identified germline alleles from 26 different human populations around the world, profiled by "1000 Genomes" data. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes. The diversity of germline alleles is the highest in Africans. Remarkably, the variants in the identified novel alleles show strikingly conserved patterns, the same as found in other IG databases, suggesting over-time evolutionary selection processes. We could relate the genetic variants to population-specific immune responses, e.g. IGHV1-69 for flu in Africans. The population matched IG (pmIG) resource will enhance our understanding of the SHM-related B-cell receptor selection processes in (infectious) diseases and vaccination within and between different human populations.
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Affiliation(s)
- Indu Khatri
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Erik B van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Cristina Teodosio
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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47
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Hughes CE, Juarez C, Yim AD. Forensic anthropology casework performance: Assessing accuracy and trends for biological profile estimates on a comprehensive sample of identified decedent cases. J Forensic Sci 2021; 66:1602-1616. [PMID: 34160079 DOI: 10.1111/1556-4029.14782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
The purpose of this study was to investigate the accuracy rates and trends in forensic anthropology casework concerning the estimation of the biological profile (sex, age, ancestry, and stature). Identified cases from the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA; n = 359) were analyzed to explore the following: accuracy rates per biological profile component, case-level performance in assessing the biological profile, and factors related to inaccuracy rates. Accuracy rates for the four biological profile components ranged from 83% to 98%, with sex estimation performing the best and stature performing the poorest. While the overall sex estimation inaccuracies were the lowest of any biological profile component, we found that females are missexed approximately ten times more often than males. Inaccurate age estimates were more frequently the result of overestimation than underestimation, while the trends are reversed for stature estimation. Regarding ancestry estimation performance, African American/Black and White decedents had the lowest inaccuracy rates, while Hispanic and Asian/Pacific Islander decedents demonstrated greater inaccuracy rates. When examining accuracy rates for each case, 81% of cases had no inaccurate biological profile estimates, while 17% and 2% inaccurately estimated one and two biological profile components, respectively. The demographic trends of identified forensic anthropology cases reflect the national unidentified decedent demographics. Biological profile accuracy rates were generally comparable to previous studies. The findings highlight the current status of forensic anthropologists' casework performance, with a greater amount of case-level inaccuracy rates than previously thought, and demonstrate the potential methodological and sampling strategies that could improve accuracy rates.
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Affiliation(s)
- Cris E Hughes
- Department of Anthropology & Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Chelsey Juarez
- Department of Anthropology, California State University-Fresno, Fresno, CA, USA
| | - An-Di Yim
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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48
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Sirugo G, Tishkoff SA, Williams SM. The quagmire of race, genetic ancestry, and health disparities. J Clin Invest 2021; 131:e150255. [PMID: 34060479 DOI: 10.1172/jci150255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Giorgio Sirugo
- Institute of Systems Pharmacology and Translational Therapeutics.,Division of Translational Medicine and Human Genetics, and
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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49
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Almeida J, Fehn AM, Ferreira M, Machado T, Hagemeijer T, Rocha J, Gayà-Vidal M. The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea. Genes (Basel) 2021; 12:833. [PMID: 34071462 PMCID: PMC8229774 DOI: 10.3390/genes12060833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022] Open
Abstract
The forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on the archipelago of São Tomé and Príncipe in the Gulf of Guinea, which hosted one of the earliest plantation societies relying exclusively on slave labor. We analyze the genetic variation in 25 individuals from three communities who speak distinct creole languages (Forros, Principenses and Angolares), using genomic data from expanded exomes in combination with a contextual dataset from Europe and Africa, including newly generated data from 28 Bantu speakers from Angola. Our findings show that while all islanders display mixed contributions from the Gulf of Guinea and Angola, the Angolares are characterized by extreme genetic differentiation and inbreeding, consistent with an admixed maroon isolate. In line with a more prominent Bantu contribution to their creole language, we additionally found that a previously reported high-frequency Y-chromosome haplotype in the Angolares has a likely Angolan origin, suggesting that their genetic, linguistic and social characteristics were influenced by a small group of dominant men who achieved disproportionate reproductive success.
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Affiliation(s)
- João Almeida
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Anne-Maria Fehn
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Department of Linguistic and Cultural Evolution, Max-Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Margarida Ferreira
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Teresa Machado
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
| | - Tjerk Hagemeijer
- Centro de Linguística da Universidade de Lisboa, 1600-214 Lisboa, Portugal;
- Faculdade de Letras, Universidade de Lisboa, 1600-214 Lisboa, Portugal
| | - Jorge Rocha
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Magdalena Gayà-Vidal
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal; (J.A.); (A.-M.F.); (M.F.); (T.M.); (M.G.-V.)
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50
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Fortes-Lima C, Verdu P. Anthropological genetics perspectives on the transatlantic slave trade. Hum Mol Genet 2020; 30:R79-R87. [PMID: 33331897 DOI: 10.1093/hmg/ddaa271] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023] Open
Abstract
During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.
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Affiliation(s)
- Cesar Fortes-Lima
- Sub-department of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
| | - Paul Verdu
- Unité Mixte de Recherche7206 Eco-Anthropology, CNRS-MNHN-Université de Paris, Musée de l'Homme, Paris, 75016, France
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