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Miller B, Kim S, Cao K, Mehta HH, Thumaty N, Kumagai H, Iida T, McGill C, Pike CJ, Nurmakova K, Levine ZA, Sullivan PM, Yen K, Ertekin‐Taner N, Atzmon G, Barzilai N, Cohen P. Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4-induced brain pathology. Aging Cell 2024; 23:e14153. [PMID: 38520065 PMCID: PMC11258485 DOI: 10.1111/acel.14153] [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: 12/04/2023] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
The APOE4 allele is recognized as a significant genetic risk factor to Alzheimer's disease (AD) and influences longevity. Nonetheless, some APOE4 carriers exhibit resistance to AD even in advanced age. Humanin, a mitochondrial-derived peptide comprising 24 amino acids, has variants linked to cognitive resilience and longevity. Our research uncovered a unique humanin variant, P3S, specifically enriched in centenarians with the APOE4 allele. Through in silico analyses and subsequent experimental validation, we demonstrated a strong affinity between humanin P3S and APOE4. Utilizing an APOE4-centric mouse model of amyloidosis (APP/PS1/APOE4), we observed that humanin P3S significantly attenuated brain amyloid-beta accumulation compared to the wild-type humanin. Transcriptomic assessments of mice treated with humanin P3S highlighted its potential mechanism involving the enhancement of amyloid beta phagocytosis. Additionally, in vitro studies corroborated humanin P3S's efficacy in promoting amyloid-beta clearance. Notably, in the temporal cortex of APOE4 carriers, humanin expression is correlated with genes associated with phagocytosis. Our findings suggest a role of the rare humanin variant P3S, especially prevalent among individuals of Ashkenazi descent, in mitigating amyloid beta pathology and facilitating phagocytosis in APOE4-linked amyloidosis, underscoring its significance in longevity and cognitive health among APOE4 carriers.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Su‐Jeong Kim
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Kevin Cao
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Hemal H. Mehta
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Neehar Thumaty
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Hiroshi Kumagai
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Tomomitsu Iida
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Cassandra McGill
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Christian J. Pike
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Kamila Nurmakova
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
| | - Zachary A. Levine
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Patrick M. Sullivan
- Department of Medicine (Geriatrics)Duke University Medical CenterDurhamNorth CarolinaUSA
| | - Kelvin Yen
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Gil Atzmon
- Department of MedicineAlbert Einstein College of MedicineBronxNew YorkUSA
- Department of Biology, Faculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Nir Barzilai
- Department of MedicineAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Pinchas Cohen
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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Amjadi M, Hayatmehr Z, Egyed B, Tavallaei M, Szécsényi-Nagy A. A comprehensive review of HVS-I mitochondrial DNA variation of 19 Iranian populations. Ann Hum Genet 2024; 88:259-277. [PMID: 38161274 DOI: 10.1111/ahg.12544] [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: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Iran is located along the Central Asian corridor, a natural artery that has served as a cross-continental route since the first anatomically modern human populations migrated out of Africa. We compiled and reanalyzed the HVS-I (hypervariable segment-I) of 3840 mitochondrial DNA (mtDNA) sequences from 19 Iranian populations and from 26 groups from adjacent countries to give a comprehensive review of the maternal genetic variation and investigate the impact of historical events and cultural factors on the maternal genetic structure of modern Iranians. We conclude that Iranians have a high level of genetic diversity. Thirty-six haplogroups were observed in Iran's populations, and most of them belong to widespread West-Eurasian haplogroups, such as H, HV, J, N, T, and U. In contrast, the predominant haplogroups observed in most of the adjacent countries studied here are H, M, D, R, U, and C haplogroups. Using principal component analysis, clustering, and genetic distance-based calculations, we estimated moderate genetic relationships between Iranian and other Eurasian groups. Further, analyses of molecular variance and comparing geographic and genetic structures indicate that mtDNA HVS-I sequence diversity does not exhibit any sharp geographic structure in the country. Barring a few from some culturally distinct and naturally separated minorities, most Iranian populations have a homogenous maternal genetic structure.
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Affiliation(s)
- Motahareh Amjadi
- Department of Genetics, ELTE Doctoral School of Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
| | - Zahra Hayatmehr
- Faculty of Management and Financial Science, Department of Management, Khatam University, Tehran, Iran
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | | | - Anna Szécsényi-Nagy
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
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Roberts E, van Veen EM, Byers H, Barnett-Griness O, Gronich N, Lejbkowicz F, Pinchev M, Smith MJ, Howell A, Newman WG, Woodward ER, Harkness EF, Brentnall AR, Cuzick J, Rennert G, Howell SJ, Evans DG. Breast cancer polygenic risk scores derived in White European populations are not calibrated for women of Ashkenazi Jewish descent. Genet Med 2023; 25:100846. [PMID: 37061873 DOI: 10.1016/j.gim.2023.100846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
PURPOSE Polygenic risk scores (PRSs) are a major component of accurate breast cancer (BC) risk prediction but require ethnicity-specific calibration. Ashkenazi Jewish (AJ) population is assumed to be of White European (WE) origin in some commercially available PRSs despite differing effect allele frequencies (EAFs). We conducted a case-control study of WE and AJ women from the Predicting Risk of Cancer at Screening Study. The Breast Cancer in Northern Israel Study provided a separate AJ population-based case-control validation series. METHODS All women underwent Illumina OncoArray single-nucleotide variation (SNV; formerly single-nucleotide polymorphism [SNP]) analysis. Two PRSs were assessed, SNV142 and SNV78. A total of 221 of 2243 WE women (discovery: cases = 111; controls = 110; validation: cases = 651; controls = 1772) and 221 AJ women (cases = 121; controls = 110) were included from the UK study; the Israeli series consisted of 2045 AJ women (cases = 1331; controls = 714). EAFs were obtained from the Genome Aggregation Database. RESULTS In the UK study, the mean SNV142 PRS demonstrated good calibration and discrimination in WE population, with mean PRS of 1.33 (95% CI 1.18-1.48) in cases and 1.01 (95% CI 0.89-1.13) in controls. In AJ women from Manchester, the mean PRS of 1.54 (1.38-1.70) in cases and 1.20 (1.08-1.32) in controls demonstrated good discrimination but overestimation of BC relative risk. After adjusting for EAFs for the AJ population, mean risk was corrected (mean SNV142 PRS cases = 1.30 [95% CI 1.16-1.44] and controls = 1.02 [95% CI 0.92-1.12]). This was recapitulated in the larger Israeli data set with good discrimination (area under the curve = 0.632 [95% CI 0.607-0.657] for SNV142). CONCLUSION AJ women should not be given BC relative risk predictions based on PRSs calibrated to EAFs from the WE population. PRSs need to be recalibrated using AJ-derived EAFs. A simple recalibration using the mean PRS adjustment ratio likely performs well.
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Affiliation(s)
- Eleanor Roberts
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Helen Byers
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ofra Barnett-Griness
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Naomi Gronich
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Anthony Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elaine F Harkness
- Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Informatics, Imaging & Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Adam R Brentnall
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Population Health, Charterhouse Square, London, United Kingdom
| | - Jack Cuzick
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Population Health, Charterhouse Square, London, United Kingdom
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sacha J Howell
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom
| | - D Gareth Evans
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom; Nightingale/Prevent Breast Cancer Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The Christie Hospital, Manchester, United Kingdom.
