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Miranda-Acuña J, Casallas-Vanegas A, McCauley J, Castro-Castro P, Amezcua L. Multiple sclerosis in Colombia: A review of the literature. Mult Scler J Exp Transl Clin 2024; 10:20552173241293921. [PMID: 39600996 PMCID: PMC11590136 DOI: 10.1177/20552173241293921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/09/2024] [Indexed: 11/29/2024] Open
Abstract
Background The prevalence of multiple sclerosis (MS) in Latin America is generally considered low to moderate. However, accurate data regarding MS epidemiology in Colombia is lacking. Objective This study aims to discuss the situation of MS in Colombia. Results Analysis reveals a lack of accurate data regarding MS epidemiology in Colombia, however, there have been notable improvements in diagnosis and ultimately leading to better access to treatment for MS patients. While ethnic diversity may potentially influence MS prevalence, there is currently no strong data supporting this claim. MS treatment in Colombia, focuses on early disease-modifying therapy, nevertheless, MS is considered an orphan disease in Colombia, contributing to MS patients not receiving comprehensive evaluation in MS centers. Regional efforts are ongoing to improve diagnostic access and access to treatment for MS patients. Conclusion Despite the challenges in accurately defining MS epidemiology in Colombia, an increase in neurological training, diagnostic capabilities, and access to treatment has been observed. However, the status of MS as an orphan disease in Colombia poses challenges to comprehensive care for affected individuals. Further studies are needed to elucidate risk factors and improve care conditions for MS patients in the region.
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Affiliation(s)
| | | | - Jacob McCauley
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | | | - Lilyana Amezcua
- Multiple Sclerosis Comprehensive Care Center, University of Southern California, Los Angeles, CA, USA/Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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2
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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3
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Lomstein FB, Kjærgaard M, Skovgaard N, Pedersen ML, Backe MB. Reporting chronic kidney disease in Greenland. Int J Circumpolar Health 2023; 82:2261223. [PMID: 37742312 PMCID: PMC10519261 DOI: 10.1080/22423982.2023.2261223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023] Open
Abstract
Background: Chronic kidney disease (CKD) is a major health burden affecting more than 10% of the global population. It is a multifactorial disease with many risk factors attributed lifestyle diseases. The prevalence of CKD in Greenland is unknown; however, the prevalence of risk factors contributing to CKD is increasing.Objectives: To estimate the prevalence of CKD in Greenland.Methods: The study was a cross-sectional register-study including all Greenlandic residents aged ≥20 years with serum creatinine analysis within the last 2 years. We identified those with CKD based on eGFR and UACR and those registered with a CKD diagnosis code. Two limitations of the study are possible lack of data completeness and the reliance of a single time point to report CKD.Results: A total of 2,157 patients were identified with CKD with an age-standardised prevalence of 3.01%. Only 75 patients were registered with a diagnosis code for CKD. Approximately 80% of patients were classified with CKD stages 1-2.Conclusion: This is the first study reporting CKD in Greenland. We found a lower prevalence of CKD than reported by other studies, and a low number of patients correctly diagnosed with CKD. We call for increased awareness and diagnosis coding of CKD in Greenland.
