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Gurwitz D, Steeg R. Enriching iPSC research diversity: Harnessing human biobank collections for improved ethnic representation. Drug Dev Res 2024; 85:e22227. [PMID: 38943497 DOI: 10.1002/ddr.22227] [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: 04/21/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Biobanks of human biosamples and cell lines are indispensable for biomedical research on human health and disease and for drug development projects. Many human cell line biobanks worldwide hold collections of lymphoblastoid cell lines (LCLs), representing thousands of affected and control donors from diverse ethnic/ancestry groups. In recent years, induced human pluripotent stem cells (iPSCs) and differentiated human cells derived from these iPSCs have become indispensable for applied biomedical research. Establishing iPSCs remains a laborious and costly step towards generating differentiated human cells. To address this research need, several non-profit and commercial biobanks have established iPSC collections for distribution to researchers, thereby serving as a resource for generating differentiated human cells. The most common starting materials for generation of iPSCs are a skin biopsy for harvesting fibroblasts, or a blood sample for collection of peripheral blood mononuclear cells. However untapped resources include the large established collections of biobanked human LCLs which can be reprogrammed to iPSCs using a variety of published protocols including the use of non-integrating episomal vectors. Many biobanks curate LCLs from diverse ethnic/ancestry populations, an aspect largely absent in most established iPSC biobanks which tend to primarily reflect populations from developed countries. Here, we call upon researchers across the breadth of iPSC research to tap the unique resource of existing and diverse human LCL collections for establishing biobanked iPSC panels that better represent the varied human ethnic (and hence genomic) diversity, thereby benefiting precision medicine and drug development research on a global scale.
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Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Steeg
- European Bank for Induced Pluripotent Stem Cells, Fraunhofer UK Research Ltd, Glasgow, UK
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2
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Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome wide association study and genomic risk prediction of age related macular degeneration in Israel. Sci Rep 2024; 14:13034. [PMID: 38844476 PMCID: PMC11156861 DOI: 10.1038/s41598-024-63065-0] [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: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
The risk of developing age-related macular degeneration (AMD) is influenced by genetic background. In 2016, the International AMD Genomics Consortium (IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score (PRS) from these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish (AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study (GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Our discovery set recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary-statistics excluding our study and developed PRSs via clumping/thresholding or LDpred2. In our discovery set, 31/34 loci reported by IAMDGC were AMD-associated (P < 0.05). Of those, all effects were directionally consistent with IAMDGC and 11 loci had a P-value under Bonferroni-corrected threshold (0.05/34 = 0.0015). At a 5 × 10-5 threshold, we discovered four suggestive associations in FAM189A1, IGDCC4, C7orf50, and CNTNAP4. Only the FAM189A1 variant was AMD-associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS + covariates had an AUC of 0.82 (95% CI 0.79-0.85) and performed better than covariates-only model (P = 5.1 × 10-9). Therefore, previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
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Affiliation(s)
- Michelle Grunin
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Daria Triffon
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
| | - Gala Beykin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Elior Rahmani
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Regev Schweiger
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Genetics, University of Cambridge, CB21TN, Cambridge, UK
| | - Liran Tiosano
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Shira Hagbi-Levi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Batya Rinsky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Refael Munitz
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Eran Halperin
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel.
| | - Itay Chowers
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel.
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3
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Gretzinger J, Schmitt F, Mötsch A, Carlhoff S, Lamnidis TC, Huang Y, Ringbauer H, Knipper C, Francken M, Mandt F, Hansen L, Freund C, Posth C, Rathmann H, Harvati K, Wieland G, Granehäll L, Maixner F, Zink A, Schier W, Krausse D, Krause J, Schiffels S. Evidence for dynastic succession among early Celtic elites in Central Europe. Nat Hum Behav 2024:10.1038/s41562-024-01888-7. [PMID: 38831077 DOI: 10.1038/s41562-024-01888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
The early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the 'West-Hallstattkreis', stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as 'early Celtic', suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felicitas Schmitt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Angela Mötsch
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Selina Carlhoff
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Corina Knipper
- Curt Engelhorn Zentrum Archäometrie gGmbH, Mannheim, Germany
| | - Michael Francken
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Franziska Mandt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Leif Hansen
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Hannes Rathmann
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Katerina Harvati
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
- DFG Center for Advanced Studies in the Humanities 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Günther Wieland
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Lena Granehäll
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Wolfram Schier
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Dirk Krausse
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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4
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Saint-André V, Charbit B, Biton A, Rouilly V, Possémé C, Bertrand A, Rotival M, Bergstedt J, Patin E, Albert ML, Quintana-Murci L, Duffy D. Smoking changes adaptive immunity with persistent effects. Nature 2024; 626:827-835. [PMID: 38355791 PMCID: PMC10881394 DOI: 10.1038/s41586-023-06968-8] [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: 11/01/2022] [Accepted: 12/13/2023] [Indexed: 02/16/2024]
Abstract
Individuals differ widely in their immune responses, with age, sex and genetic factors having major roles in this inherent variability1-6. However, the variables that drive such differences in cytokine secretion-a crucial component of the host response to immune challenges-remain poorly defined. Here we investigated 136 variables and identified smoking, cytomegalovirus latent infection and body mass index as major contributors to variability in cytokine response, with effects of comparable magnitudes with age, sex and genetics. We find that smoking influences both innate and adaptive immune responses. Notably, its effect on innate responses is quickly lost after smoking cessation and is specifically associated with plasma levels of CEACAM6, whereas its effect on adaptive responses persists long after individuals quit smoking and is associated with epigenetic memory. This is supported by the association of the past smoking effect on cytokine responses with DNA methylation at specific signal trans-activators and regulators of metabolism. Our findings identify three novel variables associated with cytokine secretion variability and reveal roles for smoking in the short- and long-term regulation of immune responses. These results have potential clinical implications for the risk of developing infections, cancers or autoimmune diseases.
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Affiliation(s)
- Violaine Saint-André
- Translational Immunology Unit, Department of Immunology, Institut Pasteur, Université Paris Cité, Paris, France.
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France.
| | - Bruno Charbit
- Cytometry and Biomarkers UTechS, Center for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anne Biton
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | | | - Céline Possémé
- Translational Immunology Unit, Department of Immunology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anthony Bertrand
- Translational Immunology Unit, Department of Immunology, Institut Pasteur, Université Paris Cité, Paris, France
- Frontiers of Innovation in Research and Education PhD Program, LPI Doctoral School, Université Paris Cité, Paris, France
| | - Maxime Rotival
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Jacob Bergstedt
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | | | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Chair Human Genomics and Evolution, Collège de France, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Department of Immunology, Institut Pasteur, Université Paris Cité, Paris, France.
- Cytometry and Biomarkers UTechS, Center for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France.
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5
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Nitzan I, Shakarchy N, Megreli J, Akavian I, Derazne E, Afek A, Peled A. Body mass index and visual impairment in Israeli adolescents: A nationwide study. Pediatr Obes 2024; 19:e13083. [PMID: 37989292 DOI: 10.1111/ijpo.13083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Previous research on the association between body mass index (BMI) and visual impairment (VI) in youth has reported inconsistent findings. We aimed to investigate this association in a national cohort of Israeli adolescents. METHODS This retrospective, population-based, cross-sectional study included 1 697 060 adolescents (56.4% men; mean age 17 years) who underwent mandatory pre-military service assessments from 1993 to 2017. BMI was classified based on the US age- and sex-matched percentiles. Unilateral or bilateral VI was classified as best-corrected visual acuity (BCVA) worse than 6/9 in either or both eyes, respectively. Sex-stratified regression models adjusted for sociodemographic variables were used to analyse the BMI-VI relationship. RESULTS Overall, 17 871 (1.05%) and 5148 (0.30%) adolescents had unilateral and bilateral VI, respectively. Compared with high-normal BMI (50th to 85th percentile), adjusted odds ratios (ORs) for unilateral and bilateral VI gradually increased with higher BMI, reaching 1.33 (1.13-1.55) and 1.80 (1.37-2.35) in men with severe obesity, and 1.51 (1.24-1.84) and 1.52 (1.08-2.14) in women with severe obesity, respectively. Men with underweight also had increased ORs for unilateral and bilateral VI (1.23; 1.14-1.33 and 1.59; 1.37-1.84, respectively), a pattern not observed in women (0.96; 0.86-1.07 and 1.02; 0.83-1.25, respectively). Results were maintained when the outcome was restricted to mild VI, as well as in subgroups of adolescents with unimpaired health and those without moderate-to-severe myopia. CONCLUSIONS Abnormal BMI, and particularly obesity, is associated with increased OR for VI in late adolescence.
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Affiliation(s)
- Itay Nitzan
- Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Department of Military Medicine and 'Tzameret', Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nitzan Shakarchy
- Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Department of Military Medicine and 'Tzameret', Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jacob Megreli
- Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Department of Military Medicine and 'Tzameret', Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbal Akavian
- Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Department of Military Medicine and 'Tzameret', Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Estela Derazne
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Central Management, Chaim Sheba Medical Center at Tel Hashomer, Ramat Gan, Israel
| | - Alon Peled
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Ophthalmology, Assaf-Harofeh Medical Center, Zerifin, Israel
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6
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Kumar L, Chowdhari A, Sequeira JJ, Mustak MS, Banerjee M, Thangaraj K. Genetic Affinities and Adaptation of the South-West Coast Populations of India. Genome Biol Evol 2023; 15:evad225. [PMID: 38079532 PMCID: PMC10745260 DOI: 10.1093/gbe/evad225] [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] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Evolutionary event has not only altered the genetic structure of human populations but also associated with social and cultural transformation. South Asian populations were the result of migration and admixture of genetically and culturally diverse groups. Most of the genetic studies pointed to large-scale admixture events between Ancestral North Indian (ANI) and Ancestral South Indian (ASI) groups, also additional layers of recent admixture. In the present study, we have analyzed 213 individuals inhabited in South-west coast India with traditional warriors and feudal lord status and historically associated with migratory events from North/North West India and possible admixture with West Eurasian populations, whose genetic links are still missing. Analysis of autosomal Single Nucleotide Polymorphism (SNP) markers suggests that these groups possibly derived their ancestry from some groups of North West India having additional Middle Eastern genetic components. Higher distribution of West Eurasian mitochondrial haplogroups also points to female-mediated admixture. Estimation of Effective Migration Surface (EEMS) analysis indicates Central India and Godavari basin as a crucial transition zone for population migration from North and North West India to South-west coastal India. Selection screen using 3 distinct outlier-based approaches revealed genetic signatures related to Immunity and protection from Viral infections. Thus, our study suggests that the South-west coastal groups with traditional warriors and feudal lords' status are of a distinct lineage compared to Dravidian and Gangetic plain Indo-Europeans and are remnants of very early migrations from North West India following the Godavari basin to Karnataka and Kerala.