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Kovalenko E, Vergasova E, Shoshina O, Popov I, Ilinskaya A, Kim A, Plotnikov N, Barenbaum I, Elmuratov A, Ilinsky V, Volokh O, Rakitko A. Lactase deficiency in Russia: multiethnic genetic study. Eur J Clin Nutr 2023:10.1038/s41430-023-01294-8. [PMID: 37311868 DOI: 10.1038/s41430-023-01294-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lactase persistence-the ability to digest lactose through adulthood-is closely related to evolutionary adaptations and has affected many populations since the beginning of cattle breeding. Nevertheless, the contrast initial phenotype, lactase non-persistence or adult lactase deficiency, is still observed in large numbers of people worldwide. METHODS We performed a multiethnic genetic study of lactase deficiency on 24,439 people, the largest in Russia to date. The percent of each population group was estimated according to the local ancestry inference results. Additionally, we calculated frequencies of rs4988235 GG genotype in Russian regions using the information of current location and birthplace data from the client's questionnaire. RESULTS The attained results show that among all studied population groups, the frequency of GG genotype in rs4988235 is higher than the average in the European populations. In particular, the prevalence of lactase deficiency genotype in the East Slavs group was 42.8% (95% CI: 42.1-43.4%). We also investigated the regional prevalence of lactase deficiency based on the current place of residence. CONCLUSIONS Our study emphasizes the significance of genetic testing for diagnostics, i.e., specifically for lactose intolerance parameter, as well as the scale of the problem of lactase deficiency in Russia which needs to be addressed by the healthcare and food sectors.
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Affiliation(s)
| | | | - Olesya Shoshina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | | | | | | | | | | | | | | | - Olesya Volokh
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
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Drath J, Machalski G, Holicki M, Dowejko J, Szargut M, Spradley K, Parafiniuk M, Ossowski A. Title: Skeletal evidence of the ethnic cleansing actions in the Free City of Danzig (1939-1942) based on the KL Stutthof victims analysis. Sci Justice 2023; 63:313-326. [PMID: 37169456 DOI: 10.1016/j.scijus.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023]
Abstract
In the early days of World War II, many of the prominent and influential people of Polish nationality from the Free City of Danzig were arrested by the Germans and sent to the nearby concentration camp KL Stutthof. Nearly a hundred of them died within the next seven months upon their arrival, and were buried in a clandestine mass grave in a nearby forest. However, the exact nature of their death is unknown, as it is unclear what the attitude of the aggressors was toward the victims. We do not know whether there was only one executioner or there were several assassins, nor if the killing methodology was consistent with the other state-regulated executions. The studied material represents the commingled remains of a minimum thirty-four people, possibly all male, aged from under eighteen to over sixty at the time of death. Perimortem traumatic lesions are shown mainly on the skull bones. We asked whether the perimortem trauma lesions visible on the victims' skeletons could be informative on the cause and manner of their death. Our results show the prevalence of the perimortem trauma inflicted by a blunt object are on the parietal bones above the Hat Brim Line (HBL), which is commonly associated with a violent attack. The gunshot trauma was usually localized on the occipital bone or posterior parietal, which could indicate a shot to the back of the head, and this was commonly encountered during executions. No signs of defensive injuries can be explained either by restraining of the hands or by a surprise attack. The abundance and variability of the trauma type can be evident of multiple assailants. Moreover, the multiple impact points detected on several crania prove unnecessary overkill and brutality, which reflects the personal attitudes of the executioners towards the victims.
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Zhou Y, Nevosadová L, Eliasson E, Lauschke VM. Global distribution of functionally important CYP2C9 alleles and their inferred metabolic consequences. Hum Genomics 2023; 17:15. [PMID: 36855170 PMCID: PMC9976394 DOI: 10.1186/s40246-023-00461-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Genetic variability in the cytochrome P450 CYP2C9 constitutes an important predictor for efficacy and safety of various commonly prescribed drugs, including coumarin anticoagulants, phenytoin and multiple non-steroidal anti-inflammatory drugs (NSAIDs). A global map of CYP2C9 variability and its inferred functional consequences has been lacking. RESULTS Frequencies of eight functionally relevant CYP2C9 alleles (*2, *3, *5, *6, *8, *11, *13 and *14) were analyzed. In total, 108 original articles were identified that included genotype data from a total of 81,662 unrelated individuals across 70 countries and 40 unique ethnic groups. The results revealed that CYP2C9*2 was most abundant in Europe and the Middle East, whereas CYP2C9*3 was the main reason for reduced CYP2C9 activity across South Asia. Our data show extensive variation within superpopulations with up to tenfold differences between geographically adjacent populations in Malaysia, Thailand and Vietnam. Translation of genetic CYP2C9 variability into functional consequences indicates that up to 40% of patients in Southern Europe and the Middle East might benefit from warfarin and phenytoin dose reductions, while 3% of patients in Southern Europe and Israel are recommended to reduce starting doses of NSAIDs. CONCLUSIONS This study provides a comprehensive map of the genetic and functional variability of CYP2C9 with high ethnogeographic resolution. The presented data can serve as a useful resource for CYP2C9 allele and phenotype frequencies and might guide the optimization of genotyping strategies, particularly for indigenous and founder populations with distinct genetic profiles.
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Affiliation(s)
- Yitian Zhou
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52, Huddinge, Sweden.
| | - Lenka Nevosadová
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Erik Eliasson
- grid.4714.60000 0004 1937 0626Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden ,grid.24381.3c0000 0000 9241 5705Medical Diagnostics, Clinical Pharmacology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Volker M. Lauschke
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden ,grid.502798.10000 0004 0561 903XDr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany ,grid.10392.390000 0001 2190 1447University of Tübingen, Tübingen, Germany
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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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Font-Porterias N, García-Fernández C, Aizpurua-Iraola J, Comas D, Torrents D, de Cid R, Calafell F. Sequence diversity of the uniparentally transmitted portions of the genome in the resident population of Catalonia. Forensic Sci Int Genet 2022; 61:102783. [DOI: 10.1016/j.fsigen.2022.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
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Diepenbroek M, Amory C, Niederstätter H, Zimmermann B, Szargut M, Zielińska G, Dür A, Teul I, Mazurek W, Persak K, Ossowski A, Parson W. Genetic and phylogeographic evidence for Jewish Holocaust victims at the Sobibór death camp. Genome Biol 2021; 22:200. [PMID: 34353344 PMCID: PMC8343952 DOI: 10.1186/s13059-021-02420-0] [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: 01/04/2021] [Accepted: 06/29/2021] [Indexed: 11/24/2022] Open
Abstract
Six million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibór, Poland, revealed ten sets of human skeletal remains presumptively assigned to Polish victims of the totalitarian regimes. However, their genetic analyses indicate that the remains are of Ashkenazi Jews murdered as part of the mass extermination of European Jews by the Nazi regime and not of otherwise hypothesised non-Jewish partisan combatants. In accordance with traditional Jewish rite, the remains were reburied in the presence of a Rabbi at the place of their discovery.
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Affiliation(s)
- Marta Diepenbroek
- Department of Forensic Genetics, Pomeranian Medical University, Szczecin, Poland.,Institute of Legal Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University, Szczecin, Poland
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University, Szczecin, Poland
| | - Arne Dür
- Institute of Mathematics, University of Innsbruck, Innsbruck, Austria
| | - Iwona Teul
- Institute of Anatomy, Pomeranian Medical University, Szczecin, Poland
| | | | - Krzysztof Persak
- Institute of Political Studies, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University, Szczecin, Poland.
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria. .,Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America. Politics Life Sci 2021; 39:56-86. [PMID: 32697057 DOI: 10.1017/pls.2020.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
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11
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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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Brownstein Z, Gulsuner S, Walsh T, Martins FTA, Taiber S, Isakov O, Lee MK, Bordeynik-Cohen M, Birkan M, Chang W, Casadei S, Danial-Farran N, Abu-Rayyan A, Carlson R, Kamal L, Arnþórsson ÁÖ, Sokolov M, Gilony D, Lipschitz N, Frydman M, Davidov B, Macarov M, Sagi M, Vinkler C, Poran H, Sharony R, Samara N, Zvi N, Baris-Feldman H, Singer A, Handzel O, Hertzano R, Ali-Naffaa D, Ruhrman-Shahar N, Madgar O, Sofrin E, Peleg A, Khayat M, Shohat M, Basel-Salmon L, Pras E, Lev D, Wolf M, Steingrimsson E, Shomron N, Kelley MW, Kanaan M, Allon-Shalev S, King MC, Avraham KB. Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1. Clin Genet 2020; 98:353-364. [PMID: 33111345 PMCID: PMC8045518 DOI: 10.1111/cge.13817] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
Mutations in more than 150 genes are responsible for inherited hearing loss, with thousands of different, severe causal alleles that vary among populations. The Israeli Jewish population includes communities of diverse geographic origins, revealing a wide range of deafness-associated variants and enabling clinical characterization of the associated phenotypes. Our goal was to identify the genetic causes of inherited hearing loss in this population, and to determine relationships among genotype, phenotype, and ethnicity. Genomic DNA samples from informative relatives of 88 multiplex families, all of self-identified Jewish ancestry, with either non-syndromic or syndromic hearing loss, were sequenced for known and candidate deafness genes using the HEar-Seq gene panel. The genetic causes of hearing loss were identified for 60% of the families. One gene was encountered for the first time in human hearing loss: ATOH1 (Atonal), a basic helix-loop-helix transcription factor responsible for autosomal dominant progressive hearing loss in a five-generation family. Our results show that genomic sequencing with a gene panel dedicated to hearing loss is effective for genetic diagnoses in a diverse population. Comprehensive sequencing enables well-informed genetic counseling and clinical management by medical geneticists, otolaryngologists, audiologists, and speech therapists and can be integrated into newborn screening for deafness.
