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McQuillan MA, Verhulst S, Hansen MEB, Beggs W, Meskel DW, Belay G, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Njamnshi AK, Chanock SJ, Aviv A, Tishkoff SA. Association between telomere length and Plasmodium falciparum malaria endemicity in sub-Saharan Africans. Am J Hum Genet 2024; 111:927-938. [PMID: 38701745 PMCID: PMC11080607 DOI: 10.1016/j.ajhg.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
Leukocyte telomere length (LTL) varies significantly across human populations, with individuals of African ancestry having longer LTL than non-Africans. However, the genetic and environmental drivers of LTL variation in Africans remain largely unknown. We report here on the relationship between LTL, genetics, and a variety of environmental and climatic factors in ethnically diverse African adults (n = 1,818) originating from Botswana, Tanzania, Ethiopia, and Cameroon. We observe significant variation in LTL among populations, finding that the San hunter-gatherers from Botswana have the longest leukocyte telomeres and that the Fulani pastoralists from Cameroon have the shortest telomeres. Genetic factors explain ∼50% of LTL variation among individuals. Moreover, we observe a significant negative association between Plasmodium falciparum malaria endemicity and LTL while adjusting for age, sex, and genetics. Within Africa, adults from populations indigenous to areas with high malaria exposure have shorter LTL than those in populations indigenous to areas with low malaria exposure. Finally, we explore to what degree the genetic architecture underlying LTL in Africa covaries with malaria exposure.
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Affiliation(s)
- Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dawit Wolde Meskel
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania (KIUT), Dares Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Abraham Aviv
- The Center of Human Development and Aging, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Belay S, Belay G, Nigussie H, Jian-Lin H, Tijjani A, Ahbara AM, Tarekegn GM, Woldekiros HS, Mor S, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci Data 2024; 11:139. [PMID: 38287052 PMCID: PMC10825132 DOI: 10.1038/s41597-024-02973-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species' evolutionary trajectory.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Tigray, Ethiopia.
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
| | - Helen Nigussie
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- ILRI-CAAS Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
| | - Abdulfatai Tijjani
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Siobhan Mor
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- School of Philosophical and Historical Inquiry, University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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4
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Zenebe B, Nigussie H, Belay G, Seboka N. A review on characterization of BCR - ABL transcript variants for molecular monitoring of chronic myeloid leukemia phenotypes. Hematology 2023; 28:2284038. [PMID: 37982440 DOI: 10.1080/16078454.2023.2284038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal myeloproliferative growth of human pluripotent stem cells which is estimated to occur at a rate of 1/100000 populations every year worldwide. A characteristic feature of this disease is the presence of the Philadelphia chromosome genotype, which results from the reciprocal translocation between human chromosomes 9 and 22. Two types of major genotypes are involved, which consequently result in two major types of expressed fusion mRNA transcripts: b3a2 and b2a2, i.e. major breakpoint segments (happening after exon 13 & after exon 14) of the BCR gene on chromosome 22 fuze with the ABL1 gene breakpoint (happening after exon 2) on chromosome 9, forming two genotypes coding for two transcripts: b3a2 (e14a2) and b2a2 (e13a2). The protein 'p210 BCR-ABL1', a protein which characteristically exhibits a high tyrosine kinase activity which is followed by the activation of various cellular processes that lead to increased cellular proliferation and cancer, is coded by both major BCR - ABL1 mRNA transcripts. Recent developments in the treatment of CML through molecular monitoring of the disease have managed to reduce patient morbidity and mortality. Advanced molecular techniques are aimed at detecting BCR-ABL1 transcript levels to monitor treatment response. Transcript typing is necessary to detect minimal residual disease and to achieve molecular response by helping to provide selective therapy based on the type of transcript identified, as transcript type is correlated with the disease course.The purpose of this review is to discuss: the role of the BCR-ABL1 fusion gene in the pathogenesis of CML; the role of BCR-ABL1 transcript characterization in the molecular monitoring of CML therapy; the association of BCR - ABL1 transcript types with different CML phenotypes, molecular responses, and treatment responses; and the laboratory techniques employed to detect and characterize BCR - ABL1 transcripts.
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Affiliation(s)
- Benyam Zenebe
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nigussie Seboka
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
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5
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Agonafir M, Belay G, Maningi NE, Feleke A, Reta MA, Olifant SL, Hassen MS, Girma T, Fourie PB. Genetic diversity of Mycobacterium tuberculosis isolates from the central, eastern and southeastern Ethiopia. Heliyon 2023; 9:e22898. [PMID: 38125463 PMCID: PMC10731068 DOI: 10.1016/j.heliyon.2023.e22898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The population structure of Mycobacterium tuberculosis complex (MTBC) in Ethiopia is diverse but dominated by Euro-American (Lineage 4) and East-African-Indian (Lineage 3) lineages. The objective of this study was to describe the genetic diversity of MTBC isolates in Central, Eastern and Southeastern Ethiopia. Methods A total of 223 MTBC culture isolates obtained from patients referred to Adama and Harar TB reference laboratories were spoligotyped. Demographic and clinical characteristics were collected. Results Six major lineages: Euro-American (Lineage 4), East-African-Indian (Lineage 3), East Asian (Lineage 2), Indo-Oceanic (Lineage 1), Mycobacterium africanum (Lineage 5 and Lineage 6) and Ethiopian (Lineage 7) were identified. The majority (94.6 %) of the isolates were Euro-American and East-African-Indian, with proportions of 75.3 % and 19.3 %, respectively. Overall, 77 different spoligotype patterns were identified of which 42 were registered in the SITVIT2 database. Of these, 27 spoligotypes were unique, while 15 were clustered with 2-49 isolates. SIT149/T3_ETH (n = 49), SIT53/T1 (n = 33), SIT21/CAS1_Kili (n = 24) and SIT41/Turkey (n = 11) were the dominant spoligotypes. A rare Beijing spoligotype pattern, SIT541, has also been identified in Eastern Ethiopia. The overall clustering rate of sub-lineages with known SIT was 71.3 %. Age group (25-34) was significantly associated with clustering. Conclusion We found a heterogeneous population structure of MTBC dominated by T and CAS families, and the Euro-American lineage. The identification of the Beijing strain, particularly the rare SIT541 spoligotype in Eastern Ethiopia, warrants a heightened surveillance plan, as little is known about this genotype. A large-scale investigation utilizing a tool with superior discriminatory power, such as whole genome sequencing, is necessary to gain a thorough understanding of the genetic diversity of MTBC in the nation, which would help direct the overall control efforts.
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Affiliation(s)
- Mulualem Agonafir
- Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Ethiopia
| | - Nontuthuko E. Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Adey Feleke
- Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Ethiopia
| | - Melese Abate Reta
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - Sharon L. Olifant
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Tewodros Girma
- Harar Health Research and Regional Laboratory, Harar, Ethiopia
| | - P. Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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6
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Chen N, Xia X, Hanif Q, Zhang F, Dang R, Huang B, Lyu Y, Luo X, Zhang H, Yan H, Wang S, Wang F, Chen J, Guan X, Liu Y, Li S, Jin L, Wang P, Sun L, Zhang J, Liu J, Qu K, Cao Y, Sun J, Liao Y, Xiao Z, Cai M, Mu L, Siddiki AZ, Asif M, Mansoor S, Babar ME, Hussain T, Silva GLLP, Gorkhali NA, Terefe E, Belay G, Tijjani A, Zegeye T, Gebre MG, Ma Y, Wang Y, Huang Y, Lan X, Chen H, Migliore NR, Colombo G, Semino O, Achilli A, Sinding MHS, Lenstra JA, Cheng H, Lu W, Hanotte O, Han J, Jiang Y, Lei C. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nat Commun 2023; 14:7803. [PMID: 38016956 PMCID: PMC10684552 DOI: 10.1038/s41467-023-43626-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University, Kunming, 650500, China
| | - Huixuan Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yanhong Cao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Junli Sun
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, 530001, China
| | - Zhengzhong Xiao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Ming Cai
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Lan Mu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, 650224, China
| | - Amam Zonaed Siddiki
- Genomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, 4225, Bangladesh
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Masroor Ellahi Babar
- The University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Islamabad, 44100, Pakistan
| | | | - Neena Amatya Gorkhali
- National Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, 45200, Nepal
| | - Endashaw Terefe
- College of Agriculture and Environmental Science, Department of Animal Science, Arsi University, Asella, Ethiopia
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
| | - Gurja Belay
- College of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University, 1000, Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Tsadkan Zegeye
- Mekelle Agricultural Research Center, P.O. Box 258, 7000, Mekelle, Tigray, Ethiopia
| | - Mebrate Genet Gebre
- School of Animal and Rangeland Science, College of Agriculture, Haramaya University, 2040, Haramaya, Oromia, Ethiopia
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, 250100, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China.
- Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100, Nairobi, Kenya.
- Yazhouwan National Laboratory, Sanya, 572024, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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Harris DN, Platt A, Hansen MEB, Fan S, McQuillan MA, Nyambo T, Mpoloka SW, Mokone GG, Belay G, Fokunang C, Njamnshi AK, Tishkoff SA. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Curr Biol 2023; 33:4905-4916.e5. [PMID: 37837965 PMCID: PMC10841429 DOI: 10.1016/j.cub.2023.09.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.
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Affiliation(s)
- Daniel N Harris
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Platt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaoundé, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Pagkrati I, Duke JL, Mbunwe E, Mosbruger TL, Ferriola D, Wasserman J, Dinou A, Tairis N, Damianos G, Kotsopoulou I, Papaioannou J, Giannopoulos D, Beggs W, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi AK, Fokunang C, Woldemeskel D, Belay G, Maiers M, Tishkoff SA, Monos DS. Genomic characterization of HLA class I and class II genes in ethnically diverse sub-Saharan African populations: A report on novel HLA alleles. HLA 2023; 102:192-205. [PMID: 36999238 PMCID: PMC10524506 DOI: 10.1111/tan.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/11/2023] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
HLA allelic variation has been well studied and documented in many parts of the world. However, African populations have been relatively under-represented in studies of HLA variation. We have characterized HLA variation from 489 individuals belonging to 13 ethnically diverse populations from rural communities from the African countries of Botswana, Cameroon, Ethiopia, and Tanzania, known to practice traditional subsistence lifestyles using next generation sequencing (Illumina) and long-reads from Oxford Nanopore Technologies. We identified 342 distinct alleles among the 11 HLA targeted genes: HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1, with 140 of those alleles containing novel sequences that were submitted to the IPD-IMGT/HLA database. Sixteen of the 140 alleles contained novel content within the exonic regions of the genes, while 110 alleles contained novel intronic variants. Four alleles were found to be recombinants of already described HLA alleles and 10 alleles extended the sequence content of already described alleles. All 140 alleles include complete allelic sequence from the 5' UTR to the 3' UTR that are inclusive of all exons and introns. This report characterizes the HLA allelic variation from these individuals and describes the novel allelic variation present within these specific African populations.
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Affiliation(s)
- Ioanna Pagkrati
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jamie L. Duke
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Eric Mbunwe
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy L. Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jenna Wasserman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Amalia Dinou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Nikolaos Tairis
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Georgios Damianos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Ioanna Kotsopoulou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Joanna Papaioannou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Diamantoula Giannopoulos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - William Beggs
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania (KIUT), Dar es Salaam, Tanzania
| | - Sununguko W. Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Gaonyadiwe G. Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Alfred K. Njamnshi
- Department of Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Department of Neurology & Neuroscience, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Dawit Woldemeskel
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitri S. Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Zegeye T, Belay G, Vallejo-Trujillo A, Han J, Hanotte O. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Front Genet 2023; 14:1050365. [PMID: 37600659 PMCID: PMC10432725 DOI: 10.3389/fgene.2023.1050365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%-0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and KCNG4), milk yield (GABRG1), meat quality (MMRN2, VWC2), feed efficiency (PCDH8 and SLC26A3), immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5), heat resistance (NPFFR1 and HTR7) and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments. Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6-0.7 times higher than homozygous ones. The within-breed average number of ROHs ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp. The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals. Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%-88.7%) and African taurine (11.3%-14.1%) cattle, with very small, if any, European taurine introgression. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
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Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adriana Vallejo-Trujillo
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jianlin Han
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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10
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Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, Ranciaro A, Hirbo J, Beggs W, Thomas N, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi A, Folkunang C, Meskel DW, Belay G, Song YS, Tishkoff SA. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 2023; 186:923-939.e14. [PMID: 36868214 PMCID: PMC10568978 DOI: 10.1016/j.cell.2023.01.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.
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Affiliation(s)
- Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey P Spence
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neil Thomas
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, P.O. Box 9790, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Alfred Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Charles Folkunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Dawit Wolde Meskel
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Kelly DE, Ramdas S, Ma R, Rawlings-Goss RA, Grant GR, Ranciaro A, Hirbo JB, Beggs W, Yeager M, Chanock S, Nyambo TB, Omar SA, Woldemeskel D, Belay G, Li H, Brown CD, Tishkoff SA. The genetic and evolutionary basis of gene expression variation in East Africans. Genome Biol 2023; 24:35. [PMID: 36829244 PMCID: PMC9951478 DOI: 10.1186/s13059-023-02874-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies have focused on individuals of European descent. While important progress has been made to study a greater diversity of human populations, many groups remain unstudied, particularly among indigenous populations within Africa. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations. RESULTS We find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine-mapping of causal variation. Integrating our QTL scans with signatures of natural selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation. CONCLUSION Extending QTL mapping studies beyond European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.
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Affiliation(s)
- Derek E Kelly
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Ramdas
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rong Ma
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Jibril B Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Beggs
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meredith Yeager
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Institutes of Health, Rockville, MD, USA
| | - Thomas B Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar Es Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dawit Woldemeskel
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hongzhe Li
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher D Brown
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, USA.
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12
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Agonafir M, Belay G, Feleke A, Maningi N, Girmachew F, Reta M, Fourie PB. Profile and Frequency of Mutations Conferring Drug-Resistant Tuberculosis in the Central, Southeastern and Eastern Ethiopia. Infect Drug Resist 2023; 16:2953-2961. [PMID: 37201127 PMCID: PMC10187580 DOI: 10.2147/idr.s408567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023] Open
Abstract
Purpose Advances in molecular tools that assess genes harboring drug resistance mutations have greatly improved the detection and treatment of drug-resistant tuberculosis (DR-TB). This study was conducted to determine the frequency and type of mutations that are responsible for resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolones (FLQs) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis (MTB) isolates obtained from culture-positive pulmonary tuberculosis (TB) patients in the central, southeastern and eastern Ethiopia. Patients and Methods In total, 224 stored culture-positive MTB isolates from pulmonary TB patients referred to Adama and Harar regional TB laboratories between August 2018 and January 2019 were assessed for mutations conferring RIF, INH, FLQs and SLIDs resistance using GenoType®MTBDRplus (MTBDRplus) and GenoType®MTBDRsl (MTBDRsl). Results RIF, INH, FLQs and SLIDs resistance-conferring mutations were identified in 88/224 (39.3%), 85/224 (38.0%), 7/77 (9.1%), and 3/77% (3.9%) of MTB isolates, respectively. Mutation codons rpoB S531L (59.1%) for RIF, katG S315T (96.5%) for INH, gyrA A90V (42.1%) for FLQs and WT1 rrs (100%) for SLIDs were observed in the majority of the isolates tested. Over a 10th of rpoB mutations detected in the current study were unknown. Conclusion In this study, the most common mutations conferring drug resistance to RIF, INH, FLQs were identified. However, a significant proportion of RIF-resistant isolates manifested unknown rpoB mutations. Similarly, although few in number, all SLID-resistant isolates had unknown rrs mutations. To further elucidate the entire spectrum of mutations, tool such as whole-genome sequencing is imperative. Furthermore, the expansion of molecular drug susceptibility testing services is critical for tailoring patient treatment and preventing disease transmission.