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Affiliation(s)
- Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Anuhya Chowdhari
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Jaison J Sequeira
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore 574199, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
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7
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Levi H, Carmi S, Rosset S, Yerushalmi R, Zick A, Yablonski-Peretz T, Wang Q, Bolla MK, Dennis J, Michailidou K, Lush M, Ahearn T, Andrulis IL, Anton-Culver H, Antoniou AC, Arndt V, Augustinsson A, Auvinen P, Beane Freeman L, Beckmann M, Behrens S, Bermisheva M, Bodelon C, Bogdanova NV, Bojesen SE, Brenner H, Byers H, Camp N, Castelao J, Chang-Claude J, Chirlaque MD, Chung W, Clarke C, Collee MJ, Colonna S, Couch F, Cox A, Cross SS, Czene K, Daly M, Devilee P, Dork T, Dossus L, Eccles DM, Eliassen AH, Eriksson M, Evans G, Fasching P, Fletcher O, Flyger H, Fritschi L, Gabrielson M, Gago-Dominguez M, García-Closas M, Garcia-Saenz JA, Genkinger J, Giles GG, Goldberg M, Guénel P, Hall P, Hamann U, He W, Hillemanns P, Hollestelle A, Hoppe R, Hopper J, Jakovchevska S, Jakubowska A, Jernström H, John E, Johnson N, Jones M, Vijai J, Kaaks R, Khusnutdinova E, Kitahara C, Koutros S, Kristensen V, Kurian AW, Lacey J, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Loibl S, Lori A, Lubinski J, Mannermaa A, Manoochehri M, Mavroudis D, Menon U, Mulligan A, Murphy R, Nevelsteen I, Newman WG, Obi N, O'Brien K, Offit K, Olshan A, Plaseska-Karanfilska D, Olson J, Panico S, Park-Simon TW, Patel A, Peterlongo P, Rack B, Radice P, Rennert G, Rhenius V, Romero A, Saloustros E, Sandler D, Schmidt MK, Schwentner L, Shah M, Sharma P, Simard J, Southey M, Stone J, Tapper WJ, Taylor J, Teras L, Toland AE, Troester M, Truong T, van der Kolk LE, Weinberg C, Wendt C, Yang XR, Zheng W, Ziogas A, Dunning AM, Pharoah P, Easton DF, Ben-Sachar S, Elefant N, Shamir R, Elkon R. Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel. J Med Genet 2023; 60:1186-1197. [PMID: 37451831 PMCID: PMC10715538 DOI: 10.1136/jmg-2023-109185] [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: 01/26/2023] [Accepted: 05/28/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Polygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. METHODS We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. RESULTS In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). CONCLUSIONS Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.
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Grants
- R01 CA176785 NCI NIH HHS
- NU58DP006344 NCCDPHP CDC HHS
- R37 CA070867 NCI NIH HHS
- HHSN261201800015I NCI NIH HHS
- R01 CA064277 NCI NIH HHS
- P50 CA116201 NCI NIH HHS
- G1000143 Medical Research Council
- P30 CA062203 NCI NIH HHS
- HHSN261201800015C NCI NIH HHS
- R01 CA047305 NCI NIH HHS
- HHSN261201800009I NCI NIH HHS
- R01 CA163353 NCI NIH HHS
- UM1 CA164917 NCI NIH HHS
- U01 CA199277 NCI NIH HHS
- U01 CA179715 NCI NIH HHS
- HHSN261201800032C NCI NIH HHS
- U54 CA156733 NCI NIH HHS
- HHSN261201800009C NCI NIH HHS
- Z01 CP010119 Intramural NIH HHS
- UM1 CA164973 NCI NIH HHS
- P01 CA087969 NCI NIH HHS
- UM1 CA164920 NCI NIH HHS
- NU58DP006320 CDC HHS
- UM1 CA176726 NCI NIH HHS
- R01 CA092447 NCI NIH HHS
- Z01 ES049030 Intramural NIH HHS
- R01 CA058860 NCI NIH HHS
- K07 CA092044 NCI NIH HHS
- HHSN261201800016C NCI NIH HHS
- P50 CA058223 NCI NIH HHS
- R01 CA100374 NCI NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 CA128978 NCI NIH HHS
- R01 CA047147 NCI NIH HHS
- U19 CA148537 NCI NIH HHS
- R01 CA116167 NCI NIH HHS
- R01 CA148667 NCI NIH HHS
- R01 CA063464 NCI NIH HHS
- HHSN261201800016I NCI NIH HHS
- UM1 CA186107 NCI NIH HHS
- P30 CA023100 NCI NIH HHS
- U01 CA063464 NCI NIH HHS
- R01 CA077398 NCI NIH HHS
- R01 CA054281 NCI NIH HHS
- R01 CA132839 NCI NIH HHS
- P30 CA068485 NCI NIH HHS
- U01 CA058860 NCI NIH HHS
- U01 CA164920 NCI NIH HHS
- R35 CA253187 NCI NIH HHS
- 14136 Cancer Research UK
- U19 CA148112 NCI NIH HHS
- HHSN261201800032I NCI NIH HHS
- U01 CA098758 NCI NIH HHS
- Z01 ES044005 Intramural NIH HHS
- U19 CA148065 NCI NIH HHS
- P30 CA033572 NCI NIH HHS
- R01 CA069664 NCI NIH HHS
- Wellcome Trust
- 001 World Health Organization
- Z01 ES049033 Intramural NIH HHS
- R01 CA192393 NCI NIH HHS
- U01 CA164973 NCI NIH HHS
- R37 CA054281 NCI NIH HHS
- Consellería de Industria Programa Sectorial de Investigación Aplicada
- Statistics Netherlands
- South Eastern Norway Health Authority
- Lower Saxonian Cancer Society
- Lise Boserup Fund
- Heidelberger Zentrum für Personalisierte Onkologie Deutsches Krebsforschungszentrum In Der Helmholtz-Gemeinschaft
- Lon V. Smith Foundation
- Scottish Funding Council
- Komen Foundation
- Claudia von Schilling Foundation for Breast Cancer Research
- Russian Foundation for Basic Research
- Ligue Contre le Cancer
- Sigrid Juselius Foundation
- Kuopion Yliopistollinen Sairaala
- Sheffield Experimental Cancer Medicine Centre
- Stockholm läns landsting
- Department of Health and Human Services (USA)
- Department of Defence (USA)
- Stichting Tegen Kanker
- David F. and Margaret T. Grohne Family Foundation
- Sundhed og Sygdom, Det Frie Forskningsråd
- Stavros Niarchos Foundation
- Post-Cancer GWAS initiative
- Institute of the Ruhr University Bochum
- Instituto de Salud Carlos III
- Institute of Cancer Research
- Public Health Institute
- Fondation du cancer du sein du Québec
- Institut National de la Santé et de la Recherche Médicale
- Pink Ribbon
- Institute for Prevention and Occupational Medicine
- K.G. Jebsen Centre for Breast Cancer Research
- Research Centre for Genetic Engineering and Biotechnology
- Center of Excellence (Finland)
- Robert and Kate Niehaus Clinical Cancer Genetics Initiative
- Rudolf Bartling Foundation
- Center for Disease Control and Prevention (USA)
- Karolinska Institutet
- Norges Forskningsråd
- Robert Bosch Stiftung
- Intramural Research Funds of the National Cancer Institute (USA)
- Regional Governments of Andalucía, Asturias, Basque Country, Murcia and Navarra, ISCIII RETIC
- Intramural Research Program of the Division of Cancer Epidemiology and Genetics
- Centre International de Recherche sur le Cancer
- Queensland Cancer Fund
- Red Temática de Investigación Cooperativa en Cáncer
- Intramural Research Program of the National Institutes of Health
- National Health Service (UK)
- Ministerie van Volksgezondheid, Welzijn en Sport
- National cancer institute (USA)
- KWF Kankerbestrijding
- Märit and Hans Rausings Initiative Against Breast Cancer
- Associazione Italiana per la Ricerca sul Cancro
- Fundación Científica Asociación Española Contra el Cáncer
- ERC advanced grant
- Australian National Health and Medical Research Council
- Agence Nationale de la Recherche
- Dutch Prevention Funds,
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
- American Cancer Society
- Dutch Zorg Onderzoek
- Alexander von Humboldt-Stiftung
- Ministerio de Economia y Competitividad (Spain)
- Ministère du Développement Économique, de l’Innovation et de l’Exportation
- Susan G. Komen for the Cure
- Minister of Science and Higher Education
- Medical Research Council UK
- Ministry of Science and Higher Education of the Russian Federation
- Ministry of Science and Higher Education (Sweden)
- Against Breast Cancer
- Mutuelle Générale de l’Education Nationale
- Academy of Finland
- Deutsche Krebshilfe e.V.
- Dietmar-Hopp Foundation,
- Division of Cancer Prevention, National Cancer Institute
- Deutsche Krebshilfe
- World Cancer Research Fund
- Genome Québec
- National Cancer Institute’s Surveillance, Epidemiology and End Results Program
- Breast Cancer Campaign
- National Cancer Research Network
- Berta Kamprad Foundation FBKS
- Bert von Kantzows foundation
- Biomedical Research Centre at Guy’s and St Thomas
- Genome Canada
- Freistaat Sachsen
- Biobanking and Biomolecular Resources Research Infrastructure
- Friends of Hannover Medical School
- Breast Cancer Research Foundation
- California Department of Public Health
- Government of Russian Federation
- Deutsche Forschungsgemeinschaft
- National Institute for Health and Care Research
- National Health and Medical Research Council (Australia)
- German Federal Ministry of Research and Education
- National Institute of Environmental Health Sciences
- Breast Cancer Now
- Seventh Framework Programme
- Transcan
- Centrum för idrottsforskning
- UK National Institute for Health Research Biomedical Research Centre
- University of Crete
- National Breast Cancer Foundation (Finland)
- European Regional Development Fund
- National Breast Cancer Foundation (Australia)
- United States Army Medical Research and Materiel Command
- EU Horizon 2020 Research and Innovation Programme
- Directorate-General XII, Science, Research, and Development
- Baden Württemberg Ministry of Science, Research and Arts
- VicHealth
- Fondo de Investigación Sanitario
- Victorian Breast Cancer Research Consortium.