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Affiliation(s)
- Zippora Brownstein
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Suleyman Gulsuner
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Fábio Tadeu Arrojo Martins
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Isakov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ming K. Lee
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Maria Birkan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Weise Chang
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communications Disorders, NIH, Bethesda, MD, USA
| | - Silvia Casadei
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Nada Danial-Farran
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Amal Abu-Rayyan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ryan Carlson
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Lara Kamal
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ásgeir Örn Arnþórsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Meirav Sokolov
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Dror Gilony
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Noga Lipschitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Moshe Frydman
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Bella Davidov
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Michal Macarov
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Chana Vinkler
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Hana Poran
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Reuven Sharony
- Genetics Institute, Meir Medical Center, Kfar Saba and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Na’ama Zvi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Amihood Singer
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Ophir Handzel
- Department of Otolaryngology Head and Neck Surgery and Maxillofacial Surgery, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Doaa Ali-Naffaa
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ory Madgar
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Efrat Sofrin
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Amir Peleg
- Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Morad Khayat
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
| | - Mordechai Shohat
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
- Institute of Medical Genetics, Maccabi HMO, Rehovot, Israel
| | - Lina Basel-Salmon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center–Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elon Pras
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Dorit Lev
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael Wolf
- Department of Otolaryngology - Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communications Disorders, NIH, Bethesda, MD, USA
| | - Moien Kanaan
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Stavit Allon-Shalev
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Mary-Claire King
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Karen B. Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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13
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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14
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González-Fortes G, Tassi F, Trucchi E, Henneberger K, Paijmans JLA, Díez-Del-Molino D, Schroeder H, Susca RR, Barroso-Ruíz C, Bermudez FJ, Barroso-Medina C, Bettencourt AMS, Sampaio HA, Grandal-d'Anglade A, Salas A, de Lombera-Hermida A, Fabregas Valcarce R, Vaquero M, Alonso S, Lozano M, Rodríguez-Alvarez XP, Fernández-Rodríguez C, Manica A, Hofreiter M, Barbujani G. A western route of prehistoric human migration from Africa into the Iberian Peninsula. Proc Biol Sci 2020; 286:20182288. [PMID: 30963949 DOI: 10.1098/rspb.2018.2288] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar.
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Affiliation(s)
- G González-Fortes
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - F Tassi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - E Trucchi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - K Henneberger
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - J L A Paijmans
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - D Díez-Del-Molino
- 3 Department of Bioinformatics and Genetics, Swedish Museum of Natural History , 104 05 Stockholm , Sweden
| | - H Schroeder
- 4 Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen , 1353 Copenhagen K , Denmark
| | - R R Susca
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - C Barroso-Ruíz
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - F J Bermudez
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - C Barroso-Medina
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - A M S Bettencourt
- 6 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of History, University of Minho , 4700-057 Braga , Portugal
| | - H A Sampaio
- 7 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of Hospitality and Tourism, Polytechnic Institute of Cávado and Ave , Barcelos , Portugal
| | - A Grandal-d'Anglade
- 8 Universitary Institute of Geology, University of Coruña , A Coruña 15081 , Spain
| | - A Salas
- 9 Unidade de Xenética, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, and GenPoB (IDIS-SERGAS) , Galicia , Spain
| | - A de Lombera-Hermida
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - R Fabregas Valcarce
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - M Vaquero
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - S Alonso
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - M Lozano
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - X P Rodríguez-Alvarez
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | | | - A Manica
- 14 Department of Zoology, University of Cambridge , Cambridge CB2 3EJ , UK
| | - M Hofreiter
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - G Barbujani
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
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15
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Santos-Silva R, Cardoso R, Lopes L, Fonseca M, Espada F, Sampaio L, Brandão C, Antunes A, Bragança G, Coelho R, Bernardo T, Vieira P, Morais R, Leite AL, Ribeiro L, Carvalho B, Grangeia A, Oliveira R, Oliveira MJ, Rey V, Rosmaninho-Salgado J, Marques B, Garcia AM, Meireles A, Carvalho J, Sequeira A, Mirante A, Borges T. CYP21A2 Gene Pathogenic Variants: A Multicenter Study on Genotype-Phenotype Correlation from a Portuguese Pediatric Cohort. Horm Res Paediatr 2019; 91:33-45. [PMID: 30889569 DOI: 10.1159/000497485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21OHD) is an autosomal recessive disorder characterized by 3 overlapping phenotypes: salt-wasting (SW), simple virilizing (SV), and non-classic (NC). We aimed at conducting a nationwide genotype description of the CAH pediatric patients and to establish their genotype-phenotype correlation. METHODS CAH patients were recruited from Portuguese pediatric endocrinology centers and classified as SW, SV, or NC. Genetic analysis was performed by polymerase chain reaction (sequence specific primer, restriction fragment length polymorphism) or direct Sanger sequencing. Genotypes were categorized into 4 groups (0, A, B, and C), according to their predicted enzymatic activity. In each group, the expected phenotype was compared to the observed phenotype to assess the genotype-phenotype correlation. RESULTS Our cohort comprises 212 unrelated pediatric CAH patients (29% SW, 11% SV, 60% NC). The most common pathogenic variant was p.(Val282Leu; 41.3% of the 424 alleles analyzed). The p.(Val282Leu) variant, together with c.293-13A/C>G, p.(Ile173Asn), p.(Leu308Thr), p.(Gln319*), and large deletions/conversions were responsible for 86.4% of the mutated alleles. Patients' stratification by disease subtype revealed that the most frequent pathogenic variants were c.293-13A/C>G in SW (31.1%), p.(Ile173Asn) in SV (46.9%), and p.(Val282Leu) in NC (69.5%). The most common genotype was homozygosity for p.(Val282Leu; 33.0%). Moreover, we found 2 novel variants: p.(Ile161Thr) and p.(Trp202Arg), in exons 4 and 5, respectively. The global genotype-phenotype correlation was 92.4%. Group B (associated with the SV form) showed the lowest genotype-phenotype correlation (80%). CONCLUSION Our cohort has one of the largest NC CAH pediatric populations described. We emphasize the high frequency of the p.(Val282Leu) variant and the very high genotype-phenotype correlation observed.