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Affiliation(s)
- Fabian Bøgild Lomstein
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Greenland, Queen Ingrid’s Hospital, Nuuk, Greenland
| | - Marie Kjærgaard
- Department of Internal Medicine, Queen Ingrid’s Hospital, Nuuk, Greenland
- Department of Nephrology, Sygehus Lillebælt, Kolding, Denmark
| | - Nils Skovgaard
- Steno Diabetes Center Greenland, Queen Ingrid’s Hospital, Nuuk, Greenland
- Greenland’s Centre for Health Research, Institute of Health and Nature, University of Greenland, Nuuk, Greenland
| | - Michael Lynge Pedersen
- Steno Diabetes Center Greenland, Queen Ingrid’s Hospital, Nuuk, Greenland
- Greenland’s Centre for Health Research, Institute of Health and Nature, University of Greenland, Nuuk, Greenland
| | - Marie Balslev Backe
- Steno Diabetes Center Greenland, Queen Ingrid’s Hospital, Nuuk, Greenland
- Greenland’s Centre for Health Research, Institute of Health and Nature, University of Greenland, Nuuk, Greenland
- Department of Clinical Epidemiology, Steno Diabetes Center Copenhagen, Herlev, Denmark
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4
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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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5
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Costa RDO, Pereira J, Lage LADPC, Baiocchi OCG. Extranodal NK-/T-cell lymphoma, nasal type: what advances have been made in the last decade? Front Oncol 2023; 13:1175545. [PMID: 37529691 PMCID: PMC10388588 DOI: 10.3389/fonc.2023.1175545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Extranodal NK-/T-cell lymphoma (ENKTCL) is a rare and highly aggressive malignancy with significant racial and geographic variations worldwide. In addition to the formerly "nasal-type" initial description, these lymphomas are predominantly extranodal in origin and typically cause vascular damage and tissue destruction, and although not fully understood, Epstein-Barr virus (EBV) has an important role in its pathogenesis. Initial assessment must include a hematopathology review of representative and viable tumor areas without necrosis for adequate immunohistochemistry studies, including EBV-encoded small RNA (EBER) in situ hybridization (ISH). Positron emission tomography with 18-fluorodeoxyglucose (18F-FDG-PET/CT) for accurate staging is essential, and most patients will have localized disease (IE/IIE) at diagnosis. Apart from other T-cell malignancies, the best treatment even for localized cases is combined modality therapy (chemotherapy plus radiotherapy) with non-anthracycline-based regimens. For advanced-stage disease, l-asparaginase-containing regimens have shown improved survival, but relapsed and refractory cases have very poor outcomes. Nowadays, even with a better understanding of pathogenic pathways, up-front therapy is completely based on chemotherapy and radiotherapy, and treatment-related mortality is not low. Future strategies targeting signaling pathways and immunotherapy are evolving, but we need to better identify those patients with dismal outcomes in a pre-emptive way. Given the rarity of the disease, international collaborations are urgently needed, and clinical trials are the way to change the future.
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Affiliation(s)
- Renata de Oliveira Costa
- Department of Hematology, Faculdade de Ciências Médicas de Santos (FCMS), Centro Universitário Lusíadas (Unilus), Santos, São Paulo, Brazil
- Hospital Alemao Osvaldo Cruz (HAOC), São Paulo, Brazil
| | - Juliana Pereira
- Hospital Alemao Osvaldo Cruz (HAOC), São Paulo, Brazil
- Department of Hematology, Hemotherapy and Cell Therapy, Faculdade de Medicina da Universidade de Sao Paulo (FM-USP), São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of Sao Paulo (USP), São Paulo, Brazil
| | - Luís Alberto de Pádua Covas Lage
- Department of Hematology, Hemotherapy and Cell Therapy, Faculdade de Medicina da Universidade de Sao Paulo (FM-USP), São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of Sao Paulo (USP), São Paulo, Brazil
| | - Otávio César Guimarães Baiocchi
- Hospital Alemao Osvaldo Cruz (HAOC), São Paulo, Brazil
- Department of Hematology, Universidade Federal de Sao Paulo (Unifesp), São Paulo, Brazil
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6
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Lake J, Warly Solsberg C, Kim JJ, Acosta-Uribe J, Makarious MB, Li Z, Levine K, Heutink P, Alvarado CX, Vitale D, Kang S, Gim J, Lee KH, Pina-Escudero SD, Ferrucci L, Singleton AB, Blauwendraat C, Nalls MA, Yokoyama JS, Leonard HL. Multi-ancestry meta-analysis and fine-mapping in Alzheimer's disease. Mol Psychiatry 2023; 28:3121-3132. [PMID: 37198259 PMCID: PMC10615750 DOI: 10.1038/s41380-023-02089-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
Genome-wide association studies (GWAS) of Alzheimer's disease are predominantly carried out in European ancestry individuals despite the known variation in genetic architecture and disease prevalence across global populations. We leveraged published GWAS summary statistics from European, East Asian, and African American populations, and an additional GWAS from a Caribbean Hispanic population using previously reported genotype data to perform the largest multi-ancestry GWAS meta-analysis of Alzheimer's disease and related dementias to date. This method allowed us to identify two independent novel disease-associated loci on chromosome 3. We also leveraged diverse haplotype structures to fine-map nine loci with a posterior probability >0.8 and globally assessed the heterogeneity of known risk factors across populations. Additionally, we compared the generalizability of multi-ancestry- and single-ancestry-derived polygenic risk scores in a three-way admixed Colombian population. Our findings highlight the importance of multi-ancestry representation in uncovering and understanding putative factors that contribute to risk of Alzheimer's disease and related dementias.