- Finnish Cancer Foundation
- University of Southern California San Francisco
- Fomento de la Investigación Clínica Independiente
- the Cancer Biology Research Center (CBRC), Djerassi Oncology Center
- Bundesministerium für Bildung und Forschung
- Cancerfonden
- Tel Aviv University Center for AI and Data Science
- University of Oulu
- National Breast Cancer Foundation (JS)
- Safra Center for Bioinformatics
- Fondation de France, Institut National du Cancer
- Israeli Science Foundation
- University of Utah
- National Cancer Center Research and Development Fund (Japan)
- Chief Scientist Office, Scottish Government Health and Social Care Directorate
- Oak Foundation
- Health Research Fund (FIS)
- Ontario Familial Breast Cancer Registry
- New South Wales Cancer Council
- North Carolina University Cancer Research Fund
- Kreftforeningen
- Northern California Breast Cancer Family Registry
- Institut Gustave Roussy
- Huntsman Cancer Institute, University of Utah
- Ovarian Cancer Research Fund
- NIHR Oxford Biomedical Research Centre
- Hellenic Health Foundation
- Oulun Yliopistollinen Sairaala
- Helmholtz Society
- Herlev and Gentofte Hospital
- PSRSIIRI-701
- Helsinki University Hospital Research Fund
- Cancer Council Victoria
- National Research Council (Italy)
- Cancer Council Tasmania
- Cancer Council Western Australia
- Hamburger Krebsgesellschaft
- Gustav V Jubilee foundation
- National Program of Cancer Registries
- Canadian Cancer Society
- Cancer Council South Australia
- Canadian Institutes of Health Research
- Cancer Council NSW
- Guy's & St. Thomas' NHS Foundation Trust
- Netherlands Organisation of Scientific Research
- Cancer Institute NSW
- National Institutes of Health (USA)
- National Research Foundation of Korea
- Syöpäsäätiö
- Cancer Foundation of Western Australia
- Netherlands Cancer Registry (NKR),
- Cancer Fund of North Savo
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Affiliation(s)
- Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Rinat Yerushalmi
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviad Zick
- Department of oncology, Hadassah Medical Center, Jerusalem, Israel
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Yablonski-Peretz
- Department of oncology, Hadassah Medical Center, Jerusalem, Israel
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annelie Augustinsson
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
- Department of Oncology, Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Laura Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthias Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Helen Byers
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nicola Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt lake city, UT, USA
| | - Jose Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Christine Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Margriet J Collee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Sarah Colonna
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt lake city, UT, USA
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Department of Human Genetics, Leiden University Medical, Leiden, Netherlands
| | - Thilo Dork
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gareth Evans
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lin Fritschi
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jeanine Genkinger
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Mark Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, QU, Canada
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hamburg, Germany
| | | | - Reiner Hoppe
- Dr Margarete Fischer Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tubingen, Germany
| | - John Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Simona Jakovchevska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Skopje, North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Joseph Vijai
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Cari Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vessela Kristensen
- Institute of Clinical Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Allison W Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - James Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Annika Lindblom
- Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College, London, UK
| | - AnnaMarie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Rachel Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Ines Nevelsteen
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - William G Newman
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ken Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Janet Olson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Salvatore Panico
- Dipertimento Di Medicina Clinca e Chirurgia, Federico II University, Naples, Italy
| | | | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Atocha Romero
- Laboratorio de Oncología Molecular, Hospital Clínico San Carlos, Madrid, Spain
| | | | - Dale Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas Schwentner
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Jacques Simard
- Genomics Center, Molecular Medicine, Université Laval, Quebec, Quebec, Canada
| | - Melissa Southey
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia
| | - William J Tapper
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jack Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Melissa Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | | | - Clarice Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Camilla Wendt
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
| | - Xiaohong Rose Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Shay Ben-Sachar
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
| | - Naama Elefant
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
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8
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Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome-wide association study and genomic risk prediction of age-related macular degeneration in Israel. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.06.23295126. [PMID: 37732190 PMCID: PMC10508791 DOI: 10.1101/2023.09.06.23295126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Purpose The risk of developing age-related macular degeneration(AMD) is influenced by genetic background. In 2016, International AMD Genomics Consortium(IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score(PRS) based on these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish(AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study(GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Methods For our discovery set, we recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped all individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary statistics excluding our study and developed PRSs via either clumping/thresholding or LDpred2. Results In our discovery set, 31/34 loci previously reported by the IAMDGC were AMD associated with P<0.05. Of those, all effects were directionally consistent with the IAMDGC and 11 loci had a p-value under Bonferroni-corrected threshold(0.05/34=0.0015). At a threshold of 5x10 -5 , we discovered four suggestive associations in FAM189A1 , IGDCC4 , C7orf50 , and CNTNAP4 . However, only the FAM189A1 variant was AMD associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS and other covariates had an AUC of 0.82(95%CI:0.79-0.85) and performed better than a covariates-only model(P=5.1x10 -9 ). Conclusions Previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
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9
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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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10
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Gershoni M, Braun T, Hauser R, Barda S, Lehavi O, Malcov M, Frumkin T, Kalma Y, Pietrokovski S, Arama E, Kleiman SE. A pathogenic variant in the uncharacterized RNF212B gene results in severe aneuploidy male infertility and repeated IVF failure. HGG ADVANCES 2023; 4:100189. [PMID: 37124137 PMCID: PMC10133878 DOI: 10.1016/j.xhgg.2023.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Quantitative and qualitative spermatogenic impairments are major causes of men's infertility. Although in vitro fertilization (IVF) is effective, some couples persistently fail to conceive. To identify causal variants in patients with severe male infertility factor and repeated IVF failures, we sequenced the exome of two consanguineous family members who underwent several failed IVF cycles and were diagnosed with low sperm count and motility. We identified a rare homozygous nonsense mutation in a previously uncharacterized gene, RNF212B, as the causative variant. Recurrence was identified in another unrelated, infertile patient who also faced repeated failed IVF treatments. scRNA-seq demonstrated meiosis-specific expression of RNF212B. Sequence analysis located a protein domain known to be associated with aneuploidy, which can explain multiple IVF failures. Accordingly, FISH analysis revealed a high aneuploidy rate in the patients' sperm cells and their IVF embryos. Finally, inactivation of the Drosophila orthologs significantly reduced male fertility. Given that members of the evolutionary conserved RNF212 gene family are involved in meiotic recombination and crossover maturation, our findings indicate a critical role of RNF212B in meiosis, genome stability, and in human fertility. Since recombination is completely absent in Drosophila males, our findings may indicate an additional unrelated role for the RNF212-like paralogs in spermatogenesis.
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Affiliation(s)
- Moran Gershoni
- ARO-The Volcani Center Institute of Animal Science, Bet Dagan, Israel
- Corresponding author
| | - Tslil Braun
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Hauser
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shimi Barda
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Lehavi
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mira Malcov
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tsvia Frumkin
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Kalma
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Corresponding author
| | - Eli Arama
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Corresponding author
| | - Sandra E. Kleiman
- Racine IVF Unit and Male Fertility Clinic and Sperm Bank, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, affiliated with the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Corresponding author
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11
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Bardugo A, Bendor CD, Rotem RS, Tsur AM, Derazne E, Gerstein HC, Tzur D, Pinhas-Hamiel O, Cukierman-Yaffe T, Raz I, Hod M, Tirosh A, Lebenthal Y, Afek A, Chodick G, Twig G. Glucose intolerance in pregnancy and risk of early-onset type 2 diabetes: a population-based cohort study. Lancet Diabetes Endocrinol 2023; 11:333-344. [PMID: 37011646 DOI: 10.1016/s2213-8587(23)00062-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND The risk of type 2 diabetes among women with glucose intolerance during pregnancy that does not meet gestational diabetes criteria requires further investigation. We aimed to explore the associations between various degrees of gestational glucose intolerance and the risk of type 2 diabetes in young adulthood. METHODS For this population-based cohort study, the national Israeli conscription database was linked to Maccabi Healthcare Services (MHS), the second-largest state-mandated health provider in Israel. We included 177 241 women who underwent a pre-recruitment evaluation at adolescence (age 16-20 years), 1 year before mandatory military service, and later underwent, from Jan 1, 2001, to Dec 31, 2019, two-step gestational diabetes screening with a 50 g glucose challenge test (GCT) based on a threshold of 140 mg/dL (7·8 mmol/L), followed as needed by a 100 g oral glucose tolerance test (OGTT). Abnormal OGTT values were defined according to the Carpenter-Coustan thresholds: 95 mg/dL (5·3 mmol/L) or higher in the fasting state; 180 mg/dL (10·0 mmol/L) or higher at 1 h; 155 mg/dL (8·6 mmol/L) or higher at 2 h; and 140 mg/dL (7·8 mmol/L) or higher at 3 h. The primary outcome was incident type 2 diabetes in the MHS diabetes registry. Cox proportional hazards models were applied to estimate adjusted hazard ratios (HRs) with 95% CIs for incident type 2 diabetes. FINDINGS During a cumulative follow-up of 1 882 647 person-years, and with a median follow-up of 10·8 (IQR 5·2-16·4) years, 1262 women were diagnosed with type 2 diabetes. Crude incidence rates of type 2 diabetes were 2·6 (95% CI 2·4-2·9) per 10 000 person-years in women with gestational normoglycaemia, 8·9 (7·4-10·6) per 10 000 person-years in women with an abnormal GCT and normal OGTT, 26·1 (22·4-30·1) per 10 000 person-years in women with one abnormal OGTT value (in the fasting state or 1 h, 2 h, or 3 h post-challenge), and 71·9 (66·0-78·3) per 10 000 person-years in women with gestational diabetes. After adjustment for sociodemographic characteristics, adolescent BMI, and age at gestational screening, the risk of type 2 diabetes was higher, compared to the gestational normoglycaemia group, in women with an abnormal GCT and normal OGTT (adjusted hazard ratio [HR] 3·39 [95% CI 2·77-4·16]; p<0·0001), in women with one abnormal OGTT value (9·11 [7·64-10·86]; p<0·0001), and in women with gestational diabetes (24·84 [21·78-28·34]; p<0·0001). The risk of type 2 diabetes was modestly increased in women with isolated elevated fasting glucose (adjusted HR 11·81 [95% CI 8·58-16·25]; p<0·0001), and in women with gestational diabetes and an abnormal fasting glucose (38·02 [32·41-44·61]; p<0·0001). INTERPRETATION Gestational glucose intolerance, including conditions not meeting gestational diabetes criteria of the two-step strategy, confers a high risk of type 2 diabetes in young adulthood. These conditions should be recognised as risk factors for type 2 diabetes, especially among women with abnormal fasting glucose concentrations during pregnancy. FUNDING None.
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Affiliation(s)
- Aya Bardugo
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Cole D Bendor
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Ran Shmuel Rotem
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, USA; Kahn-Sagol-Maccabi Research and Innovation Institute, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Avishai M Tsur
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Medicine "B," Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Estela Derazne
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Dorit Tzur
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Orit Pinhas-Hamiel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Tali Cukierman-Yaffe
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Ramat Gan, Israel
| | - Itamar Raz
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Moshe Hod
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Diabetes in Pregnancy Clinic, Perinatal Division, Department of Obstetrics and Gynecology, Beilinson Medical Campus, Petah Tiqva, Israel
| | - Amir Tirosh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Ramat Gan, Israel
| | - Yael Lebenthal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Central Management, Sheba Medical Center, Ramat Gan, Israel
| | - Gabriel Chodick
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Maccabitech, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Gilad Twig
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Ramat Gan, Israel; The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan, Israel.
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12
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Begg TJA, Schmidt A, Kocher A, Larmuseau MHD, Runfeldt G, Maier PA, Wilson JD, Barquera R, Maj C, Szolek A, Sager M, Clayton S, Peltzer A, Hui R, Ronge J, Reiter E, Freund C, Burri M, Aron F, Tiliakou A, Osborn J, Behar DM, Boecker M, Brandt G, Cleynen I, Strassburg C, Prüfer K, Kühnert D, Meredith WR, Nöthen MM, Attenborough RD, Kivisild T, Krause J. Genomic analyses of hair from Ludwig van Beethoven. Curr Biol 2023; 33:1431-1447.e22. [PMID: 36958333 DOI: 10.1016/j.cub.2023.02.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/11/2022] [Accepted: 02/13/2023] [Indexed: 03/25/2023]
Abstract
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.
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Affiliation(s)
- Tristan James Alexander Begg
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| | - Axel Schmidt
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Arthur Kocher
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Maarten H D Larmuseau
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Laboratory of Human Genetic Genealogy, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ARCHES - Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, 2000 Antwerp, Belgium; Histories vzw, 9000 Gent, Belgium
| | | | | | - John D Wilson
- Austrian Academy of Sciences, 1030 Vienna, Austria; University of Vienna, 1010 Vienna, Austria
| | - Rodrigo Barquera
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Carlo Maj
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | | | - Stephen Clayton
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Alexander Peltzer
- Quantitative Biology Center (QBiC) University of Tübingen, Tübingen, Germany
| | - Ruoyun Hui
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; Alan Turing Institute, 2QR, John Dodson House, London NW1 2DB, UK
| | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Marta Burri
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Franziska Aron
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Anthi Tiliakou
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Joanna Osborn
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Guido Brandt
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Isabelle Cleynen
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Strassburg
- Department of Internal Medicine I, University Hospital Bonn, 53127 Bonn, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - William Rhea Meredith
- American Beethoven Society, San Jose State University, San Jose, CA 95192, USA; Ira F. Brilliant Center for Beethoven Studies, San Jose State University, San Jose, CA 95192, USA; School of Music and Dance, San Jose State University, San Jose, CA 95192, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Robert David Attenborough
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
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13
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Wilke F, Herrick N, Matthews H, Hoskens H, Singh S, Shaffer JR, Weinberg SM, Shriver MD, Claes P, Walsh S. Exploring regional aspects of 3D facial variation within European individuals. Sci Rep 2023; 13:3708. [PMID: 36879022 PMCID: PMC9988837 DOI: 10.1038/s41598-023-30855-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Facial ancestry can be described as variation that exists in facial features that are shared amongst members of a population due to environmental and genetic effects. Even within Europe, faces vary among subregions and may lead to confounding in genetic association studies if unaccounted for. Genetic studies use genetic principal components (PCs) to describe facial ancestry to circumvent this issue. Yet the phenotypic effect of these genetic PCs on the face has yet to be described, and phenotype-based alternatives compared. In anthropological studies, consensus faces are utilized as they depict a phenotypic, not genetic, ancestry effect. In this study, we explored the effects of regional differences on facial ancestry in 744 Europeans using genetic and anthropological approaches. Both showed similar ancestry effects between subgroups, localized mainly to the forehead, nose, and chin. Consensus faces explained the variation seen in only the first three genetic PCs, differing more in magnitude than shape change. Here we show only minor differences between the two methods and discuss a combined approach as a possible alternative for facial scan correction that is less cohort dependent, more replicable, non-linear, and can be made open access for use across research groups, enhancing future studies in this field.