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Affiliation(s)
- Rita Santos-Silva
- Department of Pediatric Endocrinology, Centro Hospitalar Universitário de S. João, Porto, Portugal,
| | - Rita Cardoso
- Department of Pediatric Endocrinology, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Lurdes Lopes
- Department of Pediatric Endocrinology, Hospital D. Estefânia, Lisboa, Portugal
| | - Marcelo Fonseca
- Department of Pediatric Endocrinology, Unidade Local de Saúde de Matosinhos, Matosinhos, Portugal
| | - Filipa Espada
- Department of Pediatric Endocrinology, Unidade Local de Saúde de Matosinhos, Matosinhos, Portugal
| | - Lurdes Sampaio
- Department of Pediatric Endocrinology, Centro Hospitalar de Lisboa Norte, Lisboa, Portugal
| | - Carla Brandão
- Department of Pediatrics, Centro Hospitalar do Tâmega e Vouga, Penafiel, Portugal
| | - Ana Antunes
- Department of Pediatric Endocrinology, Hospital de Braga, Braga, Portugal
| | - Graciete Bragança
- Department of Pediatric Endocrinology, Hospital Fernando Fonseca, Lisboa, Portugal
| | - Raquel Coelho
- Department of Pediatric Endocrinology, Hospital Fernando Fonseca, Lisboa, Portugal
| | - Teresa Bernardo
- Department of Pediatrics, Unidade Local de Saúde do Alto Minho, Viana do Castelo, Portugal
| | - Paula Vieira
- Department of Pediatrics, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
| | - Rita Morais
- Department of Pediatrics, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
| | - Ana Luísa Leite
- Department of Pediatric Endocrinology, Centro Hospitalar de Vila Nova Gaia e Espinho, Vila Nova de Gaia, Portugal
| | - Luís Ribeiro
- Department of Pediatrics, Unidade Local de Saúde do Nordeste, Bragança, Portugal
| | - Berta Carvalho
- Genetics Unit, Department of Pathology, Oporto Medical School, Porto, Portugal
| | - Ana Grangeia
- Department of Medical Genetics, Centro Hospitalar Universitário de S. João, Porto, Portugal
| | - Renata Oliveira
- Department of Medical Genetics, Centro Hospitalar Universitário de S. João, Porto, Portugal
| | - Maria João Oliveira
- Department of Pediatric Endocrinology, Centro Materno-infantil do Norte, Porto, Portugal
| | - Vicente Rey
- Department of Pediatrics, Centro Hospitalar Universitário de S. João, Porto, Portugal
| | - Joana Rosmaninho-Salgado
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Bernardo Marques
- Department of Endocrinology, Instituto Português de Oncologia de Coimbra Francisco Gentil, Coimbra, Portugal
| | | | - Andreia Meireles
- Department of Pediatrics, Unidade Local de Saúde de Matosinhos, Matosinhos, Portugal
| | - Joana Carvalho
- Department of Pediatrics, Unidade Local de Saúde de Matosinhos, Matosinhos, Portugal
| | - Ana Sequeira
- Department of Pediatrics, Centro Hospitalar de Lisboa Norte, Lisboa, Portugal
| | - Alice Mirante
- Department of Pediatric Endocrinology, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Teresa Borges
- Department of Pediatric Endocrinology, Centro Materno-infantil do Norte, Porto, Portugal
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16
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Poma A, Cesare P, Bonfigli A, Vecchiotti G, Colafarina S, Savini F, Redi F, Zarivi O. Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy. Heliyon 2019; 5:e02586. [PMID: 31646208 PMCID: PMC6804371 DOI: 10.1016/j.heliyon.2019.e02586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy. The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.
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Affiliation(s)
- Anna Poma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Corresponding author.
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Vecchiotti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Savini
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Fabio Redi
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions. Sci Rep 2019; 9:14751. [PMID: 31611588 PMCID: PMC6791841 DOI: 10.1038/s41598-019-48596-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023] Open
Abstract
Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.
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Yardumian A, Schurr TG. The Geography of Jewish Ethnogenesis. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2019. [DOI: 10.1086/702709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Mitochondrial DNA variability of the Polish population. Eur J Hum Genet 2019; 27:1304-1314. [PMID: 30903113 PMCID: PMC6777467 DOI: 10.1038/s41431-019-0381-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 01/24/2023] Open
Abstract
The aim of the present study was to define the mtDNA variability of Polish population and to visualize the genetic relations between Poles. For the first time, the study of Polish population was conducted on such a large number of individuals (5852) representing administrative units of both levels of local administration in Poland (voivodeships and counties). Additionally, clustering was used as a method of population subdivision. Performed genetic analysis, included FST, MDS plot, AMOVA and SAMOVA. Haplogroups were classified and their geographical distribution was visualized using surface interpolation maps. Results of the present study showed that Poles are characterized by the main West Eurasian mtDNA haplogroups. Furthermore, the level of differentiation within the Polish population was quite low but the existing genetic differences could be explained well with geographic distances. This may lead to a conclusion that Poles can be considered as genetically homogenous but with slight differences, highlighted at the regional level. Some patterns of variability were observed and could be explained by the history of demographic processes in Poland such as resettlements and migrations of women or relatively weaker urbanisation and higher rural population retention of some regions.
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Patel D, Mez J, Vardarajan BN, Staley L, Chung J, Zhang X, Farrell JJ, Rynkiewicz MJ, Cannon-Albright LA, Teerlink CC, Stevens J, Corcoran C, Gonzalez Murcia JD, Lopez OL, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg G, Kauwe JSK, Lunetta KL, Farrer LA. Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry. JAMA Netw Open 2019; 2:e191350. [PMID: 30924900 PMCID: PMC6450321 DOI: 10.1001/jamanetworkopen.2019.1350] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
Importance Some of the unexplained heritability of Alzheimer disease (AD) may be due to rare variants whose effects are not captured in genome-wide association studies because very large samples are needed to observe statistically significant associations. Objective To identify genetic variants associated with AD risk using a nonstatistical approach. Design, Setting, and Participants Genetic association study in which rare variants were identified by whole-exome sequencing in unrelated individuals of European ancestry from the Alzheimer's Disease Sequencing Project (ADSP). Data were analyzed between March 2017 and September 2018. Main Outcomes and Measures Minor alleles genome-wide and in 95 genes previously associated with AD, AD-related traits, or other dementias were tabulated and filtered for predicted functional impact and occurrence in participants with AD but not controls. Support for several findings was sought in a whole-exome sequencing data set comprising 19 affected relative pairs from Utah high-risk pedigrees and whole-genome sequencing data sets from the ADSP and Alzheimer's Disease Neuroimaging Initiative. Results Among 5617 participants with AD (3202 [57.0%] women; mean [SD] age, 76.4 [9.3] years) and 4594 controls (2719 [59.0%] women; mean [SD] age, 86.5 [4.5] years), a total of 24 variants with moderate or high functional impact from 19 genes were observed in 10 or more participants with AD but not in controls. These variants included a missense mutation (rs149307620 [p.A284T], n = 10) in NOTCH3, a gene in which coding mutations are associated with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), that was also identified in 1 participant with AD and 1 participant with mild cognitive impairment in the whole genome sequencing data sets. Four participants with AD carried the TREM2 rs104894002 (p.Q33X) high-impact mutation that, in homozygous form, causes Nasu-Hakola disease, a rare disorder characterized by early-onset dementia and multifocal bone cysts, suggesting an intermediate inheritance model for the mutation. Compared with controls, participants with AD had a significantly higher burden of deleterious rare coding variants in dementia-associated genes (2314 vs 3354 cumulative variants, respectively; P = .006). Conclusions and Relevance Different mutations in the same gene or variable dose of a mutation may be associated with result in distinct dementias. These findings suggest that minor differences in the structure or amount of protein may be associated with in different clinical outcomes. Understanding these genotype-phenotype associations may provide further insight into the pathogenic nature of the mutations, as well as offer clues for developing new therapeutic targets.