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Affiliation(s)
- Mulualem Agonafir
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Correspondence: Mulualem Agonafir, Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 34738, Addis Ababa, Ethiopia, Tel +251911446959, Email
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adey Feleke
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nontuthuko Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Melese Reta
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - P Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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13
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Terefe E, Belay G, Han J, Hanotte O, Tijjani A. Genomic adaptation of Ethiopian indigenous cattle to high altitude. Front Genet 2022; 13:960234. [PMID: 36568400 PMCID: PMC9780680 DOI: 10.3389/fgene.2022.960234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
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Affiliation(s)
- Endashaw Terefe
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
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14
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Gebru G, Belay G, Vallejo-Trujillo A, Dessie T, Gheyas A, Hanotte O. Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia). Front Genet 2022; 13:968961. [PMID: 36246589 PMCID: PMC9561088 DOI: 10.3389/fgene.2022.968961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800–400 BCE. Since then, the farming communities of the region have integrated chicken into their livelihoods. The region is also recognised for its high chicken-to-human population ratio and diverse and complex geography, ranging from 500 to 4,000 m above sea level (m.a.s.l.). More than 15 agro-ecological zones have been described. Following exotic chicken introductions, the proportion of indigenous chicken is now 70% only in the region. It calls for the characterisation of indigenous Tigrayan chicken ecotypes and their habitats. This study reports an Ecological Niche Modelling using MaxEnt to characterise the habitats of 16 indigenous village chicken populations of Tigray. A total of 34 ecological and landscape variables: climatic (22), soil (eight), vegetation, and land cover (four), were included. We applied Principal Component Analysis correlation, and MaxentVariableSelection procedures to select the most contributing and uncorrelated variables. The selected variables were three climatic (bio5 = maximum temperature of the warmest month, bio8 = mean temperature of the wettest quarter, bio13 = precipitation of the wettest month), three vegetation and land cover (grassland, forest land, and cultivated land proportional areas), and one soil (clay content). Following our analysis, we identified four main chicken agro-ecologies defining four candidates indigenous Tigrayan chicken ecotypes. The study provides baseline information for phenotypic and genetic characterisation as well as conservation interventions of indigenous Tigrayan chickens.
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Affiliation(s)
- Gebreslassie Gebru
- Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Addis Ababa University, College of Natural and Computational Science, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- *Correspondence: Gebreslassie Gebru, ; Olivier Hanotte,
| | - Gurja Belay
- Addis Ababa University, College of Natural and Computational Science, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | | | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Almas Gheyas
- Centre for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Gebreslassie Gebru, ; Olivier Hanotte,
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15
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McQuillan MA, Ranciaro A, Hansen MEB, Fan S, Beggs W, Belay G, Woldemeskel D, Tishkoff SA. Signatures of Convergent Evolution and Natural Selection at the Alcohol Dehydrogenase Gene Region are Correlated with Agriculture in Ethnically Diverse Africans. Mol Biol Evol 2022; 39:6677382. [PMID: 36026493 PMCID: PMC9547508 DOI: 10.1093/molbev/msac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The alcohol dehydrogenase (ADH) family of genes encodes enzymes that catalyze the metabolism of ethanol into acetaldehyde. Nucleotide variation in ADH genes can affect the catalytic properties of these enzymes and is associated with a variety of traits, including alcoholism and cancer. Some ADH variants, including the ADH1B*48His (rs1229984) mutation in the ADH1B gene, reduce the risk of alcoholism and are under positive selection in multiple human populations. The advent of Neolithic agriculture and associated increase in fermented foods and beverages is hypothesized to have been a selective force acting on such variants. However, this hypothesis has not been tested in populations outside of Asia. Here, we use genome-wide selection scans to show that the ADH gene region is enriched for variants showing strong signals of positive selection in multiple Afroasiatic-speaking, agriculturalist populations from Ethiopia, and that this signal is unique among sub-Saharan Africans. We also observe strong selection signals at putatively functional variants in nearby lipid metabolism genes, which may influence evolutionary dynamics at the ADH region. Finally, we show that haplotypes carrying these selected variants were introduced into Northeast Africa from a West-Eurasian source within the last ∼2,000 years and experienced positive selection following admixture. These selection signals are not evident in nearby, genetically similar populations that practice hunting/gathering or pastoralist subsistence lifestyles, supporting the hypothesis that the emergence of agriculture shapes patterns of selection at ADH genes. Together, these results enhance our understanding of how adaptations to diverse environments and diets have influenced the African genomic landscape.
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Affiliation(s)
| | - Alessia Ranciaro
- Current address: Department of Biological Sciences, Human and Evolutionary Biology Section, University of Southern California, Los Angeles, CA
| | | | - Shaohua Fan
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dawit Woldemeskel
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
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16
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Beshah D, Desta A, Belay G, Abebe T, Gebreselasie S, Sisay Tessema T. Antimicrobial Resistance and Associated Risk Factors of Gram-Negative Bacterial Bloodstream Infections in Tikur Anbessa Specialized Hospital, Addis Ababa. Infect Drug Resist 2022; 15:5043-5059. [PMID: 36068835 PMCID: PMC9441145 DOI: 10.2147/idr.s371654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background Bloodstream infections (BSIs) are significant causes of morbidity and mortality in Ethiopia and worldwide. Alarming is the rapid global spread of antimicrobial resistance (AMR) in bacteria. Objective To determine the microbial profile, antimicrobial susceptibility pattern, and associated risk factors for bloodstream infections in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa Ethiopia. Methods A cross-sectional study was conducted between September 2018 and March 2019. Blood collected twice from each septicemia suspected patient were processed following standard bacteriological procedures. AST was performed by using the disk diffusion test according to CLSI 2017 and 2018 guidelines. Data captured in Epidata were cleaned and analyzed by SPSS version 21 software. Results The prevalence of BSI was 28.06% and a higher proportion of pathogene detected were gram-negative bacteria (GNB) (54.5%) and gram-positive bacteria (GPB) (45.43%). The most abundant bacterial species were Klebsiella pneumoniae 17.6%, CoNS 15.2%, and Acinetobacter spp 11.0%. Culture positivity was associated with age below 6 years, neonates AOR p=<0.001, infants AOR p=<0.001, Pre-school P=0.002, ICU admission COR p=<0.001, length of admission >5 days COR P=0.016, temperature greater than 38°C, AOR p=0.013, instrument usage during medical care AOR, p=<0.001, chronic illness AOR p=0.027, and neonatal incubation AOR p=0.013. GNB average drug resistance rate was 57.9% of the commonly used antibiotics and the most efficient and inefficient drugs were amikacin (10.8%) and ampicillin (94.6%). The gram-negative isolates showed a 95.3% rate of multi-drug resistance; and MDR, XDR, and PDR were observed at 55.8%, 32.2%, and 7.3%, of isolates respectively. This finding shows children especially neonates were highly affected by drug resistant BSI. Conclusion Pediatric patients and ICU patients are more affected by BSI, and drug-resistant bacteria are a major problem. Therefore, appropriate intervention approaches need to be implemented.