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Affiliation(s)
- Franziska Wilke
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Noah Herrick
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Sylvia Singh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA.
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14
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [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: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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15
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Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14 th century. Cell 2022; 185:4703-4716.e16. [PMID: 36455558 PMCID: PMC9793425 DOI: 10.1016/j.cell.2022.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022]
Abstract
We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14th century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.
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16
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Brace S, Diekmann Y, Booth T, Macleod R, Timpson A, Stephen W, Emery G, Cabot S, Thomas MG, Barnes I. Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century. Curr Biol 2022; 32:4350-4359.e6. [PMID: 36044903 PMCID: PMC10499757 DOI: 10.1016/j.cub.2022.08.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/26/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews. We identify four alleles associated with genetic disease in Ashkenazi Jewish populations and infer variation in pigmentation traits, including the presence of red hair. Simulations indicate that Ashkenazi-associated genetic disease alleles were already at appreciable frequencies, centuries earlier than previously hypothesized. These findings provide new insights into a significant historical crime, into Ashkenazi population history, and into the origins of genetic diseases associated with modern Jewish populations.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Thomas Booth
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Francis Crick Institute, London NW1 1AT, UK; UCL Genetics Institute, University College London, London, UK
| | - Ruairidh Macleod
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Adrian Timpson
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Will Stephen
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Giles Emery
- Norvic Archaeology, 7 Foxburrow Road, Norwich NR7 8QU, UK
| | - Sophie Cabot
- Norfolk Record Office, The Archive Centre, Martineau Lane, Norwich, Norfolk NR1 2DQ, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Ian Barnes
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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17
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Gretzinger J, Sayer D, Justeau P, Altena E, Pala M, Dulias K, Edwards CJ, Jodoin S, Lacher L, Sabin S, Vågene ÅJ, Haak W, Ebenesersdóttir SS, Moore KHS, Radzeviciute R, Schmidt K, Brace S, Bager MA, Patterson N, Papac L, Broomandkhoshbacht N, Callan K, Harney É, Iliev L, Lawson AM, Michel M, Stewardson K, Zalzala F, Rohland N, Kappelhoff-Beckmann S, Both F, Winger D, Neumann D, Saalow L, Krabath S, Beckett S, Van Twest M, Faulkner N, Read C, Barton T, Caruth J, Hines J, Krause-Kyora B, Warnke U, Schuenemann VJ, Barnes I, Dahlström H, Clausen JJ, Richardson A, Popescu E, Dodwell N, Ladd S, Phillips T, Mortimer R, Sayer F, Swales D, Stewart A, Powlesland D, Kenyon R, Ladle L, Peek C, Grefen-Peters S, Ponce P, Daniels R, Spall C, Woolcock J, Jones AM, Roberts AV, Symmons R, Rawden AC, Cooper A, Bos KI, Booth T, Schroeder H, Thomas MG, Helgason A, Richards MB, Reich D, Krause J, Schiffels S. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 2022; 610:112-119. [PMID: 36131019 PMCID: PMC9534755 DOI: 10.1038/s41586-022-05247-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | | | - Maria Pala
- University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- University of Huddersfield, Huddersfield, UK
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ceiridwen J Edwards
- University of Huddersfield, Huddersfield, UK
- University of Oxford, Oxford, UK
| | | | - Laura Lacher
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susanna Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Åshild J Vågene
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Haak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Rita Radzeviciute
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Martina Abenhus Bager
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luka Papac
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Frank Both
- Landesmuseum Natur und Mensch, Oldenburg, Germany
| | | | | | - Lars Saalow
- Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany
| | - Stefan Krabath
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK
- Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Neil Faulkner
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Chris Read
- The Atlantic Technological University, Sligo, Ireland
| | | | | | | | | | | | - Verena J Schuenemann
- University of Zurich, Zurich, Switzerland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | - Andrew Richardson
- Canterbury Archaeological Trust, Canterbury, UK
- Isle Heritage CIC, Sandgate, UK
| | | | | | | | | | - Richard Mortimer
- Oxford Archaeology East, Cambridge, UK
- Cotswold Archaeology, Needham Market, UK
| | - Faye Sayer
- University of Birmingham, Birmingham, UK
| | - Diana Swales
- Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK
| | | | | | - Robert Kenyon
- East Dorset Antiquarian Society (EDAS), West Bexington, UK
| | - Lilian Ladle
- Department of Archaeology and Anthropology, Bournemouth University, Poole, UK
| | - Christina Peek
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | | | | | | | | | | | | | | | | | - Anooshka C Rawden
- Fishbourne Roman Palace, Fishbourne, UK
- South Downs Centre, Midhurst, UK
| | - Alan Cooper
- BlueSkyGenetics, Adelaide, South Australia, Australia
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Agnar Helgason
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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18
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Manzali SB, Yu E, Ravona-Springer R, Livny A, Golan S, Ouyang Y, Lesman-Segev O, Liu L, Ganmore I, Alkelai A, Gan-Or Z, Lin HM, Heymann A, Schnaider Beeri M, Greenbaum L. Alzheimer’s Disease Polygenic Risk Score Is Not Associated With Cognitive Decline Among Older Adults With Type 2 Diabetes. Front Aging Neurosci 2022; 14:853695. [PMID: 36110429 PMCID: PMC9468264 DOI: 10.3389/fnagi.2022.853695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesMultiple risk loci for late-onset Alzheimer’s disease (LOAD) have been identified. Type 2 diabetes (T2D) is a risk factor for cognitive decline, dementia and Alzheimer’s disease (AD). We investigated the association of polygenic risk score (PRS) for LOAD with overall cognitive functioning and longitudinal decline, among older adults with T2D.MethodsThe study included 1046 Jewish participants from the Israel Diabetes and Cognitive Decline (IDCD) study, aged ≥ 65 years, diagnosed with T2D, and cognitively normal at baseline. The PRS included variants from 26 LOAD associated loci (at genome-wide significance level), and was calculated with and without APOE. Outcome measures, assessed in 18 months intervals, were global cognition and the specific domains of episodic memory, attention/working memory, executive functions, and language/semantic categorization. Random coefficient models were used for analysis, adjusting for demographic variables, T2D-related characteristics, and cardiovascular factors. Additionally, in a subsample of 202 individuals, we analyzed the association of PRS with the volumes of total gray matter, frontal lobe, hippocampus, amygdala, and white matter hyperintensities. Last, the association of PRS with amyloid beta (Aβ) burden was examined in 44 participants who underwent an 18F-flutemetamol PET scan.ResultsThe PRS was not significantly associated with overall functioning or decline in global cognition or any of the specific cognitive domains. Similarly, following correction for multiple testing, there was no association with Aβ burden and other brain imaging phenotypes.ConclusionOur results suggest that the cumulative effect of LOAD susceptibility loci is not associated with a greater rate of cognitive decline in older adults with T2D, and other pathways may underlie this link.
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Affiliation(s)
- Sigalit B. Manzali
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Israel
| | - Sapir Golan
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yuxia Ouyang
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Orit Lesman-Segev
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Israel
| | - Lang Liu
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Hung-Mo Lin
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- *Correspondence: Lior Greenbaum,
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19
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Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022; 12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
Principal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
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Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
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20
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Bendor CD, Bardugo A, Rotem RS, Derazne E, Gerstein HC, Tzur D, Pinhas-Hamiel O, Tsur AM, Cukierman-Yaffe T, Lebenthal Y, Afek A, Chodick G, Twig G. Glucose Intolerance in Pregnancy and Offspring Obesity in Late Adolescence. Diabetes Care 2022; 45:1540-1548. [PMID: 35670776 DOI: 10.2337/dc21-2634] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/25/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Gestational hyperglycemia is associated with deleterious neonatal outcomes, but long-term risks for offspring obesity are less clear. We estimated the odds for offspring adolescent overweight and obesity among mothers with gestational glucose intolerance. RESEARCH DESIGN AND METHODS In a mother-offspring historical cohort, the Israel military conscription data set was linked to a large health maintenance organization. Included were women who were evaluated at adolescence and underwent two-step gestational diabetes screening (mean age, 31 years) with a 50-g glucose challenge test (GCT), followed by a 100-g oral glucose tolerance test (OGTT) if the result was abnormal. Glucose tolerance categories included gestational normoglycemia, abnormal GCT with normal OGTT, impaired glucose tolerance (IGT; one abnormal OGTT value), and gestational diabetes. The primary outcome was offspring overweight/obesity (BMI ≥85th percentile) at adolescence, measured prior to military conscription. Logistic regression models were applied. RESULTS Of 33,482 mother-offspring pairs, overweight and obesity were observed in 6,516 offspring. Across increasing categories of pregnancy glycemia, the proportions of offspring with adolescent overweight/obesity increased: normoglycemia, 19%; abnormal GCT with normal OGTT, 22%; gestational IGT, 24%; and gestational diabetes, 25% (P < 0.0001). Corresponding odds ratios after adjustment for the mother's late adolescent characteristics (sociodemographic confounders and BMI) and pregnancy age were 1.2 (95% CI 1.1-1.4), 1.3 (1.2-1.5), and 1.4 (1.3-1.6), respectively. Further adjustment for offspring birth weight percentile and sociodemographic variables did not materially change results. Associations were more pronounced with increasing obesity severity. CONCLUSIONS Gestational glucose intolerance, including categories not meeting the gestational diabetes threshold, was associated with increased odds for offspring overweight/obesity at late adolescence.
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Affiliation(s)
- Cole D Bendor
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Aya Bardugo
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Ran Shmuel Rotem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA.,Kahn-Sagol-Maccabi Research and Innovation Institute, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Estela Derazne
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Dorit Tzur
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Orit Pinhas-Hamiel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Avishai M Tsur
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Medicine "B," Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Tali Cukierman-Yaffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Endocrinology, Sheba Medical Center, Ramat Gan, Israel
| | - Yael Lebenthal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Management, Sheba Medical Center, Ramat Gan, Israel
| | - Gabriel Chodick
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabitech, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Gilad Twig
- Department of Military Medicine, Hebrew University, Jerusalem, and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Institute of Endocrinology, Sheba Medical Center, Ramat Gan, Israel.,Department of Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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21
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Wangkumhang P, Greenfield M, Hellenthal G. An efficient method to identify, date, and describe admixture events using haplotype information. Genome Res 2022; 32:gr.275994.121. [PMID: 35794007 PMCID: PMC9435750 DOI: 10.1101/gr.275994.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
We present fastGLOBETROTTER, an efficient new haplotype-based technique to identify, date, and describe admixture events using genome-wide autosomal data. With simulations, we show how fastGLOBETROTTER reduces computation time by an order of magnitude relative to the related technique GLOBETROTTER without suffering loss of accuracy. We apply fastGLOBETROTTER to a cohort of more than 6000 Europeans from 10 countries, revealing previously unreported admixture signals. In particular, we infer multiple periods of admixture related to East Asian or Siberian-like sources, starting >2000 yr ago, in people living in countries north of the Baltic Sea. In contrast, we infer admixture related to West Asian, North African, and/or Southern European sources in populations south of the Baltic Sea, including admixture dated to ∼300-700 CE, overlapping the fall of the Roman Empire, in people from Belgium, France, and parts of Germany. Our new approach scales to analyzing hundreds to thousands of individuals from a putatively admixed population and, hence, is applicable to emerging large-scale cohorts of genetically homogeneous populations.