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Affiliation(s)
- Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Jesse Mez
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | | | - Lyndsay Staley
- Department of Biology, Brigham Young University, Provo, Utah
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Lisa A. Cannon-Albright
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Craig C. Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | - Jeffery Stevens
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City
| | | | | | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York, New York
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia
| | | | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
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Granot-Hershkovitz E, Karasik D, Friedlander Y, Rodriguez-Murillo L, Dorajoo R, Liu J, Sewda A, Peter I, Carmi S, Hochner H. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. Eur J Hum Genet 2018; 26:1848-1858. [PMID: 30108283 PMCID: PMC6244281 DOI: 10.1038/s41431-018-0230-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/24/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022] Open
Abstract
Genetic studies in isolated populations often increase power for identifying loci associated with complex diseases and traits. We present here the Kibbutzim Family Study (KFS), aimed at investigating the genetic basis of cardiometabolic traits in extended Israeli families characterized by long-term social stability and a homogeneous environment. Extensive information on cardiometabolic traits, as well as genome-wide genotypes, were collected on 901 individuals. We observed that most KFS participants were of Ashkenazi Jewish (AJ) genetic origin, confirmed a recent severe bottleneck in the AJ recent history, and detected a subtle within-AJ population structure. Focusing on genetic variants relatively common in the KFS but very rare in Europeans, we observed that AJ-enriched variants appear in cancer-related pathways more than expected by chance. We conducted an association study of the AJ-enriched variants against 16 cardiometabolic traits, and found seven loci (24 variants) to be significantly associated. The strongest association, which we also replicated in an independent study, was between a variant upstream of MSRA (frequency ≈1% in the KFS and nearly absent in Europeans) and weight (P = 3.6∙10-8). In conclusion, the KFS is a valuable resource for the study of the population genetics of Israel as well as the genetics of cardiometabolic traits.
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Affiliation(s)
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Laura Rodriguez-Murillo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anshuman Sewda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shai Carmi
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Hagit Hochner
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
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22
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Peled Y, Loewenthal R, Kassif Y, Raichlin E, Younis A, Younis A, Nachum E, Freimark D, Goldenberg I, Lavee J. Donor-recipient ethnic mismatching impacts short- and long-term results of heart transplantation. Clin Transplant 2018; 32:e13389. [DOI: 10.1111/ctr.13389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/28/2018] [Accepted: 08/20/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Yael Peled
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Ron Loewenthal
- Tissue Typing Laboratory Sheba Medical Center; Tel Hashomer Israel
| | - Yigal Kassif
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Eugenia Raichlin
- Cardiology Department; Loyola University Medical Center; Maywood Illinois
| | - Arwa Younis
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Anan Younis
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Eyal Nachum
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Dov Freimark
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Ilan Goldenberg
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Jacob Lavee
- The Olga and Lev Leviev Heart Center; Sheba Medical Center; Ramat Gan Israel
- The Sackler School of Medicine; Tel Aviv University; Tel Aviv Israel
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23
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ElHefnawi M, Jeon S, Bhak Y, ElFiky A, Horaiz A, Jun J, Kim H, Bhak J. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes. Gene 2018; 668:129-134. [DOI: 10.1016/j.gene.2018.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/13/2018] [Indexed: 12/27/2022]
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24
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Miller EF, Manica A, Amos W. Global demographic history of human populations inferred from whole mitochondrial genomes. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180543. [PMID: 30225046 PMCID: PMC6124094 DOI: 10.1098/rsos.180543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.
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25
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Zhou Y, Lauschke VM. Comprehensive overview of the pharmacogenetic diversity in Ashkenazi Jews. J Med Genet 2018; 55:617-627. [PMID: 29970487 DOI: 10.1136/jmedgenet-2018-105429] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 05/28/2018] [Accepted: 06/10/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Adverse drug reactions are a major concern in drug development and clinical therapy. Genetic polymorphisms in genes involved in drug metabolism and transport are major determinants of treatment efficacy and adverse reactions, and constitute important biomarkers for drug dosing, efficacy and safety. Importantly, human populations and subgroups differ substantially in their pharmacogenetic variability profiles, with important consequences for personalised medicine strategies and precision public health approaches. Despite their long migration history, Ashkenazi Jews constitute a rather isolated population with a unique genetic signature that is distinctly different from other populations. OBJECTIVE To provide a comprehensive overview of the pharmacogenetic profile in Ashkenazim. METHODS We analysed next-generation sequencing data from 5076 Ashkenazim individuals and used sequence data from 117 425 non-Jewish individuals as reference. RESULTS We derived frequencies of 164 alleles in 17 clinically relevant pharmacogenes and derived profiles of putative functional consequences, providing the most comprehensive data set of Jewish pharmacogenetic diversity published to date. Furthermore, we detected 127 variants with an aggregated frequency of 20.7% that were specifically found in Ashkenazim, of which 55 variants were putatively deleterious (aggregated frequency of 9.4%). CONCLUSION The revealed pattern of pharmacogenetic variability in Ashkenazi Jews is distinctly different from other populations and is expected to translate into unique functional consequences, especially for the metabolism of CYP2A6, CYP2C9, NAT2 and VKORC1 substrates. We anticipate that the presented data will serve as a powerful resource for the guidance of pharmacogenetic treatment decisions and the optimisation of population-specific genotyping strategies in the Ashkenazi diaspora.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
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26
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Zhu X, Zhang WY, Chen C, Ye Q, Fu DW. Challenge in optoelectronic duplex switches: a red emission large-size single crystal and a unidirectional flexible thin film of a hybrid multifunctional material. Dalton Trans 2018; 47:2344-2351. [PMID: 29372192 DOI: 10.1039/c7dt04489e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectric dual-function features in bulk crystals or flexible thin films make them excellent candidates for important and thriving applications in storage, sensing and other information fields. Based on superior advantages such as easy and environmentally friendly processing, mechanical flexibility, and ability to fabricate films and bulk single crystals; we designed a type of molecular material with a photoelectric multi-function switch, [N(NH2CH2CH2)3]2Mn2Cl12 (compound 1), which exhibits intriguing temperature-dependent dielectric and red emission switchable characteristics. This material perfectly explains the advantages of molecular materials, while 1 can also be used to fabricate a transparent unidirectional film with ultra-flexibility. Moreover, this material shows the highest record in signal contrast of ∼5 (exceeding all the known molecular materials/crystalline switches, revealing its potential to obtain high-efficiency signal-to-noise ratio), sensitive dielectric bi-stability, and excellent switching anti fatigue. These features give it a high application value in integrated circuits, optoelectronic seamless integration devices and flexible multifunctional devices.
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Affiliation(s)
- Xiao Zhu
- Ordered Matter Science Research Center, Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics, Southeast University, Nanjing, 211189, P.R. China.
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27
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Caporali L, Iommarini L, La Morgia C, Olivieri A, Achilli A, Maresca A, Valentino ML, Capristo M, Tagliavini F, Del Dotto V, Zanna C, Liguori R, Barboni P, Carbonelli M, Cocetta V, Montopoli M, Martinuzzi A, Cenacchi G, De Michele G, Testa F, Nesti A, Simonelli F, Porcelli AM, Torroni A, Carelli V. Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber's hereditary optic neuropathy. PLoS Genet 2018; 14:e1007210. [PMID: 29444077 PMCID: PMC5828459 DOI: 10.1371/journal.pgen.1007210] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/27/2018] [Accepted: 01/21/2018] [Indexed: 12/23/2022] Open
Abstract
We here report on the existence of Leber’s hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband’s fibroblasts into the cybrid cell model. Finally, all but one of these missense mtDNA variants cluster along the same predicted fourth E-channel deputed to proton translocation within the transmembrane domain of Complex I, involving the ND1, ND4L and ND6 subunits. Hence, the definition of the pathogenic role of a specific mtDNA mutation becomes blurrier than ever and only an accurate evaluation of mitogenome sequence variation data from the general population, combined with functional analyses using the cybrid cell model, may lead to final validation. Our study conclusively shows that even in the absence of a clearly established LHON primary mutation, unprecedented combinations of missense mtDNA variants, individually known as polymorphisms, may lead to reduced OXPHOS efficiency sufficient to trigger LHON. In this context, we introduce a new diagnostic perspective that implies the complete sequence analysis of mitogenomes in LHON as mandatory gold standard diagnostic approach. Leber’s hereditary optic neuropathy (LHON) is a common cause of maternally inherited vision loss. In the large majority of cases LHON is due to mitochondrial DNA (mtDNA) point mutations, clearly distinct from common polymorphisms normally found in the general population, affecting the mitochondrial function, thus defined as pathogenic. For the first time, we here demonstrate, on the genetic and functional ground, that unusual combinations of otherwise polymorphic and non-pathogenic mtDNA variants are sufficient for causing low-penetrance maternally inherited optic neuropathy in pedigrees fitting the LHON clinical diagnosis. Our findings bridge the blurry border between “pathogenic” and “neutral” mutations in an overall continuum that truly depends on the specific and sometime unique combination of variants characterizing each mitogenome. As a result, we conclude that, for an accurate diagnosis of LHON and possibly of other mitochondrial diseases, the only approach that can disclose all possible causative sources is complete mitogenome sequencing.