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Affiliation(s)
- Daniel Beshah
- Microbial Cellular Molecular Biology Infection Biology Stream, College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Diagnostic Laboratory, Tikur Anbessa Specialized Hospital, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Correspondence: Daniel Beshah, Microbial Cellular Molecular Biology infection Biology stream, College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia, Tel +251 911151317, Email ;
| | - Adey Desta
- Microbial Cellular Molecular Biology Infection Biology Stream, College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular Molecular Biology Infection Biology Stream, College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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17
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Zhang C, Verma A, Feng Y, Melo MCR, McQuillan M, Hansen M, Lucas A, Park J, Ranciaro A, Thompson S, Rubel MA, Campbell MC, Beggs W, Hirbo J, Wata Mpoloka S, George Mokone G, Nyambo T, Wolde Meskel D, Belay G, Fokunang C, Njamnshi AK, Omar SA, Williams SM, Rader DJ, Ritchie MD, de la Fuente-Nunez C, Sirugo G, Tishkoff SA. Impact of natural selection on global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2022; 119:e2123000119. [PMID: 35580180 PMCID: PMC9173769 DOI: 10.1073/pnas.2123000119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/29/2022] [Indexed: 01/09/2023] Open
Abstract
Human genomic diversity has been shaped by both ancient and ongoing challenges from viruses. The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating impact on population health. However, genetic diversity and evolutionary forces impacting host genes related to SARS-CoV-2 infection are not well understood. We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (angiotensin converting enzyme 2 [ACE2], transmembrane protease serine 2 [TMPRSS2], dipeptidyl peptidase 4 [DPP4], and lymphocyte antigen 6 complex locus E [LY6E]). We analyzed data from 2,012 ethnically diverse Africans and 15,977 individuals of European and African ancestry with electronic health records and integrated with global data from the 1000 Genomes Project. At ACE2, we identified 41 nonsynonymous variants that were rare in most populations, several of which impact protein function. However, three nonsynonymous variants (rs138390800, rs147311723, and rs145437639) were common among central African hunter-gatherers from Cameroon (minor allele frequency 0.083 to 0.164) and are on haplotypes that exhibit signatures of positive selection. We identify signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage compared with the chimpanzee genome. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19. Our study provides insights into global variation at host genes related to SARS-CoV-2 infection, which have been shaped by natural selection in some populations, possibly due to prior viral infections.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Yuanqing Feng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcelo C. R. Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael McQuillan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Matthew Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Meagan A. Rubel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael C. Campbell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jibril Hirbo
- Department of Medicine, Vanderbilt University, Nashville, TN 37232
| | | | | | | | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | - Dawit Wolde Meskel
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
- Brain Research Africa Initiative, Neuroscience Laboratory, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sabah A. Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106
| | - Daniel J. Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Sarah A. Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA 19104
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18
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Jang J, Terefe E, Kim K, Lee YH, Belay G, Tijjani A, Han JL, Hanotte O, Kim H. Correction to: Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics 2022; 23:207. [PMID: 35291938 PMCID: PMC8922724 DOI: 10.1186/s12864-022-08409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Endashaw Terefe
- Addis Ababa University, MCMB Department, Addis Ababa, Ethiopia.,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,Arsi University, Asella, Ethiopia
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Gurja Belay
- Addis Ababa University, MCMB Department, Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, UK
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc., Seoul, South Korea.
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19
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Zhang C, Verma A, Feng Y, Melo MCR, McQuillan M, Hansen M, Lucas A, Park J, Ranciaro A, Thompson S, Rubel MA, Campbell MC, Beggs W, Hirbo J, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi AK, Omar SA, Williams SM, Rader D, Ritchie MD, de la Fuente Nunez C, Sirugo G, Tishkoff S. Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. medRxiv 2021:2021.06.28.21259529. [PMID: 34230933 PMCID: PMC8259910 DOI: 10.1101/2021.06.28.21259529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuanqing Feng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo C. R. Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael McQuillan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meghan A. Rubel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | - Dawit Wolde Meskel
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Gurja Belay
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sabah A. Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Daniel Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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Zegeye T, Belay G, Hanotte O. Multivariate characterization of phenotypic traits of five native cattle populations from Tigray, Northern Ethiopia. Trop Anim Health Prod 2021; 53:212. [PMID: 33738653 DOI: 10.1007/s11250-021-02652-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/09/2021] [Indexed: 11/28/2022]
Abstract
Abergelle, Arado, Begait, Irob, and Raya are important native cattle populations that are well adapted to the harsh natural conditions in Tigray, Ethiopia. However, little is known about their phenotypic characteristics and inter-population variability. Understanding the phenotypic characteristics is the crucial step in an effort of maintaining genetic diversity and conserving important traits for adaptation. A total of 1650 native matured cattle from the five populations were used to investigate the phenotypic characteristics and variability based on 21 qualitative traits and 21 body measurements using uni- and multivariate, and discriminant analysis. All the qualitative traits and body measurements showed highly significant breed difference except the tail base thickness. Values for most of the body measurements were higher in Begait cattle compared to the other cattle populations. The stepwise discriminant analysis extracted eighteen variables for characterizing the female populations and thirteen variables for the male populations. The pair-wise Mahalanobis distance showed the highest morphological distance between Begait and Irob, and the closest distance between Abergelle and Irob cattle populations. High correct assignment to source population was obtained for both sexes of all breeds except Abergelle and Irob. The discriminant function graph discerned each population with no clear distinction between Abergelle and Irob. These results indicate that the five cattle populations under investigation are clustered into four distinct breeds. However, the present phenotypic characterization should be confirmed with molecular genetic diversity investigation to use as a base in their conservation, breeding, and selection strategies.
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Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, P.O. Box 492, Mekelle, Tigray, Ethiopia. .,Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Live Gene - CTLGH, International Livestock Research Institute (ILRI), P.O Box 5689, Addis Ababa, Ethiopia.,Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK
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21
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Hunt SC, Hansen MEB, Verhulst S, McQuillan MA, Beggs W, Lai TP, Mokone GG, Mpoloka SW, Meskel DW, Belay G, Nyambo TB, Abnet CC, Yeager M, Chanock SJ, Province MA, Williams SM, Aviv A, Tishkoff SA. Genetics and geography of leukocyte telomere length in sub-Saharan Africans. Hum Mol Genet 2020; 29:3014-3020. [PMID: 32821950 PMCID: PMC7645709 DOI: 10.1093/hmg/ddaa187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/09/2020] [Accepted: 08/15/2020] [Indexed: 01/10/2023] Open
Abstract
Leukocyte telomere length (LTL) might be causal in cardiovascular disease and major cancers. To elucidate the roles of genetics and geography in LTL variability across humans, we compared LTL measured in 1295 sub-Saharan Africans (SSAs) with 559 African-Americans (AAms) and 2464 European-Americans (EAms). LTL differed significantly across SSAs (P = 0.003), with the San from Botswana (with the oldest genomic ancestry) having the longest LTL and populations from Ethiopia having the shortest LTL. SSAs had significantly longer LTL than AAms [P = 6.5(e-16)] whose LTL was significantly longer than EAms [P = 2.5(e-7)]. Genetic variation in SSAs explained 52% of LTL variance versus 27% in AAms and 34% in EAms. Adjustment for genetic variation removed the LTL differences among SSAs. LTL genetic variation among SSAs, with the longest LTL in the San, supports the hypothesis that longer LTL was ancestral in humans. Identifying factors driving LTL variation in Africa may have important ramifications for LTL-associated diseases.