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Affiliation(s)
- Pongsakorn Wangkumhang
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Matthew Greenfield
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Garrett Hellenthal
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
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22
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Fishman B, Sharon A, Itelman E, Tsur AM, Fefer P, Barbash IM, Segev A, Matetzky S, Guetta V, Grossman E, Maor E. Invasive Management in Older Adults (≥80 Years) With Non-ST Elevation Myocardial Infarction. Mayo Clin Proc 2022; 97:1247-1256. [PMID: 35787854 DOI: 10.1016/j.mayocp.2022.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/08/2022] [Accepted: 03/15/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To evaluate the association of invasive management (coronary angiogram) with all-cause mortality among older adult (≥80 years of age) patients presenting with non-ST elevation myocardial infarction (NSTEMI) by frailty status. PATIENTS AND METHODS This study used a retrospective cohort of consecutive older adult patients who were hospitalized with NSTEMI as their primary clinical diagnosis between August 1, 2008, and December 31, 2019. Cox regression models were applied with stratification by frailty status (low, medium, and high). Extensive sensitivity analyses were conducted including propensity score matching and inverse probability treatment weighting models. RESULTS The study population included 2317 patients with median age of 86 years (IQR, 83-90 years) of whom 1243 (53.6%) were men. Patients who were managed invasively (n=581 [25%]) were less likely to be frail (7% vs 44%, P<.001). During the follow-up (median, 19 months, IQR, 4-41 months), 1599 (69%) patients died. In a multivariable Cox model, invasive approach was associated with adjusted hazard ratio (HR) of 0.61 (95% CI, 0.53 to 0.71) for the risk of death. The benefit of invasive approach was consistent among low, medium, and high frailty subgroups with adjusted HRs of 0.74 (95% CI, 0.58 to 0.93), 0.65 (95% CI, 0.50 to 0.85), and 0.52 (95% CI, 0.34 to 0.78), respectively (P for interaction = 0.48). Results were consistent with propensity score matching and inverse probability treatment weighting analyses (HR, 0.6; 95% CI, 0.50 to 0.71 and HR, 0.67; 95% CI, 0.55 to 0.82, respectively). Sensitivity analysis addressing potential immortal time bias and residual confounding yielded similar results. CONCLUSION Invasive approach is associated with improved survival among older adults with NSTEMI irrespective of frailty status.
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Affiliation(s)
- Boris Fishman
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Department of Medicine D and the Hypertension Unit, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Edward Itelman
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Medicine T, Sheba Medical Center, Tel-Hashomer, Israel
| | - Avishai M Tsur
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Israel Defense Forces, Medical Corps, Tel Hashomer, Ramat Gan, Israel; Department of Military Medicine, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
| | - Paul Fefer
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Israel Moshe Barbash
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amit Segev
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shlomi Matetzky
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Victor Guetta
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Grossman
- Department of Medicine D and the Hypertension Unit, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elad Maor
- Olga and Lev Leviev Heart Center, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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23
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Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [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: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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24
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Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 2022; 11:77625. [PMID: 35635751 PMCID: PMC9293011 DOI: 10.7554/elife.77625] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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25
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Ádám V, Bánfai Z, Sümegi K, Büki G, Szabó A, Magyari L, Miseta A, Kásler M, Melegh B. Genome-Wide Marker Data-Based Comparative Population Analysis of Szeklers From Korond, Transylvania, and From Transylvania Living Non-Szekler Hungarians. Front Genet 2022; 13:841769. [PMID: 35419037 PMCID: PMC9000985 DOI: 10.3389/fgene.2022.841769] [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: 12/22/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide genotype data from 48 carefully selected population samples of Transylvania-living Szeklers and non-Szekler Hungarians were analyzed by comparative analysis. Our analyses involved contemporary Hungarians living in Hungary, other Europeans, and Eurasian samples counting 530 individuals altogether. The source of the Szekler samples was the commune of Korond, Transylvania. The analyzed non-Szekler Hungarian samples were collected from villages with a history dating back to the era of the Árpád Dynasty. Population structure by principal component analysis and ancestry analysis also revealed a great within-group similarity of the analyzed Szeklers and non-Szekler Transylvanian Hungarians. These groups also showed similar genetic patterns with each other. Haplotype analyses using identity-by-descent segment discovering tools showed that average pairwise identity-by-descent sharing is similar in the investigated populations, but the Korond Szekler samples had higher average sharing with the Hungarians from Hungary than non-Szekler Transylvanian Hungarians. Average sharing results showed that both groups are isolated compared to other Europeans, and pointed out that the non-Szekler Transylvanian Hungarian inhabitants of the investigated Árpád Age villages are more isolated than investigated Szeklers from Korond. This was confirmed by our autozygosity analysis as well. Identity-by-descent segment analyses and 4-population tests also confirmed that these Hungarian-speaking Transylvanian ethnic groups are strongly related to Hungarians living in Hungary.
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Affiliation(s)
- Valerián Ádám
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - Zsolt Bánfai
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Katalin Sümegi
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gergely Büki
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - András Szabó
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Lili Magyari
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Miseta
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | | | - Béla Melegh
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
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26
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Elliott KS, Haber M, Daggag H, Busby GB, Sarwar R, Kennet D, Petraglia M, Petherbridge LJ, Yavari P, Heard-Bey FU, Shobi B, Ghulam T, Haj D, Al Tikriti A, Mohammad A, Antony S, Alyileili M, Alaydaroos S, Lau E, Butler M, Yavari A, Knight JC, Ashrafian H, Barakat MT. Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture, Population History, and Geography. Mol Biol Evol 2022; 39:msac039. [PMID: 35192718 PMCID: PMC8911814 DOI: 10.1093/molbev/msac039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.
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Affiliation(s)
- Katherine S Elliott
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Hinda Daggag
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - George B Busby
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Rizwan Sarwar
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Derek Kennet
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Parisa Yavari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Bindu Shobi
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - Tariq Ghulam
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | - Dalia Haj
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | | | | | - Suma Antony
- Imperial College London Diabetes Centre, Abu Dhabi, UAE
| | | | | | - Evelyn Lau
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mark Butler
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Arash Yavari
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Houman Ashrafian
- Experimental Therapeutics, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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27
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Recurring pathogenic variants in the BRCA2 gene in the Ethiopian Jewish population. Founder mutations? Fam Cancer 2022; 21:121-123. [PMID: 35166990 DOI: 10.1007/s10689-021-00255-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/07/2021] [Indexed: 11/04/2022]
Abstract
Mutations in the BRCA1 and BRCA2 genes increase the risk for various cancers including breast, ovarian, prostate, pancreas and melanoma. Identifying BRCA1/2 mutation carriers enables risk assessment, surveillance, early detection and risk reduction. In certain Israeli sub-populations recurring and founder mutations have been identified and for these, testing for founder mutations is simple, efficient and cost-effective. Founder mutations in the Jewish Ethiopian population have not been described. We report here the identification of a recurring BRCA2 mutation in the Ethiopian Jewish population; c.5159C>A; p.Ser1720Ter, which has only been described once before in this population. In addition, in another family of the same origin we found the BRCA2 c.7579delG; p.Val2527Ter mutation that has been previously described in two different Jewish Ethiopian families. In Israel genetic testing is performed in a sequential stepwise manner, first testing a panel of predominant mutations and if negative further testing by gene sequencing is offered. Recently it has been decided to expand the founder mutation panel to include mutations which have been found in two or more separate families. This new panel will include the BRCA2 c.7579delG; p.Val2527Ter mutation, and we recommend that the BRCA2 c.5159C>A; p.Ser1720Ter mutation should also be added to the new predominant mutation panel.
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28
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Fishman B, Zloof Y, Orr O, Tsur AM, Furer A, Omer Gilon M, Chodick G, Leiba A, Derazne E, Tzur D, Afek A, Grossman E, Twig G. The opposing trends of body mass index and blood pressure during 1977-2020; nationwide registry of 2.8 million male and female adolescents. Cardiovasc Diabetol 2021; 20:242. [PMID: 34963457 PMCID: PMC8715587 DOI: 10.1186/s12933-021-01433-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 12/30/2022] Open
Abstract
Background Elevated blood pressure among adolescents has been shown to be associated with future adverse cardiovascular outcomes and early onset diabetes. Most data regarding systolic and diastolic blood pressure trends are based on surveys of selected populations within 10–20-year periods. The goal of this study was to characterize the secular trend of blood pressure given the rising prevalence of adolescent obesity. Methods This nationwide population-based study included 2,785,515 Israeli adolescents (41.6% females, mean age 17.4 years) who were medically evaluated and whose weight, height and blood pressure were measured, prior to mandatory military service between 1977 and 2020. The study period was divided into 5-year intervals. Linear regression models were used to describe the P for trend along the time intervals. Analysis of covariance was used to calculate means of blood pressure adjusted for body mass index. Results During the study period, the mean body mass index increased by 2.1 and 1.6 kg/m2 in males and females, respectively (P for trend < 0.001 in both sexes). The mean diastolic blood pressure decreased by 3.6 mmHg in males and by 2.9 mmHg in females (P < 0.001 in both sexes). The mean systolic blood pressure increased by 1.6 mmHg in males and decreased by 1.9 mmHg in females. These trends were also consistent when blood pressure values were adjusted to body mass index. Conclusion Despite the increase in body mass index over the last four decades, diastolic blood pressure decreased in both sexes while systolic blood pressure increased slightly in males and decreased in females. Supplementary Information The online version contains supplementary material available at 10.1186/s12933-021-01433-0.
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Affiliation(s)
- Boris Fishman
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Division of Cardiology, The Leviev Heart Center, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Talpiot Sheba Medical Leadership Program, Ramat Gan, Israel
| | - Yair Zloof
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Omri Orr
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Orthopedic Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Avishai M Tsur
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Medicine 'B', Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Ariel Furer
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Division of Cardiology, The Leviev Heart Center, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ma'ayan Omer Gilon
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Chodick
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabitech, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Adi Leiba
- Division of Nephrology and Hypertension, Assuta Ashdod Academic Medical Center affiliated to Ben Gurion University, Beer Sheva, Israel.,Harvard Medical School, Boston, MA, USA
| | - Estela Derazne
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dorit Tzur
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Management, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Ehud Grossman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Hypertension Unit and the Internal Division, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Gilad Twig
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
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29
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A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia. Hum Genet 2021; 141:697-707. [PMID: 34839402 DOI: 10.1007/s00439-021-02405-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Mutations in the GJB2 gene are known to be a major cause of autosomal recessive deafness 1A (OMIM 220290). The most common pathogenic variants of the GJB2 gene have a high ethno-geographic specificity in their distribution, being attributed to a founder effect related to the Neolithic migration routes of Homo sapiens. The c.-23 + 1G > A splice site variant is frequently found among deaf patients of both Caucasian and Asian origins. It is currently unknown whether the spread of this mutation across Eurasia is a result of the founder effect or if it could have multiple local centers of origin. To determine the origin of c.-23 + 1G > A, we reconstructed haplotypes by genotyping SNPs on an Illumina OmniExpress 730 K platform of 23 deaf individuals homozygous for this variant from different populations of Eurasia. The analyses revealed the presence of common regions of homozygosity in different individual genomes in the sample. These data support the hypothesis of the common founder effect in the distribution of the c.-23 + 1G > A variant of the GJB2 gene. Based on the published data on the c.-23 + 1G > A prevalence among 16,177 deaf people and the calculation of the TMRCA of the modified f2-haplotypes carrying this variant, we reconstructed the potential migration routes of the carriers of this mutation around the world. This analysis indicates that the c.-23 + 1G > A variant in the GJB2 gene may have originated approximately 6000 years ago in the territory of the Caucasus or the Middle East then spread throughout Europe, South and Central Asia and other regions of the world.