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Affiliation(s)
- Leonardo Caporali
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandra Maresca
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Maria Lucia Valentino
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Francesca Tagliavini
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Valentina Del Dotto
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Rocco Liguori
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Michele Carbonelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Studio Oculistico D’Azeglio, Bologna, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Andrea Martinuzzi
- IRCCS "E. Medea" Scientific Institute Conegliano-Pieve di Soligo Research Center, Pieve di Soligo, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Giuseppe De Michele
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Nesti
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
- Health Sciences & Technologies (HST) CIRI, University of Bologna, Bologna, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valerio Carelli
- Neurology Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- * E-mail:
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28
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Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB. Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proc Biol Sci 2018; 284:rspb.2016.1976. [PMID: 28330913 DOI: 10.1098/rspb.2016.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/14/2017] [Indexed: 11/12/2022] Open
Abstract
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
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Affiliation(s)
- Joana B Pereira
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Marta D Costa
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniel Vieira
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Lisa Bamford
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nourdin Harich
- Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.,Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Jiři Hatina
- Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic
| | | | | | - Turi King
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Luísa Pereira
- Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Martin B Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK .,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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Kimchi A, Khateb S, Wen R, Guan Z, Obolensky A, Beryozkin A, Kurtzman S, Blumenfeld A, Pras E, Jacobson SG, Ben-Yosef T, Newman H, Sharon D, Banin E. Nonsyndromic Retinitis Pigmentosa in the Ashkenazi Jewish Population: Genetic and Clinical Aspects. Ophthalmology 2017; 125:725-734. [PMID: 29276052 DOI: 10.1016/j.ophtha.2017.11.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 01/19/2023] Open
Abstract
PURPOSE To analyze the genetic and clinical findings in retinitis pigmentosa (RP) patients of Ashkenazi Jewish (AJ) descent, aiming to identify genotype-phenotype correlations. DESIGN Cohort study. PARTICIPANTS Retinitis pigmentosa patients from 230 families of AJ origin. METHODS Sanger sequencing was performed to detect specific founder mutations known to be prevalent in the AJ population. Ophthalmologic analysis included a comprehensive clinical examination, visual acuity (VA), visual fields, electroretinography, color vision testing, and retinal imaging by OCT, pseudocolor, and autofluorescence fundus photography. MAIN OUTCOME MEASURES Inheritance pattern and causative mutation; retinal function as assessed by VA, visual fields, and electroretinography results; and retinal structural changes observed on clinical funduscopy as well as by pseudocolor, autofluorescence, and OCT imaging. RESULTS The causative mutation was identified in 37% of families. The most prevalent RP-causing mutations are the Alu insertion (c.1297_8ins353, p.K433Rins31*) in the male germ cell-associated kinase (MAK) gene (39% of families with a known genetic cause for RP) and c.124A>G, p.K42E in dehydrodolichol diphosphate synthase (DHDDS) (33%). Additionally, disease-causing mutations were identified in 11 other genes. Analysis of clinical parameters of patients with mutations in the 2 most common RP-causing genes revealed that MAK patients had better VA and visual fields at relatively older ages in comparison with DHDDS patients. Funduscopic findings of DHDDS patients matched those of MAK patients who were 20 to 30 years older. Patients with DHDDS mutations were referred for electrophysiologic evaluation at earlier ages, and their cone responses became nondetectable at a much younger age than MAK patients. CONCLUSIONS Our AJ cohort of RP patients is the largest reported to date and showed a substantial difference in the genetic causes of RP compared with cohorts of other populations, mainly a high rate of autosomal recessive inheritance and a unique composition of causative genes. The most common RP-causing genes in our cohort, MAK and DHDDS, were not described as major causative genes in other populations. The clinical data show that in general, patients with biallelic MAK mutations had a later age of onset and a milder retinal phenotype compared with patients with biallelic DHDDS mutations.
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Affiliation(s)
- Adva Kimchi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rong Wen
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
| | - Ziqiang Guan
- Duke University Medical Center, Durham, North Carolina
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shoshi Kurtzman
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Anat Blumenfeld
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eran Pras
- Department of Ophthalmology, Assaf Harofeh Medical Center, Zerifin, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tamar Ben-Yosef
- The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hadas Newman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Ophthalmology, Sourasky Medical Center, Tel-Aviv, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
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30
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Olivieri A, Sidore C, Achilli A, Angius A, Posth C, Furtwängler A, Brandini S, Capodiferro MR, Gandini F, Zoledziewska M, Pitzalis M, Maschio A, Busonero F, Lai L, Skeates R, Gradoli MG, Beckett J, Marongiu M, Mazzarello V, Marongiu P, Rubino S, Rito T, Macaulay V, Semino O, Pala M, Abecasis GR, Schlessinger D, Conde-Sousa E, Soares P, Richards MB, Cucca F, Torroni A. Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past. Mol Biol Evol 2017; 34:1230-1239. [PMID: 28177087 PMCID: PMC5400395 DOI: 10.1093/molbev/msx082] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-specific haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.,Center for Advanced Studies, Research and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e Tecnologico della Sardegna, Pula, Italy
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy.,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | | | | | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, United Kingdom
| | | | | | - Michele Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
| | | | - Patrizia Marongiu
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences & ICVS/3B's-PT Government Associate Laboratory, University of Minho, Braga, Portugal
| | - Vincent Macaulay
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging US National Institutes of Health, Baltimore, Maryland, MD
| | - Eduardo Conde-Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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31
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Mitochondrial DNA haplogroup K as a contributor to protection against thyroid cancer in a population from southeast Europe. Mitochondrion 2017; 39:43-50. [PMID: 28851673 DOI: 10.1016/j.mito.2017.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022]
Abstract
We aimed to analyze the contribution of mitochondrial DNA (mtDNA) haplogroups of the mtDNA control region to thyroid cancer risk in a population from southeastern Europe consisting of 235 thyroid tumor patients, including 114 patients with thyroid follicular adenoma, 121 patients with papillary thyroid carcinoma, and 419 healthy controls. Binary logistic regression with adjustment for age and gender revealed that mtDNA haplogroup K was significantly associated with a protective role for thyroid cancer in the combined tumor group versus controls. These results indicate a potential role for mtDNA haplogroups as important candidate susceptibility markers for the patients with thyroid nodules.
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32
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Elhaik E. Editorial: Population Genetics of Worldwide Jewish People. Front Genet 2017; 8:101. [PMID: 28804494 PMCID: PMC5532521 DOI: 10.3389/fgene.2017.00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/14/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eran Elhaik
- Department of Animal and Plant Sciences, University of SheffieldSheffield, United Kingdom
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33
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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34
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Hernández CL, Dugoujon JM, Novelletto A, Rodríguez JN, Cuesta P, Calderón R. The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean. BMC Genet 2017; 18:46. [PMID: 28525980 PMCID: PMC5437654 DOI: 10.1186/s12863-017-0514-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/11/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature. RESULTS Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean. CONCLUSIONS Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.