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Affiliation(s)
- Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Warly Solsberg
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonggeol Jeffrey Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Preventive Neurology Unit, Centre for Prevention Diagnosis and Detection, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute and the department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Zizheng Li
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kristin Levine
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Peter Heutink
- Alector, Inc. 131 Oyster Point Blvd, Suite 600, South San Francisco, CA, 94080, USA
| | - Chelsea X Alvarado
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Dan Vitale
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Sarang Kang
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
| | - Jungsoo Gim
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea
| | - Kun Ho Lee
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea
- Korea Brain Research Institute, Daegu, 41062, Korea
| | - Stefanie D Pina-Escudero
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer S Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Data Tecnica International LLC, Washington, DC, USA.
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
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Peng J, Rajeevan H, Kubatko L, RoyChoudhury A. A fast likelihood approach for estimation of large phylogenies from continuous trait data. Mol Phylogenet Evol 2021; 161:107142. [PMID: 33713799 DOI: 10.1016/j.ympev.2021.107142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/15/2020] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Despite the recent availability of large-scale genomic data for many individuals, few methods for phylogenetic inference are both computationally efficient and highly accurate for trees with hundreds of taxa. Model-based methods such as those developed in the maximum likelihood and Bayesian frameworks are especially time-consuming, as they involve both computationally intensive calculations on fixed phylogenies and searches through the space of possible phylogenies, and they are known to scale poorly with the addition of taxa. Here, we propose a fast approximation to the maximum likelihood estimator that directly uses continuous trait data, such as allele frequency data. The approximation works by first computing the maximum likelihood estimates of some internal branch lengths, and then inferring the tree-topology using these estimates. Our approach is more computationally efficient than existing methods for such data while still achieving comparable accuracy. This method is innovative in its use of the mathematical properties of tree-topologies for inference, and thus serves as a useful addition to the collection of methods available for estimating phylogenies from continuous trait data.
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Affiliation(s)
- Jing Peng
- Division of Biostatistics, College of Public Health, The Ohio State University, United States; Department of Statistics, The Ohio State University, United States
| | | | - Laura Kubatko
- Department of Statistics, The Ohio State University, United States; Department of Evolution, Ecology and Organismal Biology, The Ohio State University, United States.
| | - Arindam RoyChoudhury
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, United States
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8
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Hoh BP, Rahman TA. The indigenous populations as the model by nature to understand human genomic-phenomics interactions. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Tezel T, Ruff A. Retinal cell transplantation in retinitis pigmentosa. Taiwan J Ophthalmol 2021; 11:336-347. [PMID: 35070661 PMCID: PMC8757529 DOI: 10.4103/tjo.tjo_48_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/10/2021] [Indexed: 11/25/2022] Open
Abstract
Retinitis pigmentosa is the most common hereditary retinal disease. Dietary supplements, neuroprotective agents, cytokines, and lately, prosthetic devices, gene therapy, and optogenetics have been employed to slow down the retinal degeneration or improve light perception. Completing retinal circuitry by transplanting photoreceptors has always been an appealing idea in retinitis pigmentosa. Recent developments in stem cell technology, retinal imaging techniques, tissue engineering, and transplantation techniques have brought us closer to accomplish this goal. The eye is an ideal organ for cell transplantation due to a low number of cells required to restore vision, availability of safe surgical and imaging techniques to transplant and track the cells in vivo, and partial immune privilege provided by the subretinal space. Human embryonic stem cells, induced pluripotential stem cells, and especially retinal organoids provide an adequate number of cells at a desired developmental stage which may maximize integration of the graft to host retina. However, stem cells must be manufactured under strict good manufacturing practice protocols due to known tumorigenicity as well as possible genetic and epigenetic stabilities that may pose a danger to the recipient. Immune compatibility of stem cells still stands as a problem for their widespread use for retinitis pigmentosa. Transplantation of stem cells from different sources revealed that some of the transplanted cells may not integrate the host retina but slow down the retinal degeneration through paracrine mechanisms. Discovery of a similar paracrine mechanism has recently opened a new therapeutic path for reversing the cone dormancy and restoring the sight in retinitis pigmentosa.