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30
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Shapiro M, Arbel C, Zucker I, Balmor GR, Lutski M, Derazne E, Beer Z, Pinhas-Hamiel O, Mosenzon O, Tzur D, Afek A, Tirosh A, Cukierman-Yaffe T, Gerstein HC, Rosenberg V, Chodick G, Raz I, Twig G. Asthma in Youth and Early-onset Type 2 Diabetes: A Nationwide Study of 1.72 Million Israeli Adolescents. J Clin Endocrinol Metab 2021; 106:e5043-e5053. [PMID: 34291806 DOI: 10.1210/clinem/dgab542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND The prevalence of both asthma and early-onset diabetes is on the rise; however, the association between them remains unclear. We examined a possible association of asthma at adolescence with type 2 diabetes in young adulthood. METHODS This is a nationwide, population-based study of 1 718 541 Israeli adolescents (57% males; mean age 17.3 years; range 16-19 years), examined before compulsory military service between 1992 and 2016, with data linked to the Israeli National Diabetes Registry. Asthma diagnosis and severity were determined by a board-certified pulmonologist and based on spirometry tests. RESULTS Type 2 diabetes developed in 58/9090 (0.64%), 507/97 059 (0.52%), 114/23 332 (0.49%), and 7095/1 589 060 (0.44%) persons with moderate-to-severe, mild, inactive, and no history of asthma, respectively, during a mean follow-up >13 years. The respective odds ratios (ORs) were 1.33 (95% CI, 1.02-1.74), 1.17 (1.06-1.28), and 1.09 (0.9-1.31), considering those without asthma history as the reference, in a model adjusted for birth year, sex, body mass index, and other sociodemographic variables. The association persisted when the analysis accounted for coexisting morbidities, and when persons without asthma, individually matched by age, sex, birth year, and body mass index were the reference. Both mild and moderate-to-severe asthma were associated with type 2 diabetes before age 35 years: ORs 1.18 (1.05-1.34) and 1.44 (1.05-2.00), respectively. The strength of the association was accentuated over time. The effect was unchanged when adjusted for oral and inhaled glucocorticoid use. CONCLUSION Adolescents with active asthma have higher risk to develop type 2 diabetes. This seems related to disease severity, independent of adolescent obesity status, apparent before age 35 years, and more pronounced in recent years.
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Affiliation(s)
- Michael Shapiro
- Department of Internal Medicine T, Tel Aviv Sourasky Medical Center, Tel Aviv 6492601, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Israel Defense Forces Medical Corps, Ramat Gan 5510802, Israel
| | - Chen Arbel
- Israel Defense Forces Medical Corps, Ramat Gan 5510802, Israel
- Department of Military Medicine, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem 9112102, Israel
| | - Inbar Zucker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- The Israel Center for Disease Control, Ministry of Health, Ramat Gan 5262160, Israel
| | - Gingy Ronen Balmor
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Shamir (Assaf-Harofeh) Medical Center, Zerifin 70300, Israel
| | - Miri Lutski
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- The Israel Center for Disease Control, Ministry of Health, Ramat Gan 5262160, Israel
| | - Estela Derazne
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zivan Beer
- Israel Defense Forces Medical Corps, Ramat Gan 5510802, Israel
- Department of Military Medicine, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem 9112102, Israel
| | - Orit Pinhas-Hamiel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Pediatric Endocrinology, Safra Children Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan 5266202, Israel
| | - Ofri Mosenzon
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem 91120, Israel
| | - Dorit Tzur
- Israel Defense Forces Medical Corps, Ramat Gan 5510802, Israel
- Department of Military Medicine, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem 9112102, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Central Management, Sheba Medical Center, Tel Hashomer, Ramat Gan 5266202, Israel
| | - Amir Tirosh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan 5266202, Israel
| | - Tali Cukierman-Yaffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan 5266202, Israel
| | - Hertzel C Gerstein
- Department of Medicine, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Vered Rosenberg
- Maccabitech Research Institute, Maccabi Healthcare Services, Tel Aviv 6801296, Israel
| | - Gabriel Chodick
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Maccabitech Research Institute, Maccabi Healthcare Services, Tel Aviv 6801296, Israel
| | - Itamar Raz
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem 91120, Israel
| | - Gilad Twig
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Israel Defense Forces Medical Corps, Ramat Gan 5510802, Israel
- Department of Military Medicine, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem 9112102, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan 5266202, Israel
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Warshauer EM, Brown A, Fuentes I, Shortt J, Gignoux C, Montinaro F, Metspalu M, Youssefian L, Vahidnezhad H, Jacków J, Christiano AM, Uitto J, Fajardo-Ramírez ÓR, Salas-Alanis JC, McGrath JA, Consuegra L, Rivera C, Maier PA, Runfeldt G, Behar DM, Skorecki K, Sprecher E, Palisson F, Norris DA, Bruckner AL, Kogut I, Bilousova G, Roop DR. Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry. Am J Med Genet A 2021; 185:3390-3400. [PMID: 34435747 DOI: 10.1002/ajmg.a.62456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 11/11/2022]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare genodermatosis caused by mutations in the gene coding for type VII collagen (COL7A1). More than 800 different pathogenic mutations in COL7A1 have been described to date; however, the ancestral origins of many of these mutations have not been precisely identified. In this study, 32 RDEB patient samples from the Southwestern United States, Mexico, Chile, and Colombia carrying common mutations in the COL7A1 gene were investigated to determine the origins of these mutations and the extent to which shared ancestry contributes to disease prevalence. The results demonstrate both shared European and American origins of RDEB mutations in distinct populations in the Americas and suggest the influence of Sephardic ancestry in at least some RDEB mutations of European origins. Knowledge of ancestry and relatedness among RDEB patient populations will be crucial for the development of future clinical trials and the advancement of novel therapeutics.
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Affiliation(s)
- Emily Mira Warshauer
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Adam Brown
- Avotaynu Research Partnership LLC, Englewood, New Jersey, USA
| | - Ignacia Fuentes
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.,Fundación DEBRA Chile, Santiago, Chile
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology and Genetics, University of Bari, Bari, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joanna Jacków
- Department of Dermatology, Columbia University, New York, New York, USA.,St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | - Angela M Christiano
- Department of Dermatology, Columbia University, New York, New York, USA.,Department of Genetics and Development, Columbia University, New York, New York, USA
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Óscar R Fajardo-Ramírez
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Julio C Salas-Alanis
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Instituto Dermatologico de Jalisco, Zapopan, Mexico
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | | | - Carolina Rivera
- Fundación DEBRA Colombia, Bogotá, Colombia.,Department of Medical Genetics, Pediatric Hospital, Fundacion Cardioinfantil-Universidad del Rosario, Bogotá, Colombia
| | - Paul A Maier
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Goran Runfeldt
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Karl Skorecki
- Azrieli Faculty of Medicine of the Galilee, Bar-Ilan University, Safed, Israel
| | - Eli Sprecher
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Francis Palisson
- Fundación DEBRA Chile, Santiago, Chile.,Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David A Norris
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anna L Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Igor Kogut
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dennis R Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
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Kumar L, Farias K, Prakash S, Mishra A, Mustak MS, Rai N, Thangaraj K. Dissecting the genetic history of the Roman Catholic populations of West Coast India. Hum Genet 2021; 140:1487-1498. [PMID: 34424406 DOI: 10.1007/s00439-021-02346-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Migration and admixture history of populations have always been curious and an interesting theme. The West Coast of India harbours a rich diversity, bestowing various ethno-linguistic groups, with many of them having well-documented history of migrations. The Roman Catholic is one such distinct group, whose origin was much debated. While some historians and anthropologists relating them to ancient group of Gaud Saraswat Brahmins, others relating them for being members of the Jews Lost Tribes in the first Century migration to India. Historical records suggests that this community was later forcibly converted to Christianity by the Portuguese in Goa during the Sixteenth Century. Till date, no genetic study was done on this group to infer their origin and genetic affinity. Hence, we analysed 110 Roman Catholics from three different locations of West Coast of India including Goa, Kumta and Mangalore using both uniparental and autosomal markers to understand their genetic history. We found that the Roman Catholics have close affinity with the Indo-European linguistic groups, particularly Brahmins. Additionally, we detected genetic signal of Jews in the linkage disequilibrium-based admixture analysis, which was absent in other Indo-European populations, who are inhabited in the same geographical regions. Haplotype-based analysis suggests that the Roman Catholics consist of South Asian-specific ancestry and showed high drift. Ancestry-specific historical population size estimation points to a possible bottleneck around the time of Goan inquisition (fifteenth century). Analysis of the Roman Catholics data along with ancient DNA data of Neolithic and bronze age revealed that the Roman Catholics fits well in a basic model of ancient ancestral composition, typical of most of the Indo-European caste groups of India. Mitochondrial DNA (mtDNA) analysis suggests that most of the Roman Catholics have aboriginal Indian maternal genetic ancestry; while the Y chromosomal DNA analysis indicates high frequency of R1a lineage, which is predominant in groups with higher ancestral North Indian (ANI) component. Therefore, we conclude that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of Brahmin community of India, having Indo-Europeans genetic affinity along with cryptic Jewish admixture, which needs to be explored further.
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Affiliation(s)
- Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Kranti Farias
- Canadian Institute for Jewish Research, Montreal, Canada
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Anshuman Mishra
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, 590 53, Ulrika, Sweden
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, 574199, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, 53 University Road, Lucknow, 226007, India.
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India.
- DBT-Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, 500007, India.
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López S, Tarekegn A, Band G, van Dorp L, Bird N, Morris S, Oljira T, Mekonnen E, Bekele E, Blench R, Thomas MG, Bradman N, Hellenthal G. Evidence of the interplay of genetics and culture in Ethiopia. Nat Commun 2021; 12:3581. [PMID: 34117245 PMCID: PMC8196081 DOI: 10.1038/s41467-021-23712-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with-and shape-genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals' birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.
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Affiliation(s)
- Saioa López
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Ayele Tarekegn
- Department of Archaeology and Heritage Management, College of Social Sciences, Addis Ababa University, New Classrooms (NCR) Building, Second Floor, Office No. 214, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucy van Dorp
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Nancy Bird
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Sam Morris
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Tamiru Oljira
- Genomics & Bioinformatics Research Directorate (GBRD), Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
| | - Ephrem Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Endashaw Bekele
- College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Roger Blench
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of History, University of Jos, Jos, Nigeria
| | - Mark G Thomas
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Garrett Hellenthal
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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34
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mtDNA tests as a vehicle for Jewish recognition of Former Soviet Union Israeli citizens: religious and political debate. BIOSOCIETIES 2021. [DOI: 10.1057/s41292-021-00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Bose A, Platt DE, Parida L, Drineas P, Paschou P. Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India. Mol Biol Evol 2021; 38:1809-1819. [PMID: 33481022 PMCID: PMC8097304 DOI: 10.1093/molbev/msaa321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.