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Affiliation(s)
- Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Jean M. Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | | | | | - Pedro Cuesta
- Centro de Proceso de Datos, Universidad Complutense, Madrid, Spain
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
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35
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EINHORN YARON, WEISSGLAS-VOLKOV DAPHNA, CARMI SHAI, OSTRER HARRY, FRIEDMAN EITAN, SHOMRON NOAM. Differential analysis of mutations in the Jewish population and their implications for diseases. Genet Res (Camb) 2017; 99:e3. [PMID: 28502252 PMCID: PMC6865140 DOI: 10.1017/s0016672317000015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/10/2017] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Sequencing large cohorts of ethnically homogeneous individuals yields genetic insights with implications for the entire population rather than a single individual. In order to evaluate the genetic basis of certain diseases encountered at high frequency in the Ashkenazi Jewish population (AJP), as well as to improve variant annotation among the AJP, we examined the entire exome, focusing on specific genes with known clinical implications in 128 Ashkenazi Jews and compared these data to other non-Jewish populations (European, African, South Asian and East Asian). We targeted American College of Medical Genetics incidental finding recommended genes and the Catalogue of Somatic Mutations in Cancer (COSMIC) germline cancer-related genes. We identified previously known disease-causing variants and discovered potentially deleterious variants in known disease-causing genes that are population specific or substantially more prevalent in the AJP, such as in the ATP and HGFAC genes associated with colorectal cancer and pancreatic cancer, respectively. Additionally, we tested the advantage of utilizing the database of the AJP when assigning pathogenicity to rare variants of independent whole-exome sequencing data of 49 Ashkenazi Jew early-onset breast cancer (BC) patients. Importantly, population-based filtering using our AJP database enabled a reduction in the number of potential causal variants in the BC cohort by 36%. Taken together, population-specific sequencing of the AJP offers valuable, clinically applicable information and improves AJP filter annotation.
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Affiliation(s)
- YARON EINHORN
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - SHAI CARMI
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - HARRY OSTRER
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - EITAN FRIEDMAN
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - NOAM SHOMRON
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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36
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Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep 2017; 7:46044. [PMID: 28387361 PMCID: PMC5384202 DOI: 10.1038/srep46044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 01/17/2023] Open
Abstract
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.
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37
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Silva M, Oliveira M, Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM, Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P. A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC Evol Biol 2017; 17:88. [PMID: 28335724 PMCID: PMC5364613 DOI: 10.1186/s12862-017-0936-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging. RESULTS We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55-65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems. CONCLUSIONS Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.
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Affiliation(s)
- Marina Silva
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Marisa Oliveira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Daniel Vieira
- Department of Informatics, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreia Brandão
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Teresa Rito
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana B Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Ross M Fraser
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh, EH16 4UX, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, Sydney, NSW, 2006, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Ceiridwen Edwards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - John Koch
- University of Wales Centre for Advanced Welsh and Celtic Studies, National Library of Wales, Aberystwyth, SY23 3HH, Wales, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland, UK
| | - Luísa Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
| | - Pedro Soares
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Davidovic S, Malyarchuk B, Aleksic J, Derenko M, Topalovic V, Litvinov A, Skonieczna K, Rogalla U, Grzybowski T, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial super-haplogroup U diversity in Serbians. Ann Hum Biol 2017; 44:408-418. [PMID: 28140657 DOI: 10.1080/03014460.2017.1287954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balkans, a region having a turbulent demographic history. AIM The aim was to thoroughly study complete mitogenomes of Serbians, a population linking westward and eastward South Slavs. SUBJECTS AND METHODS Forty-six predominantly Serbian super-haplogroup U complete mitogenomes were analysed phylogenetically against ∼4000 available complete mtDNAs of modern and ancient Western Eurasians. RESULTS Serbians share a number of U mtDNA lineages with Southern, Eastern-Central and North-Western Europeans. Putative Balkan-specific lineages (e.g. U1a1c2, U4c1b1, U5b3j, K1a4l and K1a13a1) and lineages shared among Serbians (South Slavs) and West and East Slavs were detected (e.g. U2e1b1, U2e2a1d, U4a2a, U4a2c, U4a2g1, U4d2b and U5b1a1). CONCLUSION The exceptional diversity of maternal lineages found in Serbians may be associated with the genetic impact of both autochthonous pre-Slavic Balkan populations whose mtDNA gene pool was affected by migrations of various populations over time (e.g. Bronze Age pastoralists) and Slavic and Germanic newcomers in the early Middle Ages.
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Affiliation(s)
- Slobodan Davidovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Boris Malyarchuk
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Jelena Aleksic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Miroslava Derenko
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Vladanka Topalovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Andrey Litvinov
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Katarzyna Skonieczna
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Urszula Rogalla
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Tomasz Grzybowski
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Milena Stevanovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Natasa Kovacevic-Grujicic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
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39
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Shaulov A, Filon D, Rund D. Haplotype analysis of α-thalassemia chromosomes reveals heterogeneity and multiple founders in Ashkenazi Jews. Eur J Med Genet 2016; 59:555-558. [PMID: 27771472 DOI: 10.1016/j.ejmg.2016.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/16/2016] [Indexed: 11/19/2022]
Abstract
α-Thalassemia (α-thal) is among the world's most common single gene disorders, generally attributed to a selective advantage of heterozygotes against malaria mortality. A high frequency of -α3.7 deletion heterozygosity has been previously reported in Ashkenazi Jews despite lack of obvious malarial selection pressure in this population. Using haplotype and -α3.7 subtype analysis we analyzed a subset of -α3.7 homozygotes from various Israeli ethnic groups. We found a high frequency of the common Ia haplotype in Yemenite Jews and Arabs (54% and 13% respectively). Ashkenazi Jews exhibited a high frequency of IIIb alleles (67%) previously reported only in Aboriginal Australians and not found in other Israeli ethnicities. Both Yemenites and Ashkenazim carried the rare IIh alleles (18% and 15% respectively). These results may suggest multiple founder effects in Ashkenazi Jews as well a common founder for both Yemenite and Ashkenazi Jews.
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Affiliation(s)
- Adir Shaulov
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel.
| | - Dvora Filon
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel
| | - Deborah Rund
- Department of Hematology, Hadassah - Hebrew University Hospital, Jerusalem, Israel
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40
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Abstract
The latest in a series of transformative studies of DNA from prehistoric Europeans focuses on mitochondrial DNA, bringing fresh surprises and filling in important details of the early stages of a European ancestry stretching back more than 40,000 years.
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41
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Flegontov P, Kassian A, Thomas MG, Fedchenko V, Changmai P, Starostin G. Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews. Genome Biol Evol 2016; 8:2259-65. [PMID: 27389685 PMCID: PMC4987117 DOI: 10.1093/gbe/evw162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia ,
| | - Alexei Kassian
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia Russian Presidential Academy of National Economy and Public Administration (RANEPA), Moscow, Russia ,
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - George Starostin
- Russian Presidential Academy of National Economy and Public Administration (RANEPA), Moscow, Russia Russian State University for the Humanities, Moscow, Russia
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42
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Elhaik E. In Search of the jüdische Typus: A Proposed Benchmark to Test the Genetic Basis of Jewishness Challenges Notions of "Jewish Biomarkers". Front Genet 2016; 7:141. [PMID: 27547215 PMCID: PMC4974603 DOI: 10.3389/fgene.2016.00141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/20/2016] [Indexed: 11/13/2022] Open
Abstract
The debate as to whether Jewishness is a biological trait inherent from an "authentic" "Jewish type" (jüdische Typus) ancestor or a system of beliefs has been raging for over two centuries. While the accumulated biological and anthropological evidence support the latter argument, recent genetic findings, bolstered by the direct-to-consumer genetic industry, purport to identify Jews or quantify one's Jewishness from genomic data. To test the merit of claims that Jews and non-Jews are genetically distinguishable, we propose a benchmark where genomic data of Jews and non-Jews are hybridized over two generations and the observed and predicted Jewishness of the terminal offspring according to either the Orthodox religious law (Halacha) or the Israeli Law of Return are compared. Members of academia, the public, and 23andMe were invited to use the benchmark to test claims that Jews are genetically distinct from non-Jews. Here, we report the findings from these trials. We also compare the genomic similarity of ∼300 individuals from nearly thirty Afro-Eurasian Jewish communities to a simulated jüdische Typus population. The results are discussed in light of modern trends in the genetics of Jews and related fields and provide a tentative answer to the ageless question "who is a Jew?"