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Affiliation(s)
- Steven C Hunt
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tsung-Po Lai
- Center of Human Development and Aging, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - Gaonyadiwe G Mokone
- Faculty of Medicine, Department of Biomedical Sciences, University of Botswana, Gaborone, Botswana
| | | | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thomas B Nyambo
- Department of Biochemistry, Kampala International University, Tanzania
| | - Christian C Abnet
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892,USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892,USA
| | - Stephen J Chanock
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892,USA
| | - Michael A Province
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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22
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Amane A, Belay G, Nasser Y, Kyalo M, Dessie T, Kebede A, Getachew T, Entfellner JBD, Edea Z, Hanotte O, Tarekegn GM. Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography. Genes Genomics 2020; 42:1169-1178. [PMID: 32803704 PMCID: PMC7497517 DOI: 10.1007/s13258-020-00984-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/04/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. OBJECTIVE The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. METHODS A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. RESULTS Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. CONCLUSION The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations.
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Affiliation(s)
- Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- Andassa Livestock Research Center, Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia.
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya.
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Yao Nasser
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Martina Kyalo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Tadelle Dessie
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Adebabay Kebede
- Andassa Livestock Research Center, Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Tesfaye Getachew
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | | | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science (SLU), Uppsala, Sweden.
- Department of Animal Production and Technology, School of Animal Sciences and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia.
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23
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Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA. Correction to: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol 2019; 20:204. [PMID: 31597575 PMCID: PMC6784328 DOI: 10.1186/s13059-019-1821-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Present Address: State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Derek E Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Present Address: Division of Genetic Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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24
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Mbunwe E, Duke JL, Ferriola D, Mosbruger T, Damianos G, Dinou A, Kotsopoulou I, Ranciaro A, Thompson S, Beggs W, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi AK, Carrington M, Maiers M, Tishkoff S, Monos DS. P072 HLA types in ethnically diverse sub-saharan african populations. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Haile EL, Cindy S, Ina B, Belay G, Jean-Pierre VG, Sharon R, Lisbeth LR, Paul BJ. HPV testing on vaginal/cervical nurse-assisted self-samples versus clinician-taken specimens and the HPV prevalence, in Adama Town, Ethiopia. Medicine (Baltimore) 2019; 98:e16970. [PMID: 31464941 PMCID: PMC6736428 DOI: 10.1097/md.0000000000016970] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 01/11/2023] Open
Abstract
This study aimed to determine the feasibility of vaginal/cervical nurse-assisted self-sampling (NASS) and the agreement between human papilloma virus (HPV) tests on self-samples versus clinician-taken (CT) specimens.Women participated voluntarily for cervical cancer screening at St. Aklesia Memorial Hospital. Eighty-three women provided a total of 166 coupled self-taken and CT specimens collected. Specimens were stored at room temperature for a maximum of 10 months and analyzed using validated the RIATOL qPCR HPV genotyping test, a quantitative polymerase chain reaction (qPCR) high-throughput HPV E6, E7 assay. The average age of the participating women was 32 years. Seventy-three women (87.9%) felt that NASS was easy to use. An overall HPV, high-risk (HR) HPV, and low-risk HPV prevalence was 22.7% (15/66), 18.2% (12/66), and 6.1% (4/66), respectively. The overall HR HPV prevalence was 17.2% (NASS) and 15.5% (CT). The most prevalent HPV type was HPV51; HPV 16 was only detected in 1 woman (CT+NASS) and HPV18 only in 1 woman (CT). The overall measurement agreement between self-taken and CT samples was moderate with a kappa value of 0.576 (P < .001). Lifetime partnered with >2 men were associated with HR HPV positivity (P < .001). There was a strong statistical association between HR HPV positivity and visual inspection with acetic acid- positive (P < .001). The NASS for HPV testing could be seen as an alternative option and might be acceptable to Ethiopian women. The overall HR HPV prevalence was comparable with Sub-Saharan countries in the general population.
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Affiliation(s)
- Eshetu Lemma Haile
- University of Antwerp, Antwerpen, Belgium
- Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Benoy Ina
- University of Antwerp, Antwerpen, Belgium
- Algemeen Medisch Laboratorium (AML), Sonic Healthcare, Antwerpen, Belgium
| | - Gurja Belay
- Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Ransom Sharon
- International Partnership for Reproductive Health, Bryan, OH
| | | | - Bogers Johannes Paul
- University of Antwerp, Antwerpen, Belgium
- Algemeen Medisch Laboratorium (AML), Sonic Healthcare, Antwerpen, Belgium
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26
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Rume VN, Dundon WG, Belay G, Baziki JDD, Diakite A, Paul A, Tessema YD, Nwankpa N, Gizaw D, Cattoli G, Bodjo SC, Tessema TS. Molecular epidemiological update of Peste des Petits Ruminants virus (PPRV) in Ethiopia. Vet Microbiol 2019; 235:229-233. [PMID: 31383306 DOI: 10.1016/j.vetmic.2019.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/01/2019] [Accepted: 07/07/2019] [Indexed: 11/18/2022]
Abstract
Peste des Petits ruminants (PPR) is a devastating disease of small ruminants with high morbidity and mortality rates among susceptible animals. The disease is endemic in much of Africa, the Middle East and Asia and constitutes one of the major hurdles to the improvement of small-ruminant production in these countries. The causal agent of PPR, the Small Ruminant Morbillivirus (SRMV), previously known as PPR virus (PPRV) belongs to the genus Morbillivirus within the family Paramyxoviridae. SRMV can be categorized into four genetically distinct lineages (I to IV). Suspicion of PPR was first reported in Ethiopia in 1977 and since then genetic characterization of circulating viruses has identified lineages III and IV in the country. This study was undertaken to provide an update on the molecular epidemiology of PPR in Ethiopia by analysing animal tissue samples collected between 2011 and 2017. PPR positive samples were identified in four regions of the country. Sequence and phylogenetic analysis of fourteen RT-PCR positive amplicons revealed that all of the SRMV in the samples from 2010 to 2017 belong to sub-clade II of clade I of lineage IV. No lineage III viruses were identified.
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Affiliation(s)
- Veronica Nwankpa Rume
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box: 1176, Ethiopia; African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia
| | - William G Dundon
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box: 1176, Ethiopia
| | - Jean-de-Dieu Baziki
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia; Pan African University Institute for basic Sciences, Technology and Innovation (PAUSTI), JKUAT Main Campus, P.O.Box: 620000-00200, Nairobi, Kenya
| | - Adama Diakite
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia
| | - Ankeli Paul
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia
| | - Yebchaye Degefa Tessema
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia
| | - Nick Nwankpa
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia
| | - Daniel Gizaw
- National Animal Health Diagnostic and Investigation Center (NAHDIC), P.O. Box 04, Sebeta, Ethiopia
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Sanne Charles Bodjo
- African Union- Pan African Veterinary Vaccine Centre (AU-PANVAC), P. O. Box 1746, Debre Zeit, Ethiopia.
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27
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Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol 2019; 20:82. [PMID: 31023338 PMCID: PMC6485071 DOI: 10.1186/s13059-019-1679-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations. RESULTS Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations. CONCLUSIONS We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
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Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Derek E Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: Division of Genetic Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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28
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Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. Loci associated with skin pigmentation identified in African populations. Science 2017; 358:eaan8433. [PMID: 29025994 PMCID: PMC5759959 DOI: 10.1126/science.aan8433] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/03/2017] [Indexed: 12/13/2022]
Abstract
Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.