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Affiliation(s)
- Aritra Bose
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Daniel E Platt
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Laxmi Parida
- Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Petros Drineas
- Computer Science Department, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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36
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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Zhang C, Ostrom QT, Hansen HM, Gonzalez-Maya J, Hu D, Ziv E, Morimoto L, de Smith AJ, Muskens IS, Kline CN, Vaksman Z, Hakonarson H, Diskin SJ, Kruchko C, Barnholtz-Sloan JS, Ramaswamy V, Ali-Osman F, Bondy ML, Taylor MD, Metayer C, Wiemels JL, Walsh KM. European genetic ancestry associated with risk of childhood ependymoma. Neuro Oncol 2021; 22:1637-1646. [PMID: 32607579 DOI: 10.1093/neuonc/noaa130] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ependymoma is a histologically defined central nervous system tumor most commonly occurring in childhood. Population-level incidence differences by race/ethnicity are observed, with individuals of European ancestry at highest risk. We aimed to determine whether extent of European genetic ancestry is associated with ependymoma risk in US populations. METHODS In a multi-ethnic study of Californian children (327 cases, 1970 controls), we estimated the proportions of European, African, and Native American ancestry among recently admixed Hispanic and African American subjects and estimated European admixture among non-Hispanic white subjects using genome-wide data. We tested whether genome-wide ancestry differences were associated with ependymoma risk and performed admixture mapping to identify associations with local ancestry. We also evaluated race/ethnicity-stratified ependymoma incidence data from the Central Brain Tumor Registry of the United States (CBTRUS). RESULTS CBTRUS data revealed that African American and Native American children have 33% and 36%, respectively, reduced incidence of ependymoma compared with non-Hispanic whites. In genetic analyses, a 20% increase in European ancestry was associated with a 1.31-fold higher odds of ependymoma among self-reported Hispanics and African Americans (95% CI: 1.08-1.59, Pmeta = 6.7 × 10-3). Additionally, eastern European ancestral substructure was associated with increased ependymoma risk in non-Hispanic whites (P = 0.030) and in Hispanics (P = 0.043). Admixture mapping revealed a peak at 20p13 associated with increased local European ancestry, and targeted fine-mapping identified a lead variant at rs6039499 near RSPO4 (odds ratio = 1.99; 95% CI: 1.45-2.73; P = 2.2 × 10-5) but which was not validated in an independent set of posterior fossa type A patients. CONCLUSIONS Interethnic differences in ependymoma risk are recapitulated in the genomic ancestry of ependymoma patients, implicating regions to target in future association studies.
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Affiliation(s)
- Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA.,Central Brain Tumor Registry of the United States, Hinsdale, Illinois, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Julio Gonzalez-Maya
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley Berkeley, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, California, USA
| | - Ivo S Muskens
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, California, USA
| | - Cassie N Kline
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.,Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sharon J Diskin
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol Kruchko
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Francis Ali-Osman
- Department of Neurosurgery and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Catherine Metayer
- School of Public Health, University of California Berkeley Berkeley, California, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, California, USA
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA.,Department of Neurosurgery and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA
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Huang X, Wang S, Jin L, He Y. Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biol Open 2021; 10:bio056523. [PMID: 33495209 PMCID: PMC7888712 DOI: 10.1242/bio.056523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023] Open
Abstract
Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.
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Affiliation(s)
- Xin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Bardugo A, Bendor CD, Zucker I, Lutski M, Cukierman-Yaffe T, Derazne E, Mosenzon O, Tzur D, Beer Z, Pinhas-Hamiel O, Ben-Ami M, Fishman B, Ben-Ami Shor D, Raz I, Afek A, Gerstein HC, Häring HU, Tirosh A, Levi Z, Twig G. Adolescent Nonalcoholic Fatty Liver Disease and Type 2 Diabetes in Young Adulthood. J Clin Endocrinol Metab 2021; 106:e34-e44. [PMID: 33075820 DOI: 10.1210/clinem/dgaa753] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT The long-term risk of type 2 diabetes in adolescents with nonalcoholic fatty liver disease (NAFLD) is unclear. OBJECTIVE To assess type 2 diabetes risk among adolescents with NAFLD. DESIGN AND SETTING A nationwide, population-based study of Israeli adolescents who were examined before military service during 1997-2011 and were followed until December 31, 2016. PARTICIPANTS A total of 1 025 796 normoglycemic adolescents were included. INTERVENTIONS Biopsy or radiographic tests were prerequisite for NAFLD diagnosis. Data were linked to the Israeli National Diabetes Registry. MAIN OUTCOME MEASURES Type 2 diabetes incidence. RESULTS During a mean follow-up of 13.3 years, 12 of 633 adolescents with NAFLD (1.9%; all with high body mass index [BMI] at baseline) were diagnosed with type 2 diabetes compared with 2917 (0.3%) adolescents without NAFLD. The hazard ratio (HR) for type 2 diabetes was 2.59 (95% confidence interval [CI], 1.47-4.58) for the NAFLD vs. the non-NAFLD group after adjustment for BMI and sociodemographic confounders. The elevated risk persisted in several sensitivity analyses. These included an analysis of persons without other metabolic comorbidities (adjusted HR, 2.75 [95% CI, 1.48-5.14]) and of persons with high BMI; and an analysis whose outcome was type 2 diabetes by age 30 years (adjusted HR, 2.14 [95% CI, 1.02-4.52]). The results remained significant when a sex-, birth year-, and BMI-matched control group was the reference (adjusted HR, 2.98 [95% CI, 1.54-5.74]). CONCLUSIONS Among normoglycemic adolescents, NAFLD was associated with an increased adjusted risk for type 2 diabetes, which may be apparent before age 30 years.
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Affiliation(s)
- Aya Bardugo
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Cole D Bendor
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Inbar Zucker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Israel Center for Disease Control, Ministry of Health, Ramat Gan, Israel
| | - Miri Lutski
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Israel Center for Disease Control, Ministry of Health, Ramat Gan, Israel
| | - Tali Cukierman-Yaffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Estela Derazne
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofri Mosenzon
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Dorit Tzur
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Zivan Beer
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
| | - Orit Pinhas-Hamiel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Michal Ben-Ami
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Boris Fishman
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Internal Medicine D and Hypertension Unit, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Dana Ben-Ami Shor
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Gastroenterology, Tel-Aviv Medical Center, Tel Aviv, Israel
| | - Itamar Raz
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Central Management, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | | | - Hans-Ulrich Häring
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
- Institute of Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany
- German Center for Diabetes Research, Tübingen, Germany
| | - Amir Tirosh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Zohar Levi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Gastroenterology Department, Rabin Medical Center, Petach Tikva, Israel
| | - Gilad Twig
- Department of Military Medicine, Hebrew University, Jerusalem and the Israel Defense Forces Medical Corps, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Endocrinology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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Balanovska EV, Petrushenko VS, Koshel SM, Pocheshkhova EA, Chernevskiy DK, Mirzaev KB, Abdullaev S, Balanovsky OP. Cartographic atlas of frequency variation for 45 pharmacogenetic markers in populations of Russia and its neighbor states. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lack of information about the frequency of pharmacogenetic markers in Russia impedes the adoption of personalized treatment algorithms originally developed for West European populations. The aim of this paper was to study the distribution of some clinically significant pharmacogenetic markers across Russia. A total of 45 pharmacogenetic markers were selected from a few population genetic datasets, including ADME, drug target and hemostasis-controlling genes. The total number of donors genotyped for these markers was 2,197. The frequencies of these markers were determined for 50 different populations, comprised of 137 ethnic and subethnic groups. A comprehensive pharmacogenetic atlas was created, i.e. a systematic collection of gene geographic maps of frequency variation for 45 pharmacogenetic DNA markers in Russia and its neighbor states. The maps revealed 3 patterns of geographic variation. Clinal variation (a gradient change in frequency along the East-West axis) is observed in the pharmacogenetic markers that follow the main pattern of variation for North Eurasia (13% of the maps). Uniform distribution singles out a group of markers that occur at average frequency in most Russian regions (27% of the maps). Focal variation is observed in the markers that are specific to a certain group of populations and are absent in other regions (60% of the maps). The atlas reveals that the average frequency of the marker and its frequency in individual populations do not indicate the type of its distribution in Russia: a gene geographic map is needed to uncover the pattern of its variation.
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Affiliation(s)
- EV Balanovska
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia
| | - VS Petrushenko
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
| | - SM Koshel
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - EA Pocheshkhova
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Kuban State Medical Institute, Krasnodar, Russia
| | - DK Chernevskiy
- Bochkov Research Center for Medical Genetics, Moscow, Russia
| | - KB Mirzaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - ShP Abdullaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - OP Balanovsky
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
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41
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Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas. Sci Rep 2020; 10:21428. [PMID: 33293675 PMCID: PMC7722846 DOI: 10.1038/s41598-020-78487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/19/2020] [Indexed: 11/08/2022] Open
Abstract
Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.
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Hochman A. Janus-faced race: Is race biological, social, or mythical? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 175:453-464. [PMID: 33135802 DOI: 10.1002/ajpa.24169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/13/2020] [Accepted: 10/10/2020] [Indexed: 01/29/2023]
Abstract
As belief in the reality of race as a biological category among U.S. anthropologists has fallen, belief in the reality of race as a social category has risen in its place. The view that race simply does not exist-that it is a myth-is treated with suspicion. While racial classification is linked to many of the worst evils of recent history, it is now widely believed to be necessary to fight back against racism. In this article, I argue that race is indeed a biological fiction, but I critique the claim that race is socially real. I defend a form of anti-realist reconstructionism about race, which says that there are no races, only racialized groups-groups mistakenly believed to be races. I argue that this is the most attractive position about race from a metaphysical perspective, and that it is also the position most conductive to public understanding and social justice.
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Affiliation(s)
- Adam Hochman
- Department of Philosophy, Faculty of Arts, Macquarie University, Macquarie Park, New South Wales, Australia
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43
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Ádám V, Bánfai Z, Maász A, Sümegi K, Miseta A, Melegh B. Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania. J Hum Genet 2020; 65:1093-1103. [PMID: 32653894 DOI: 10.1038/s10038-020-0799-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/09/2022]
Abstract
Csango people are an East-Central European ethnographic group living mostly in the historical region of Moldavia, Romania. Their traditional language, the Csango is an old Hungarian dialect, which is a severely endangered language due to language shift. Their origin is still disputed among experts and there are many hypotheses since the 19th century. Previous genetic studies found connection with ethnic groups living in Hungary and provided evidence which might support their Hungarian origin. Another study found Inner Asian Altaic ancestry in their genetic makeup. The goal of this study was to analyze the genetic characteristics of the Csango people by comparing their genetic characteristics to contemporary Eurasian populations based on genome-wide autosomal marker data. Our findings suggest that genetic affinity of Csangos to Hungarians is more significant than to Romanians. They also have a detectable connection with Central-Asian and Siberian Turkic ethnic groups. Besides the presumable Middle Eastern/Central-Asian Turkic ancestry, Csangos show ~4% Turkic ancestry from Central Asia/Siberia, which makes them unique in comparison to all other East-Central European populations investigated in this study. The admixture that resulted in this Turkic ancestry could have occurred 30-40 generations ago, which date interval corresponds to Hungarian historical events regarding their migration and the conquest of the Carpathian basin.