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10
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Bruno CD, Fremd B, Church RJ, Daly AK, Aithal GP, Björnsson ES, Larrey D, Watkins PB, Chow CR. HLA associations with infliximab-induced liver injury. THE PHARMACOGENOMICS JOURNAL 2020; 20:681-686. [PMID: 32024945 DOI: 10.1038/s41397-020-0159-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 11/09/2022]
Abstract
Biomarkers that are able to identify patients at risk of drug-induced liver injury (DILI) after treatment with infliximab could be important in increasing the safety of infliximab use. We performed a genetic analysis to identify possible human leukocyte antigen (HLA) associations with DILI in European Caucasian users of infliximab in a retrospective study of 16 infliximab-DILI patients and 60 matched controls. In infliximab-associated liver injury, multiple potentially causal individual HLA associations were observed, as well as possible haplotypes. The strongest associated HLA allele was HLA-B*39:01 (P = 0.001; odds ratio [OR] 43.6; 95% confidence interval [CI] 2.8-infinity), which always appeared with another associated allele C*12:03 (P = 0.032; OR 6.1; 95% CI 0.9-47.4). Other associations were observed with HLAs DQB1*02:01 (P = 0.007; OR 5.7; 95% CI 1.4-24.8), DRB1*03:01 (P = 0.012; OR 4.9; 95% CI 1.2-20.5), and B*08:01 (P = 0.048; OR 3.4; 95% CI 0.9-13.2), which also appeared together whenever present in cases. Additional associations were found with HLA-DPB1*10:01 (P = 0.042; OR 20.9; 95% CI 0.7-infinity) and HLA-DRB1*04:04 (P = 0.042; OR 20.9; 95% CI 0.7-infinity). A strong association with HLA-B*39:01 was identified as a potentially causal risk factor for infliximab-induced DILI. Future work should aim to validate this finding and explore possible mechanisms through which the biologic interacts with this particular allele.
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Affiliation(s)
| | | | - Rachel J Church
- Eshelman School of Pharmacy, University of North Carolina Institute for Drug Safety Sciences, Chapel Hill, NC, USA
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Guruprasad P Aithal
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Einar S Björnsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Paul B Watkins
- Eshelman School of Pharmacy, University of North Carolina Institute for Drug Safety Sciences, Chapel Hill, NC, USA
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11
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Küçük C. Genetic susceptibility to natural killer T-cell lymphoma. Lancet Oncol 2019; 21:196-197. [PMID: 31879221 DOI: 10.1016/s1470-2045(19)30820-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Can Küçük
- İzmir Biomedicine and Genome Center, İzmir, Turkey; İzmir International Biomedicine and Genome Institute and Department of Medical Biology, Dokuz Eylül University, İzmir, Turkey.
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12
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Negrotto L, Correale J. Evolution of multiple sclerosis prevalence and phenotype in Latin America. Mult Scler Relat Disord 2018; 22:97-102. [DOI: 10.1016/j.msard.2018.03.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/17/2018] [Accepted: 03/20/2018] [Indexed: 01/10/2023]
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Absence of the tag polymorphism for the risk haplotype HLA-DR2 for multiple sclerosis in Wixárika subjects from Mexico. Immunogenetics 2018; 70:547-551. [PMID: 29397401 DOI: 10.1007/s00251-018-1052-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
The HLA-DRB1*15:01 allele has a demonstrated risk for the development of multiple sclerosis (MS) in most populations around the world. The single nucleotide polymorphism (SNP) rs3129934 is found in linkage disequilibrium with the risk haplotype formed by the HLA-DRB1*15:01 and HLA-DQB1*06:02 alleles, and it is considered a reliable marker of the presence of this haplotype. Native Americans have a null or low prevalence of MS. In this study, we sought to identify the frequency of rs3129934 in the Wixárika ethnic group as well as in Mestizo (mixed race) patients with MS and in controls from western Mexico. Through real-time polymerase chain reaction (PCR) using TaqMan probes, we analyzed the allele and genotype frequencies of rs3129934 in Mestizo individuals with and without MS and in 73 Wixárika subjects from the state of Jalisco, Mexico. The Wixárika subjects were homozygote for the C allele of rs3129934. The allele and genotype frequency in Mestizos with MS was similar to that of other MS populations with Caucasian ancestry. The absence of the T risk allele rs3129934 (associated with the haplotype HLA-DRB1*15:01, HLA-DQ1*06:02) in this sample of Wixárika subjects is consistent with the unreported MS in this Amerindian group, related to absence of such paramount genetic risk factor.