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Affiliation(s)
- Nicholas G Crawford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Derek E Kelly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shanna L Bowman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ethan Jewett
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yancy Lo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C Campbell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jake Haut
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harriet Rothschild
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard Zon
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Zhou
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Sinclair
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cecilia Rivas
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eugene Elliot
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elena Oceana
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Yun S Song
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eleazar Eskin
- Department of Computer Science and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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Megaze A, Balakrishnan M, Belay G. Current population estimate and distribution of the African buffalo in Chebera Churchura National Park, Ethiopia. Afr J Ecol 2017. [DOI: 10.1111/aje.12411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Aberham Megaze
- Department of Biology; Faculty of Natural Sciences; Wolaita Sodo University; PO Box 138, Wolaita Sodo Sodo Ethiopia
| | | | - Gurja Belay
- Department of Zoological Sciences; Addis Ababa University; PO Box 1176 Addis Ababa Ethiopia
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Megaze A, Balakrishnan M, Belay G. Human–wildlife conflict and attitude of local people towards conservation of wildlife in Chebera Churchura National Park, Ethiopia. African Zoology 2017. [DOI: 10.1080/15627020.2016.1254063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Aberham Megaze
- Department of Biology, Faculty of Natural Sciences, Wolaita Sodo University, Wolaita Sodo, Ethiopia
| | | | - Gurja Belay
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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31
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Megaze A, Balakrishnan M, Belay G. Diurnal activity budget of African buffalo (Syncerus caffer
Sparrman, 1779) in Chebera Churchura National Park, Ethiopia. Afr J Ecol 2016. [DOI: 10.1111/aje.12359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Aberham Megaze
- Department of Biology; Faculty of Natural Sciences; Wolaita Sodo University; PO Box 138 Wolaita Sodo Ethiopia
| | | | - Gurja Belay
- Department of Zoological Sciences; Addis Ababa University; PO Box 1176 Addis Ababa Ethiopia
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Sisay Z, Djikeng A, Berhe N, Belay G, Abegaz WE, Wang QH, Saif LJ. First detection and molecular characterization of sapoviruses and noroviruses with zoonotic potential in swine in Ethiopia. Arch Virol 2016; 161:2739-47. [PMID: 27424025 DOI: 10.1007/s00705-016-2974-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Noroviruses (NoVs) and sapoviruses (SaVs), which belong to the family Caliciviridae, are important human and animal enteric pathogens with zoonotic potential. In Ethiopia, no study has been done on the epidemiology of animal NoVs and SaVs. The aim of this study was to detect and characterize NoVs and SaVs from swine of various ages. Swine fecal samples (n = 117) were collected from commercial farms in Ethiopia. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analysis was conducted using a portion of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of genome sequences of caliciviruses. Among 117 samples, potential caliciviruses were detected by RT-PCR in 17 samples (14.5 %). Of the RT-PCR-positive fecal samples, four were sequenced, of which two were identified as human NoV GII.1 and the other two as porcine SaV GIII. The porcine SaV strains that were detected were genetically related to the porcine enteric calicivirus Cowden strain genogroup III (GIII), which is the prototype porcine SaV strain. No porcine NoVs were detected. Our results showed the presence of NoVs in swine that are most similar to human strains. These findings have important implications for NoV epidemiology and food safety. Therefore, continued surveillance of NoVs in swine is needed to define their zoonotic potential, epidemiology and public and animal health impact. This is the first study to investigate enteric caliciviruses (noroviruses and sapoviruses) in swine in Ethiopia.
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Affiliation(s)
- Zufan Sisay
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia. .,Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Appolinaire Djikeng
- Biosciences eastern and central Africa-International Livestock, Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Nega Berhe
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.,Centre for Imported and Tropical Diseases, Oslo University Hospital-Ulleval, Oslo, Nornway
| | - Gurja Belay
- Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Woldaregay Erku Abegaz
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Q H Wang
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, USA
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Sisay Z, Djikeng A, Berhe N, Belay G, Gebreyes W, Abegaz WE, Njahira MN, Wang QH, Saif LJ. Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia. Arch Virol 2016; 161:2169-82. [PMID: 27193022 DOI: 10.1007/s00705-016-2887-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/03/2016] [Indexed: 01/02/2023]
Abstract
Viral gastroenteritis is a major public health problem worldwide. In Ethiopia, very limited studies have been done on the epidemiology of enteropathogenic viruses. The aim of this study was to detect and characterize noroviruses (NoVs) and sapoviruses (SaVs) from acute gastroenteritis patients of all ages. Fecal samples were collected from diarrheic patients (n = 213) in five different health centers in Addis Ababa during June-September 2013. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. Of the clinical samples, 25.3 % and 4.2 % were positive for NoV and SaV RNA, respectively. Among the norovirus positives, 22 were sequenced further, and diverse norovirus strains were identified: GI (n = 4), GII (n = 17) and GIV (n = 1). Most strains were GII (n = 17/22: 77.2 %), which were further divided into three different genotypes (GII.4, GII.12/GII.g recombinant-like and GII.17), with GII.17 being the dominant (7/17) strain detected. GI noroviruses, in particular GI.4 (n = 1), GI.5 (n = 2) and GI.8 (n = 1), were also detected and characterized. The GIV strain detected is the first from East Africa. The sapoviruses sequenced were also the first reported from Ethiopia. Collectively, this study showed the high burden and diversity of noroviruses and circulation of sapoviruses in diarrheic patients in Ethiopia. Continued surveillance to assess their association with diarrhea is needed to define their epidemiology, disease burden, and impact on public health.
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Affiliation(s)
- Zufan Sisay
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia. .,Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia.
| | - Appolinaire Djikeng
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Nega Berhe
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Wondwossen Gebreyes
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Woldaregay Erku Abegaz
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Moses N Njahira
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Q H Wang
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA.
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Campbell MC, Ranciaro A, Zinshteyn D, Rawlings-Goss R, Hirbo J, Thompson S, Woldemeskel D, Froment A, Omar SA, Bodo JM, Nyambo T, Belay G, Drayna D, Breslin PAS, Tishkoff SA. Limited evidence for adaptive evolution and functional effect of allelic variation at rs702424 in the promoter of the TAS2R16 bitter taste receptor gene in Africa. J Hum Genet 2014; 59:349-52. [PMID: 24785689 PMCID: PMC4075171 DOI: 10.1038/jhg.2014.29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 11/09/2022]
Abstract
Bitter taste perception, mediated by receptors encoded by the TAS2R loci, has important roles in human health and nutrition. Prior studies have demonstrated that nonsynonymous variation at site 516 in the coding exon of TAS2R16, a bitter taste receptor gene on chromosome 7, has been subject to positive selection and is strongly correlated with differences in sensitivity to salicin, a bitter anti-inflammatory compound, in human populations. However, a recent study suggested that the derived G-allele at rs702424 in the TAS2R16 promoter has also been the target of recent selection and may have an additional effect on the levels of salicin bitter taste perception. Here, we examined alleles at rs702424 for signatures of selection using Extended Haplotype Homozygosity (EHH) and FST statistics in diverse populations from West Central, Central and East Africa. We also performed a genotype-phenotype analysis of salicin sensitivity in a subset of 135 individuals from East Africa. Based on our data, we did not find evidence for positive selection at rs702424 in African populations, suggesting that nucleotide position 516 is likely the site under selection at TAS2R16. Moreover, we did not detect a significant association between rs702424 alleles and salicin bitter taste recognition, implying that this site does not contribute to salicin phenotypic variance. Overall, this study of African diversity provides further information regarding the genetic architecture and evolutionary history of a biologically-relevant trait in humans.