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Affiliation(s)
- Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
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43
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Bhatti S, Aslamkhan M, Abbas S, Attimonelli M, Aydin HH, de Souza EMS. Genetic analysis of mitochondrial DNA control region variations in four tribes of Khyber Pakhtunkhwa, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:687-697. [PMID: 27159729 DOI: 10.3109/24701394.2016.1174222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Due to its geo strategic position at the crossroad of Asia, Pakistan has gained crucial importance of playing its pivotal role in subsequent human migratory events, both prehistoric and historic. This human movement became possible through an ancient overland network of trails called "The Silk Route" linking Asia Minor, Middle East China, Central Asia and Southeast Asia. This study was conducted to analyze complete mitochondrial control region samples of 100 individuals of four major Pashtun tribes namely, Bangash, Khattak, Mahsuds and Orakzai in the province of Khyber Pakhtunkhwa, Pakistan. All Pashtun tribes revealed high genetic diversity which is comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis and phylogenetic analysis. The results revealed that Pashtun are the composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasive movements and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroups M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Moreover, we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) pointed to a genetic connection of Jewish conglomeration in Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.
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Affiliation(s)
- Shahzad Bhatti
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan.,b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - M Aslamkhan
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan
| | - Sana Abbas
- b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - Marcella Attimonelli
- c Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari , Italy
| | - Hikmet Hakan Aydin
- d Department of Medical Biochemistry , Ege University School of Medicine , Bornova Izmir , Turkey
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44
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Das R, Wexler P, Pirooznia M, Elhaik E. Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol 2016; 8:1132-49. [PMID: 26941229 PMCID: PMC4860683 DOI: 10.1093/gbe/evw046] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Yiddish language is over 1,000 years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs). An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non-Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey's eastern border. Loss of maternal haplogroups was evident in non-Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo-Iranian confederation, which the Jews call "Ashkenazic" (i.e., "Scythian"), though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano-Turko-Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.
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Affiliation(s)
- Ranajit Das
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK Manipal Centre for Natural Sciences (MCNS), Manipal University, Manipal, Karnataka, India
| | - Paul Wexler
- Department of Linguistics, Tel Aviv University, Tel-Aviv, Israel
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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45
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Moya G, Dorado P, Ferreiro V, Naranjo MEG, Peñas-Lledó EM, LLerena A. High frequency of CYP2D6 ultrarapid metabolizer genotypes in an Ashkenazi Jewish population from Argentina. THE PHARMACOGENOMICS JOURNAL 2016; 17:378-381. [PMID: 27068265 DOI: 10.1038/tpj.2016.27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/29/2015] [Accepted: 02/26/2016] [Indexed: 11/09/2022]
Abstract
A twofold higher frequency of CYP2D6 ultrarapid metabolizers (estimated from genotype: gUMs) was reported among Ashkenazi Jews (AJ) living in New York (USA) than in other North American Caucasians, which might be important to guide the prescription for CYP2D6 substrates in AJ communities around the world. This study was aimed to determine whether the high frequency of CYP2D6 gUMs described in AJ from USA was replicated in AJ from Argentina when compared with other multiethnic admixture Argentines (GA). The frequency of the most common allelic variants and of CYP2D6 gUMs (>2 active genes) and poor metabolizers (0 active genes, gPMs) was also compared among the studied Argentine populations. CYP2D6 genotyping was performed in 173 AJ and 246 GA DNA samples of unrelated donors from the metropolitan area of Buenos Aires. CYP2D6 alleles (*2, *3, *4, *5, *6, *10, *17, *35, *41 and multiple copies), genotypes and functional phenotype frequencies were determined. The frequencies of gUMs and gPMs in AJ from Argentina were 11.5% and 5.2%, respectively, whereas in GA, the frequencies of gUM and gPMs were 6.5% and 4.9%, respectively. Comparisons between AJ and GA showed that gUMs frequencies were twofold higher (P<0.05) in AJ than GA. CYP2D6*35 allele was more frequent in GA than AJ, whereas CYP2D6*41 and *1xN were more frequent in AJ than in GA (P<0.05). This study supports the previously reported high frequency of gUMs on another Ashkenazi population in New York. The present findings also support the interethnic variability of CYP2D6 genetic polymorphism in the overall Argentine population.
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Affiliation(s)
- G Moya
- CICAB Clinical Research Center, Extremadura University and Medical School, Badajoz, Spain.,Pontifical Catholic University of Argentina, Beunos Aires, Argentina.,Genos Laboratory, Buenos Aires, Argentina
| | - P Dorado
- CICAB Clinical Research Center, Extremadura University and Medical School, Badajoz, Spain
| | - V Ferreiro
- Genos Laboratory, Buenos Aires, Argentina
| | - M E G Naranjo
- CICAB Clinical Research Center, Extremadura University and Medical School, Badajoz, Spain
| | - E M Peñas-Lledó
- CICAB Clinical Research Center, Extremadura University and Medical School, Badajoz, Spain
| | - A LLerena
- CICAB Clinical Research Center, Extremadura University and Medical School, Badajoz, Spain.,CIBERSAM, Madrid, Spain
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46
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Kimel SY, Huesmann R, Kunst JR, Halperin E. Living in a Genetic World. PERSONALITY AND SOCIAL PSYCHOLOGY BULLETIN 2016; 42:688-700. [DOI: 10.1177/0146167216642196] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/28/2016] [Indexed: 11/16/2022]
Abstract
Information about the degree of one’s genetic overlap with ethnic outgroups has been emphasized in genocides, is frequently learned about through media reporting, and is increasingly being accessed via personal genetic testing services. However, the consequence of learning about whether your own ethnic group is either genetically related to or genetically distinct from a disliked ethnic group remains unknown. Across four experiments, using diverse samples, measures and contexts, we demonstrate that altering perceptions of genetic overlap between groups in conflict—in this case Arabs and Jews—impacts factors that are directly related to interethnic hostility (e.g., aggressive behaviors, support of conflict-related policies). Our findings indicate that learning about the genetic difference between oneself and an ethnic outgroup may contribute to the promotion of violence, whereas learning about the similarities may be a vital step toward fostering peace in some contexts. Possible interventions and implications are discussed.
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Affiliation(s)
| | | | - Jonas R. Kunst
- Harvard University, Cambridge, MA, USA
- University of Oslo, Norway
- University of Aarhus, Denmark
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47
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Genetic affinities of the Jewish populations of India. Sci Rep 2016; 6:19166. [PMID: 26759184 PMCID: PMC4725824 DOI: 10.1038/srep19166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/25/2015] [Indexed: 11/09/2022] Open
Abstract
Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven't explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the 'Jewish Diaspora'.
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48
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60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Sci Rep 2015. [PMID: 26211407 PMCID: PMC4515592 DOI: 10.1038/srep12526] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70–50 ka into Eastern or Southern Africa, (2) postglacial movements (15–10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.
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49
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Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Černý V, Soares P, Richards MB, Pereira L. Genetic stratigraphy of key demographic events in Arabia. PLoS One 2015; 10:e0118625. [PMID: 25738654 PMCID: PMC4349752 DOI: 10.1371/journal.pone.0118625] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/21/2015] [Indexed: 01/01/2023] Open
Abstract
At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.
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Affiliation(s)
- Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Petr Triska
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Alison Machado
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Zuzana Fajkošová
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Martin B. Richards
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- * E-mail:
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A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road. Sci Rep 2015; 5:8377. [PMID: 25669617 PMCID: PMC4323646 DOI: 10.1038/srep08377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/14/2015] [Indexed: 11/08/2022] Open
Abstract
Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. Whether they received any genetic contribution from the Far East remains unknown, but frequent communication with the Chinese has been observed since the Silk Road period. To address this issue, mitochondrial DNA (mtDNA) variation from 55,595 Eurasians are analyzed. The existence of some eastern Eurasian haplotypes in eastern Ashkenazi Jews supports an East Asian genetic contribution, likely from Chinese. Further evidence indicates that this connection can be attributed to a gene flow event that occurred less than 1.4 kilo-years ago (kya), which falls within the time frame of the Silk Road scenario and fits well with historical records and archaeological discoveries. This observed genetic contribution from Chinese to Ashkenazi Jews demonstrates that the historical exchange between Ashkenazim and the Far East was not confined to the cultural sphere but also extended to an exchange of genes.
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