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Amezcua L. MS in self-identified Hispanic/Latino individuals living in the US. Mult Scler J Exp Transl Clin 2017; 3:2055217317725103. [PMID: 28979795 PMCID: PMC5617095 DOI: 10.1177/2055217317725103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 07/07/2017] [Indexed: 12/26/2022] Open
Abstract
Self-identified Hispanic/Latino individuals living with multiple sclerosis (MS) in the continental United States (US) are a diverse group that represents different cultural and ancestral backgrounds. A marked variability in the way MS affects various subgroups of Hispanics in the US has been observed. We reviewed and synthesized available data about MS in Hispanics in the US. There are likely a host of multifactorial elements contributing to these observations that could be explained by genetic, environmental, and social underpinnings. Barriers to adequate MS care in Hispanics are likely to include delivery of culturally competent care and social and economic disadvantages. Considerable efforts, including the formation of a national consortium known as the Alliance for Research in Hispanic Multiple Sclerosis (ARHMS), are underway to help further explore these various factors.
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Affiliation(s)
- Lilyana Amezcua
- Department of Neurology, University of Southern California, Keck School of Medicine, USA
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15
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16
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Wang W, Tian W, Zhu F, Li L, Cai J, Wang F, Liu K, Jin H, Wang J. MICA Gene Deletion in 3411 DNA Samples from Five Distinct Populations in Mainland China and Lack of Association with Nasopharyngeal Carcinoma (NPC) in a Southern Chinese Han population. Ann Hum Genet 2017; 80:319-326. [PMID: 27870115 DOI: 10.1111/ahg.12175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/23/2016] [Indexed: 12/20/2022]
Abstract
Deletion of major histocompatibility complex class I chain-related genes A (MICA*Del) was investigated in 3,411 DNA samples from two southern Chinese Han populations (Hunan Han, HNH; Guangdong Han, GDH), two northern Chinese populations (Inner Mongolia Han, IMH; Inner Mongolia Mongol, IMM) and one southeastern Chinese Han population (Fujian Han, FJH) using an in-house polymerase chain reaction-sequence specific priming (PCR-SSP) assay, which enables direct discrimination between heterozygote and homozygote for MICA*Del. MICA*Del showed a frequency ranging from 0.8% in FJH to 5.7% in IMM (Pcorrected < 0.05), indicating northward increase in frequency of MICA*Del in Chinese populations. In contrast to the association reported recently in a Taiwan Chinese population and a Malaysian Chinese cohort, MICA*Del distribution did not differ between 1,120 patients with nasopharyngeal carcinoma (NPC) and 1,483 normal controls in the HNH population (1.03% in NPC cases vs 1.18% in the controls, OR (95% CI) = 0.87 (0.51-1.47), p = 0.69). Further gender-stratified analysis also failed to disclose any male-specific association reported in a Taiwan Chinese population. Multi-locus typing of the 94 samples carrying MICA*Del revealed two new haplotypes, HLA-A*11:01-B*13:01-MICA*Del-MICB*009N-DRB1*04:06 and HLA-B*35:01-MICA*Del-MICB*009N-DRB1*15:01, in addition to HLA-B*48-MICA*Del. Unexpectedly, two samples with MICA*Del in the HNH population were each consistently found to have two distinct MICA alleles, indicating the existence of two MICA gene copies on certain HLA haplotypes. Based on the results from a sizeable case-control study, our data suggest that there is no association between MICA*Del and NPC in the southern Chinese Han population.