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Affiliation(s)
- Michael C Campbell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Zinshteyn
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Dawit Woldemeskel
- 1] Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA [2] Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Sabah A Omar
- Kenya Medical Research Institute, Centre for Biotechnology Research and Development, Nairobi, Kenya
| | - Jean-Marie Bodo
- Ministry of Scientific Research and Innovation, Yaounde, Cameroon
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Gurja Belay
- Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD, USA
| | - Paul A S Breslin
- 1] Monell Chemical Senses Center, Philadelphia, PA, USA [2] Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Sarah A Tishkoff
- 1] Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA [2] Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Kifle Z, Belay G, Bekele A. Population size, group composition and behavioural ecology of geladas (Theropithecus gelada) and human-gelada conflict in Wonchit Valley, Ethiopia. Pak J Biol Sci 2013; 16:1248-59. [PMID: 24511732 DOI: 10.3923/pjbs.2013.1248.1259] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Primates that live in protected areas are intensively studied; however, those that live outside protected areas are less studied by primatologists. Therefore, the present study was carried out outside protected areas on the endemic gelada (Theropithecus gelada) to estimate the population size and group composition and human-gelada conflict in Wonchit Valley, Ethiopia from August 2008-March 2009. Total count method was used to determine the population size and group composition of geladas. A band of geladas was selected to carry out behavioural research. Data were collected on activity, diet and ranging patterns for one band of geladas using scan samples at 15 min intervals. Data on human-gelada conflict was gathered using questionnaire interview method. The total number of geladas in the study area was 1525. The average size of one-male unit was 16.96. Adult male to adult female sex ratio was 1.00:6.61. The average size of the band was 58.03. Group size ranged from 3 to 220. Geladas spent 65.2% of their time feeding, 16.3% moving, 4.6% resting and 13.9% socializing. The total time spent feeding on grass blades was 83.8% and 11.8% for bulbs and roots. The home range size was 1.5 km2 during the dry season and 0.2 km2 during the wet season. Geladas in the study area caused crop damage and shared pasture and drinking water with livestock. They consume crops during harvesting stage more than the seedling and vegetative stages. The study has immense contribution for the conservation and management of this endemic primate in unprotected areas.
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Affiliation(s)
- Zewdu Kifle
- Department of Zoological Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Zoological Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
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Campbell MC, Ranciaro A, Zinshteyn D, Rawlings-Goss R, Hirbo J, Thompson S, Woldemeskel D, Froment A, Rucker JB, Omar SA, Bodo JM, Nyambo T, Belay G, Drayna D, Breslin PAS, Tishkoff SA. Origin and differential selection of allelic variation at TAS2R16 associated with salicin bitter taste sensitivity in Africa. Mol Biol Evol 2013; 31:288-302. [PMID: 24177185 DOI: 10.1093/molbev/mst211] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Bitter taste perception influences human nutrition and health, and the genetic variation underlying this trait may play a role in disease susceptibility. To better understand the genetic architecture and patterns of phenotypic variability of bitter taste perception, we sequenced a 996 bp region, encompassing the coding exon of TAS2R16, a bitter taste receptor gene, in 595 individuals from 74 African populations and in 94 non-Africans from 11 populations. We also performed genotype-phenotype association analyses of threshold levels of sensitivity to salicin, a bitter anti-inflammatory compound, in 296 individuals from Central and East Africa. In addition, we characterized TAS2R16 mutants in vitro to investigate the effects of polymorphic loci identified at this locus on receptor function. Here, we report striking signatures of positive selection, including significant Fay and Wu's H statistics predominantly in East Africa, indicating strong local adaptation and greater genetic structure among African populations than expected under neutrality. Furthermore, we observed a "star-like" phylogeny for haplotypes with the derived allele at polymorphic site 516 associated with increased bitter taste perception that is consistent with a model of selection for "high-sensitivity" variation. In contrast, haplotypes carrying the "low-sensitivity" ancestral allele at site 516 showed evidence of strong purifying selection. We also demonstrated, for the first time, the functional effect of nonsynonymous variation at site 516 on salicin phenotypic variance in vivo in diverse Africans and showed that most other nonsynonymous substitutions have weak or no effect on cell surface expression in vitro, suggesting that one main polymorphism at TAS2R16 influences salicin recognition. Additionally, we detected geographic differences in levels of bitter taste perception in Africa not previously reported and infer an East African origin for high salicin sensitivity in human populations.
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Megaze A, Belay G, Balakrishnan M. Population structure and ecology of the African buffalo (Syncerus cafferSparrman, 1779) in Chebera Churchura National Park, Ethiopia. Afr J Ecol 2012. [DOI: 10.1111/aje.12049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Aberham Megaze
- Department of Zoological Sciences; College of Natural Sciences; Addis Ababa University; PO Box 1176; Addis Ababa; Ethiopia
| | - Gurja Belay
- Department of Zoological Sciences; College of Natural Sciences; Addis Ababa University; PO Box 1176; Addis Ababa; Ethiopia
| | - Mundanthra Balakrishnan
- Department of Zoological Sciences; College of Natural Sciences; Addis Ababa University; PO Box 1176; Addis Ababa; Ethiopia
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Scheinfeldt LB, Soi S, Thompson S, Ranciaro A, Woldemeskel D, Beggs W, Lambert C, Jarvis JP, Abate D, Belay G, Tishkoff SA. Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biol 2012; 13:R1. [PMID: 22264333 PMCID: PMC3334582 DOI: 10.1186/gb-2012-13-1-r1] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/05/2012] [Accepted: 01/20/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP array and employed several genome-wide scans for selection and targeted association with hemoglobin levels to identify genes that play a role in adaptation to high altitude. RESULTS We have identified a set of candidate genes for positive selection in our high-altitude population sample, demonstrated significantly different hemoglobin levels between high- and low-altitude Ethiopians and have identified a subset of candidate genes for selection, several of which also show suggestive associations with hemoglobin levels. CONCLUSIONS We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.
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Affiliation(s)
- Laura B Scheinfeldt
- Department of Genetics, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet 2011; 122:77-93. [PMID: 20706706 DOI: 10.1007/s00122-010-1424-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/30/2010] [Indexed: 05/07/2023]
Abstract
Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers.
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Affiliation(s)
- M Zeid
- Department of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, NY 14853, USA
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Kajaba I, Simoncic R, Frecerova K, Belay G. Clinical studies on the hypolipidemic and antioxidant effects of selected natural substances. BRATISL MED J 2008; 109:267-272. [PMID: 18700439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND The average blood levels of cholesterol and triacylglycerol in population are generally considered to be indicators of cardiovascular risk. AIM OF THE STUDY The aim of our study was to present representative data of selected fractions of blood lipids, and the trend of their levels during the last 35 years in the adult population of Slovakia. RESULTS This study demonstrates the risk of the elevated average cholesterolaemia and triacylglycerolaemia in men aged 35-39 years and above 60 years, as compared to womens' increased blood level that were detected only in the age group above 60 years. Strong gender differences in HDL-cholesterol were found, women having higher values than men, with these differences fading in the age group above 60 years. The results of two clinical studies present the hypolipemic effects of n-3 polyunsaturated fatty acid in individuals with dyslipidaemia, the hypotriacylglycerolemic effect being dominant (p < 0.001). The hypocholesterolemic effect was less significant (p < 0.05) than in cases when lyophilized powder of the Pleurotus ostreatus was applied (p < 0.01). In both cases, a stabilizing effect on serum HDL-cholesterol had been observed. In case of polyunsaturated fatty acid n-3, its increase was borderline with statistical significance (p = 0.05). CONCLUSION The study emphasises the necessity of improving the average blood level of lipids in the population of Slovakia and the pertinence of using natural substances with a hypolipemic effect in secondary and even primary prevention of atherosclerosis and its serious complications (Tab. 3, Fig. 4, Ref. 27).
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Affiliation(s)
- I Kajaba
- Slovak Health University, Bratislava, Slovakia.