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Affiliation(s)
- Valerián Ádám
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Zsolt Bánfai
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary. .,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
| | - Anita Maász
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Katalin Sümegi
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Miseta
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary. .,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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44
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Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A. Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium. Mol Biol Evol 2020; 37:3642-3653. [DOI: 10.1093/molbev/msaa169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractInferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Irene Novo
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
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45
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Twig G, Zucker I, Afek A, Cukierman-Yaffe T, Bendor CD, Derazne E, Lutski M, Shohat T, Mosenzon O, Tzur D, Pinhas-Hamiel O, Tiosano S, Raz I, Gerstein HC, Tirosh A. Adolescent Obesity and Early-Onset Type 2 Diabetes. Diabetes Care 2020; 43:1487-1495. [PMID: 32321731 DOI: 10.2337/dc19-1988] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/01/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Type 2 diabetes (T2D) is increasingly diagnosed at younger ages. We investigated the association of adolescent obesity with incident T2D at early adulthood. RESEARCH DESIGN AND METHODS A nationwide, population-based study evaluated 1,462,362 adolescents (59% men, mean age 17.4 years) during 1996-2016. Data were linked to the Israeli National Diabetes Registry. Weight and height were measured at study entry. Cox proportional models were applied. RESULTS During 15,810,751 person-years, 2,177 people (69% men) developed T2D (mean age at diagnosis 27 years). There was an interaction among BMI, sex, and incident T2D (P interaction = 0.023). In a model adjusted for sociodemographic variables, the hazard ratios for diabetes diagnosis were 1.7 (95% CI 1.4-2.0), 2.8 (2.3-3.5), 5.8 (4.9-6.9), 13.4 (11.5-15.7), and 25.8 (21.0-31.6) among men in the 50th-74th percentile, 75th-84th percentile, overweight, mild obesity, and severe obesity groups, respectively, and 2.2 (1.6-2.9), 3.4 (2.5-4.6), 10.6 (8.3-13.6), 21.1 (16.0-27.8), and 44.7 (32.4-61.5), respectively, in women. An inverse graded relationship was observed between baseline BMI and mean age of T2D diagnosis: 27.8 and 25.9 years among men and women with severe obesity, respectively, and 29.5 and 28.5 years among low-normal BMI (5th-49th percentile; reference), respectively. The projected fractions of adult-onset T2D that were attributed to high BMI (≥85th percentile) at adolescence were 56.9% (53.8-59.9%) and 61.1% (56.8-65.2%) in men and women, respectively. CONCLUSIONS Severe obesity significantly increases the risk for incidence of T2D in early adulthood in both sexes. The rise in adolescent severe obesity is likely to increase diabetes incidence in young adults in coming decades.
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Affiliation(s)
- Gilad Twig
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, and the Israel Defense Forces Medical Corps, Tel Hashomer, Ramat Gan, Israel
| | - Inbar Zucker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Arnon Afek
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Management, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Tali Cukierman-Yaffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Cole D Bendor
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, and the Israel Defense Forces Medical Corps, Tel Hashomer, Ramat Gan, Israel
| | - Estela Derazne
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Miri Lutski
- The Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Tammy Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofri Mosenzon
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Dorit Tzur
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, and the Israel Defense Forces Medical Corps, Tel Hashomer, Ramat Gan, Israel
| | - Orit Pinhas-Hamiel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Shmuel Tiosano
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Medicine, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Itamar Raz
- The Diabetes Unit, Department of Internal Medicine, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | | | - Amir Tirosh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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46
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Uchiyama J, Gillam JC, Savelyev A, Ning C. Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e16. [PMID: 37588381 PMCID: PMC10427466 DOI: 10.1017/ehs.2020.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.
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Affiliation(s)
- Junzo Uchiyama
- The Sainsbury Institute for the Study of Japanese Arts and Cultures, University of East Anglia, 64 The Close, NorwichNR1 4DH, UK
- Center for Cultural Resource Studies, Kanazawa University, Kakuma-machi, Kanazawa-shi, 920-1192, Japan
| | - J. Christopher Gillam
- Department of Sociology, Criminology and Anthropology, Winthrop University, 319 Kinard Hall, Rock Hill, SC29733, USA
| | - Alexander Savelyev
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
- Institute of Linguistics, Russian Academy of Sciences, Bolshoy Kislovsky Pereulok 1/1, 125009Moscow, Russia
| | - Chao Ning
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
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47
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Grunin M, Beykin G, Rahmani E, Schweiger R, Barel G, Hagbi-Levi S, Elbaz-Hayoun S, Rinsky B, Ganiel M, Carmi S, Halperin E, Chowers I. Association of a Variant in VWA3A with Response to Anti-Vascular Endothelial Growth Factor Treatment in Neovascular AMD. Invest Ophthalmol Vis Sci 2020; 61:48. [PMID: 32106291 PMCID: PMC7329947 DOI: 10.1167/iovs.61.2.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose Anti–vascular endothelial growth factor (VEGF) therapy for neovascular AMD (nvAMD) obtains a variable outcome. We performed a genome-wide association study for anti-VEGF treatment response in nvAMD to identify variants potentially underlying such a variable outcome. Methods Israeli patients with nvAMD who underwent anti-VEGF treatment (n = 187) were genotyped on a whole exome chip containing approximately 500,000 variants. Genotyping was correlated with delta visual acuity (deltaVA) between baseline and after three injections of anti-VEGF. Top principal components, age, and baseline VA were included in the analysis. Two lead associated variants were genotyped in an independent validation set of patients with nvAMD (n = 108). Results Linear regression analysis on 5,353,842 variants revealed five exonic variants with an association P value of less than 6 × 10−5. The top variant in the gene VWA3A (P = 1.77 × 10−6) was tested in the validation cohort. The minor allele of the VWA3A variant was associated with worse response to treatment (P = 0.02). The average deltaVA of discovery plus validation was –0.214 logMAR (≈ a gain of 10.7 Early Treatment Diabetic Retinopathy Study letters) for homozygote for the major allele, 0.172 logMAR for heterozygotes (≈ a loss of 8.6 Early Treatment Diabetic Retinopathy Study letters), and 0.21 logMAR for homozygote for the minor allele (≈ a loss of 10.5 Early Treatment Diabetic Retinopathy Study letters). Minor allele carriers had a higher frequency of macular hemorrhage at baseline. Conclusions An VWA3A gene variant was associated with worse response to anti-VEGF treatment in Israeli patients with nvAMD. The VWA3A protein is a precursor of the multimeric von Willebrand factor which is involved in blood coagulation, a system previously associated with nvAMD.
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48
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Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Aikens RC, Aneli S, Bartoli F, Bedini A, Cheronet O, Cotter DJ, Fernandes DM, Gasperetti G, Grifoni R, Guidi A, La Pastina F, Loreti E, Manacorda D, Matullo G, Morretta S, Nava A, Fiocchi Nicolai V, Nomi F, Pavolini C, Pentiricci M, Pergola P, Piranomonte M, Schmidt R, Spinola G, Sperduti A, Rubini M, Bondioli L, Coppa A, Pinhasi R, Pritchard JK. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science 2020; 366:708-714. [PMID: 31699931 DOI: 10.1126/science.aay6826] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022]
Abstract
Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome's population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.
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Affiliation(s)
- Margaret L Antonio
- Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Ziyue Gao
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Hannah M Moots
- Stanford University, Department of Anthropology, Stanford, CA, USA
| | - Michaela Lucci
- DANTE Laboratory for the study of Diet and Ancient Technology, Sapienza Università di Roma, Rome, Italy
| | - Francesca Candilio
- School of Archaeology, University College Dublin, Dublin, Ireland.,Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Diego Calderon
- Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | | | - Rachael C Aikens
- Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Serena Aneli
- Dipartimento di Scienze Mediche, Università di Torino, Torino, Italy
| | - Fulvio Bartoli
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Alessandro Bedini
- Ministero dei Beni e delle Attività Culturali (retired), Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Daniel J Cotter
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gabriella Gasperetti
- Soprintendenza Archeologia, belle arti e paesaggio per le province di Sassari e Nuoro, Sassari, Italy
| | - Renata Grifoni
- Dipartimento di Civiltà e Forme del Sapere, Università di Pisa, Pisa, Italy
| | - Alessandro Guidi
- Dipartimento di Studi Umanistici, Università degli Studi di Roma Tre, Rome, Italy
| | | | - Ersilia Loreti
- Curatore beni culturali presso la Sovrintendenza Capitolina, Rome, Italy
| | - Daniele Manacorda
- Dipartimento di Studi Umanistici Università degli Studi di Roma Tre, Rome, Italy
| | - Giuseppe Matullo
- Dipartimento di Scienze Mediche, Università di Torino, Torino, Italy
| | - Simona Morretta
- Soprintendenza Speciale Archeologia Belle Arti e Paesaggio di Roma, Rome, Italy
| | - Alessia Nava
- DANTE Laboratory for the study of Diet and Ancient Technology, Sapienza Università di Roma, Rome, Italy.,Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy
| | | | - Federico Nomi
- Dipartimento di Studi Umanistici, Università degli Studi di Roma Tre, Rome, Italy
| | - Carlo Pavolini
- Università della Tuscia, DISUCOM Dipartimento di Scienze Umanistiche, della Comunicazione e del Turismo, Viterbo, Italy
| | - Massimo Pentiricci
- Curatore beni culturali presso la Sovrintendenza Capitolina, Rome, Italy
| | | | - Marina Piranomonte
- Soprintendenza speciale Archeologia Belle arti e paesaggio di Roma, Rome, Italy
| | | | | | - Alessandra Sperduti
- Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy.,Dipartimento di Archeologia, Università di Foggia, Foggia, Italy
| | - Mauro Rubini
- SABAP-LAZ Ministero dei Beni e delle Attività Culturali, Rome, Italy.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Luca Bondioli
- Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Jonathan K Pritchard
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. .,Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
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49
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Mohamad J, Sarig O, Malki L, Rabinowitz T, Assaf S, Malovitski K, Shkury E, Mayer T, Vodo D, Peled A, Daniely D, Pavlovsky M, Shomron N, Samuelov L, Sprecher E. Loss-of-Function Variants in SERPINA12 Underlie Autosomal Recessive Palmoplantar Keratoderma. J Invest Dermatol 2020; 140:2178-2187. [PMID: 32247861 DOI: 10.1016/j.jid.2020.02.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/09/2020] [Accepted: 02/16/2020] [Indexed: 12/14/2022]
Abstract
Inherited palmoplantar keratodermas refer to a large and heterogeneous group of conditions resulting from abnormal epidermal differentiation and featuring thickening of the skin of the palms and soles. Here, we aimed at delineating the genetic basis of an autosomal recessive form of palmoplantar keratodermas manifesting with erythematous hyperkeratotic plaques over the palms and soles, extending to non-palmoplantar areas. Whole-exome sequencing in affected individuals revealed homozygous nonsense variants in the SERPINA12 gene. SERPINA12 encodes the visceral adipose tissue-derived serpin A12, a serine protease inhibitor. The pathogenic variants were found to result in reduced visceral adipose tissue-derived serpin A12 expression in patients' skin biopsies in comparison to healthy controls. In addition, SERPINA12 downregulation in three-dimensional skin equivalents was associated with marked epidermal acanthosis and hyperkeratosis, replicating the human phenotype. Moreover, decreased SERPINA12 expression resulted in reduced visceral adipose tissue-derived serpin A12-mediated inhibition of kallikrein 7 activity as well as decreased levels of desmoglein-1 and corneodesmosin, two known kallikrein 7 substrates, which are required for normal epidermal differentiation. The present data, taken collectively, demarcate a unique type of autosomal recessive palmoplantar keratodermas, attribute to visceral adipose tissue-derived serpin A12 a role in skin biology, and emphasize the importance of mechanisms regulating proteolytic activity for normal epidermal differentiation.
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Affiliation(s)
- Janan Mohamad
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Sarig
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Liron Malki
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tom Rabinowitz
- Department of Cell and Developmental Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Sari Assaf
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kiril Malovitski
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eden Shkury
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Talia Mayer
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Dan Vodo
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Alon Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Daniely
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mor Pavlovsky
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Liat Samuelov
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eli Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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50
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Abstract
Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.
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Affiliation(s)
- Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Desislava Petkova
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL
- Department of Ecology & Evolution, University of Chicago, Chicago, IL
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