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Affiliation(s)
- WenYi Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Wei Tian
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - FaMing Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - LiXin Li
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - JinHong Cai
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Fan Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - KangLong Liu
- Department of Nuclear Medicine, Hunan Cancer Hospital (the affiliated Cancer Hospital of XiangYa School of Medicine of Central South University), Changsha, Hunan, 410006, People's Republic of China
| | - HeKun Jin
- Department of Radiotherapy, Hunan Cancer Hospital (the affiliated Cancer Hospital of XiangYa School of Medicine of Central South University), Changsha, Hunan, 410006, People's Republic of China
| | - JunLong Wang
- Department of Laboratory Medicine, The 5th Hospital of Zhangzhou City, Zhangzhou, Fujian, People's Republic of China
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Hamzeh AR, Nair P, Al-Khaja N, Al Ali MT. Association of HLA-DQA1 and -DQB1 alleles with type I diabetes in Arabs: a meta-analyses. ACTA ACUST UNITED AC 2016; 86:21-7. [PMID: 26095634 DOI: 10.1111/tan.12598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/19/2015] [Accepted: 05/31/2015] [Indexed: 12/29/2022]
Abstract
This study aimed at assessing the nature and significance of associations between various alleles of HLA-DQA1, HLA-DQB1, and type I diabetes (T1D) in Arab populations. Evidence from literature (published before 20 April 2015) was amassed and analysed through multiple meta-analyses, which yielded effect summary odds ratios and 95% confidence intervals for 24 alleles and 4 haplotypes. A total of 1273 cases and 1747 controls from 16 studies were analysed. High levels of significance were obtained to support higher T1D risk when harbouring DQA1*03:01. The alleles DQB1*02:01 and *03:02 and the haplotypes DR3 and DR4 were significant risk factors, albeit with high publication heterogeneity. The protective effects of DQA1*01:01, DQB1*05:03, *06:02, *06:03, and *06:04 were robustly suggested by all indicators of meta-analyses. The haplotypes DR7 and DR11 were strongly suggested to be protective in Arabs. A relatively small number of studies have emerged from Arab countries, mostly with inadequate power on an individual basis. This study fills the gap by providing significant size effect of human leukocyte antigen (HLA) alleles and completes the continuum of global ethnic differences in this context.
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Affiliation(s)
- A R Hamzeh
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - P Nair
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - N Al-Khaja
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - M T Al Ali
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
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Vásquez-Loarte T, Trubnykova M, Guio H. Genetic association meta-analysis: a new classification to assess ethnicity using the association of MCP-1 -2518 polymorphism and tuberculosis susceptibility as a model. BMC Genet 2015; 16:128. [PMID: 26518714 PMCID: PMC4627623 DOI: 10.1186/s12863-015-0280-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Background In meta-analyses of genetic association studies, ancestry and ethnicity are not accurately investigated. Ethnicity is usually classified using conventional race/ethnic categories or continental groupings even though they could introduce bias increasing heterogeneity between and within studies; thus decreasing the external validity of the results. In this study, we performed a meta-analysis using a novel ethnic classification system to test the association between MCP-1 -2518 polymorphism and pulmonary tuberculosis. Our new classification considers genetic distance, migration and linguistic origins, which will increase homogeneity within ethnic groups. Methods We included thirteen studies from three continents (Asia, Africa and Latin America) and considered seven ethnic groups (West Africa, South Africa, Saharan Africa, East Asia, South Asia, Persia and Latin America). Results The results were compared to the continental group classification. We found a significant association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups (OR 3.47, P = 0.08; OR 2.73, P = 0.02). This association is not observed in other ethnic groups that are usually considered in the Asian group, such as India and Persia, or in the African group. Conclusions There is an association between MCP-1 -2518 polymorphism and TB susceptibility only in the East Asian and Latin American groups. We suggest the use of our new ethnic classification in future meta-analysis of genetic association studies when ancestry markers are not available. This new classification increases homogeneity for certain ethnic groups compared to the continental classification. We recommend considering previous data about migration, linguistics and genetic distance when classifying ethnicity in further studies.
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Affiliation(s)
- Tania Vásquez-Loarte
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Milana Trubnykova
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Avenida Defensores del, Morro 2268, Lima 9, Peru.
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19
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Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu. Genetics 2015; 202:261-72. [PMID: 26500257 DOI: 10.1534/genetics.115.178673] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/19/2015] [Indexed: 12/22/2022] Open
Abstract
Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter-gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the Sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians.
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20
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Zhou XY, Zhu FM, Li JP, Mao W, Zhang DM, Liu ML, Hei AL, Dai DP, Jiang P, Shan XY, Zhang BW, Zhu CF, Shen J, Deng ZH, Wang ZL, Yu WJ, Chen Q, Qiao YH, Zhu XM, Lv R, Li GY, Li GL, Li HC, Zhang X, Pei B, Jiao LX, Shen G, Liu Y, Feng ZH, Su YP, Xu ZX, Di WY, Jiang YQ, Fu HL, Liu XJ, Liu X, Zhou MZ, Du D, Liu Q, Han Y, Zhang ZX, Cai JP. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program. PLoS One 2015; 10:e0139485. [PMID: 26421847 PMCID: PMC4589403 DOI: 10.1371/journal.pone.0139485] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/13/2015] [Indexed: 11/18/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.