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Affiliation(s)
- Demeke Datiko
- Department of Biology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
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Belay G, Mori A. Intraspecific phylogeographic mitochondrial DNA (D-loop) variation of Gelada baboon, Theropithecus gelada, in Ethiopia. BIOCHEM SYST ECOL 2006. [DOI: 10.1016/j.bse.2006.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bechere E, Belay G, Mitiku D, Merker A. Phenotypic diversity of tetraploid wheat landraces from northern and north-central regions of Ethiopia. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1996.00165.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
In 1989 a new gelada baboon ( Theropithecus gelada) population was found in Arsi, on the opposite side of the Rift Valley to that of the known gelada populations of Semien and Showa. Previous comparisons of units of the band at Gado Goro, Arsi, in the same season in consecutive years, indicated that unit structure is less stable among Arsi geladas as compared to the Semien population. Gelada units of the band at Gado-Goro were studied for 7 months in order to investigate the processes of social changes. Changes in unit structure were observed. Provisioning was carried out for 1.5 months at the beginning of the 7-month study period, in order to capture and obtain blood samples from the geladas. Following this, changes in male leadership of some units were observed, presumably as a consequence of the capture. However, natural changes also occurred. One change in unit structure occurred after a female gave birth, and changes in another unit occurred after the disappearance of the leader male. These changes involved female desertion of a unit, her subsequent transfer to a male unit, and culminated in the formation of a unit consisting of one female and one male. One successful and one attempted case of unification of units, and one case of change of a unit leader male are reported. These changes occurred among eight resident units in a period of 7 months (196 female months). Though the types of social changes were not much different from previous observations in Semien National Park, their frequencies seemed to be much higher. The characteristics of Arsi gelada social changes are proposed to be related to the small size of the units. We also describe a new confirmed case and one suspected case of infanticide, as well as one case of abortion at the time of male leader change.
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Affiliation(s)
- Akio Mori
- Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi 484-8506, Japan.
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46
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Mitrová E, Belay G. Creutzfeldt-Jakob disease with E200K mutation in Slovakia: characterization and development. Acta Virol 2003; 46:31-9. [PMID: 12197632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Creutzfeldt-Jakob disease (CJD), the most important human prion disease, occurs in sporadic, iatrogenic and familial form. Except Slovakia and Israel, the recorded familial cases have never exceeded 10-15%. In the Slovak CJD group 95 out of 136 CJD cases (74.2%) carried a CJD-specific mutation in the prion protein gene (PRNP) at codon 200 (mutation E200K). All CJD(E200K) patients carried a heterozygous E200K mutation within the alelle with methionine at codon 129. No more than 53.7% were typical familial cases. The penetrance of the E200K mutation in 1975-2000 was 59.5%. The distribution of codon 129 polymorphism showed 78.6% of methionine-homozygous and 21.4% of methionine/valine-heterozygous patients. Genetic analysis performed on 278 CJD patient relatives demonstrated the E200K mutation in 97 (34.8%) of healthy relatives tested. The E200K mutation carriers were methionine-homozygous in 64% and methionine/valine-heterozygous in 36%. The relatives without the mutation showed a 54.9% methionine homozygosity, 10.4% valine homozygosity and 34.7% methionine/valine heterozygosity. Analysis ofthe E200K carriers provided evidence that the methionine homozygosity is a CJD risk factor, more efficient in CJD patients than in asymptomatic relatives. Th influence of both the E200K mutation and methionine homozygosity at codon 129 was evident in the duration of the clinical stage of CJD and in the immunoreactivity pattern of PrP resistant to proteases (PrP(res)). In the CJD(E200K) methionine-homozygous patients the mean duration ofthe disease was significantly shorter (3.7 +/- 2.0 months) than in the methionine/valine-heterozygous patients (7.84 +/- 7.3 months). Comparison of the PrP(res) positivity in the cerebellum of familial and sporadic CJD using specific polyclonal and monoclonal antibodies (MAbs) to PrP showed less conspicuous immune reaction in CJD(E200K) cases. Methionine-homozygous CJD patients were characteristic mainly by synaptic pattern of staining, while methionine/valine-heterozygous patients by PrP(res) granules and plaque-like structures. Most of numerous plaque-like PrP(res) deposits were found in sporadic valine/valine-homozygous cases. Potential professional risk was excluded in health facility workers. The percentage of professions related to farming was significantly higher in CJD(E200K) (48%) and sporadic CJD (44%) cases as compared to the employed population (9%).
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Affiliation(s)
- E Mitrová
- Institute of Preventive and Clinical Medicine, Bratislava, Slovak Republic.
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47
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Belay G, Mitrova E. Specific diagnosis of transmissible spongiform encephalopathies. BRATISL MED J 2003; 104:371-2. [PMID: 15055725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- G Belay
- National Reference Centre of Slow Virus Neuroinfections, Bratislava, Slovakia.
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48
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Mitrova E, Belay G. Transmissible spongioform encephalopathies (TSE)--prion diseases: their causes and risks. BRATISL MED J 2003; 104:369-70. [PMID: 15055724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- E Mitrova
- National Reference Centre of Slow Virus Neuroinfections, Institute of Preventive and Clinical Medicine, Slovak Health University, Bratislava, Slovakia.
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Abstract
Creutzfeldt-Jakob disease (CJD) is the most important human transmissible spongiform encephalopathy (prion disease), recognised in sporadic, genetic but also iatrogenic forms. The identification of 8 health care workers in a group of 114 definitive CJD patients in Slovakia suggested the possibility of professionally acquired CJD and induced the investigation of potential endo- and exogenous risk factors. In CJD-affected health professionals special attention was paid to a detailed occupational history, including a possible professional contact with CJD patient and to the findings characteristic for iatrogenic CJD: early cerebellar symptomatology, long duration of the disease, absence of typical EEG finding and homozygosity of PRNP gene at codon 129. Analysis of epidemiological, clinical and molecular biological data in investigated group of CJD-affected health professionals gave no evidence of an occupational risk for CJD.
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Affiliation(s)
- E Mitrová
- Institute of Preventive and Clinical Medicine, Bratislava, Slovakia
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50
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Mitrova E, Belay G. Creutzfeldt-Jakob disease risk in Slovak recipients of human pituitary growth hormone. BRATISL MED J 1999; 100:187-91. [PMID: 10914140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
UNLABELLED Creutzfeldt-Jakob disease (CJD) is a transmissible, fatal degenerative disorder of the CNS. CJD is known in a sporadic, familial and iatrogenic form. Iatrogenic form has been accidentally induced through corneal and dura mater transplantation or surgical procedures. The largest number of iatrogenic CJD developed in patients who had received human growth hormone (hGH). The minimal incubation period appears to be 4-15 years, the maximal 21-30 years after receiving hGh treatment. An increasing number of new CJD cases in hGH recipients in France, providing evidence of unusually long incubation period and an occurrence of genetically controlled (mutation E200K carrier) CJD-risk group in Slovak population induced this second investigation of hGh treated patients. The aim of this study is to verify whether the absence of CJD in hGH recipients in Slovakia reflects the actual epidemiological situation or a lack of informations. The objective of the study was to investigate signs of clinical manifestation of CJD and to perform molecular genetic study on prion protein (PrP) gene in hGh recipients. PATIENTS AND METHODS 32 hGH treated patients (23 men and 9 women) at the age of 17-38 years were investigated. The occurrence of codon 200 (E200K) mutation and polymorphism at codon 129 of PrP gene was studied. RESULTS Neurological, including cerebellar signs of CJD, intellectual or psychological changes were not observed in investigated patients. The shortest duration of hGH treatment was 2 years, the longest 9 years. The time interval since the beginning of hGH administration was 12-19 years. Restriction endonuclease analysis of the PrP gene revealed one patient with E200K mutation, 8 patients homozygous for methionin, 2 patients homozygous for valin and 16 heterozygous patients at codon 129. CONCLUSION No evidence of CJD has been observed in investigated group of hGH recipients. Considering the long incubation period of hGH-induced CJD and the obtained results, clinical and genetic investigation on the whole relatively small group of Slovak hGH recipients is recommended. (Tab. 2, Fig. 1, Ref. 22.)
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Affiliation(s)
- E Mitrova
- Institute of Preventive and Clinical Medicine, Bratislava, Slovakia.
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