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Affiliation(s)
- Xiao-Yang Zhou
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Fa-Ming Zhu
- HLA Laboratory, Zhejiang Blood Center, Hangzhou, Zhejiang, China
| | - Jian-Ping Li
- HLA Laboratory, Liaoning Blood Center, Shenyang, Liaoning, China
| | - Wei Mao
- HLA Laboratory, Chongqing Blood Center, Chongqing, China
| | - De-Mei Zhang
- HLA Laboratory, Taiyuan Red Cross Blood Center, Taiyuan, Shanxi, China
| | - Meng-Li Liu
- HLA Laboratory, Shaanxi Blood Center, Xi’an, Shaanxi, China
| | - Ai-Lian Hei
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Ping Jiang
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
| | - Xiao-Yan Shan
- HLA Laboratory, Beijing Red Cross Blood Center, Beijing, China
| | - Bo-Wei Zhang
- HLA Laboratory, Henan Blood Center, Zhengzhou, Henan, China
| | - Chuan-Fu Zhu
- HLA Laboratory, Shandong Blood Center, Jinan, Shandong
| | - Jie Shen
- HLA Laboratory, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi-Hui Deng
- The Key Laboratory of Histocompatibility and Immunogenetics, Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Zheng-Lei Wang
- HLA Laboratory, Hebei Blood Center, Shijiazhuang, Hebei, China
| | - Wei-Jian Yu
- HLA Laboratory, Dalian Red Cross Blood Center, Dalian, Liaoning, China
| | - Qiang Chen
- HLA Laboratory, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College, Chengdu, Sichuan, China
| | - Yan-Hui Qiao
- HLA Laboratory, Xinjiang Blood Center, Urumchi, Xinjiang, China
| | - Xiang-Ming Zhu
- HLA Laboratory, Kunming Blood Center, Kunming, Yunnan, China
| | - Rong Lv
- HLA Laboratory, Hefei Red Cross Blood Center, Hefei, Anhui, China
| | - Guo-Ying Li
- HLA Laboratory, Gansu Red Cross Blood Center, Lanzhou, Gansu, China
| | - Guo-Liang Li
- HLA Laboratory, Jiangxi Blood Center, Nanchang, Jiangxi, China
| | - Heng-Cong Li
- HLA Laboratory, Nanning Blood Center, Nanning, Guangxi, China
| | - Xu Zhang
- HLA Laboratory, Liaoning Blood Center, Shenyang, Liaoning, China
| | - Bin Pei
- HLA Laboratory, Xiamen Blood Center, Xiamen, Fujian, China
| | - Li-Xin Jiao
- HLA Laboratory, Changchun Blood Center, Changchun, Jilin, China
| | - Gang Shen
- HLA Laboratory, Wuhan Blood Center, Wuhan, Hubei, China
| | - Ying Liu
- HLA Laboratory, Harbin Red Cross Blood Center, Harbin, Heilongjiang, China
| | - Zhi-Hui Feng
- HLA Laboratory, Qingdao Blood Center, Qingdao, Shandong, China
| | - Yu-Ping Su
- HLA Laboratory, Yueyang Red Cross Blood Center, Yueyang, Hunan, China
| | - Zhao-Xia Xu
- HLA Laboratory, Changsha Blood Center, Changsha, Hunan, China
| | - Wen-Ying Di
- HLA Laboratory, Soochow Red Cross Blood Center, Suzhou, Jiangsu, China
| | - Yao-Qin Jiang
- HLA Laboratory, Shanghai Blood Center, Shanghai, China
| | - Hong-Lei Fu
- HLA Laboratory, BFR Transplant Diagnostic Service Center, Beijing China
| | - Xiang-Jun Liu
- HLA Laboratory, BFR Transplant Diagnostic Service Center, Beijing China
| | - Xiang Liu
- HLA Laboratory, CapitalBio Corporation, Beijing, China
| | - Mei-Zhen Zhou
- HLA Laboratory, Beijing Genomics Institute, Shenzhen, Guangdong, China
| | - Dan Du
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Qi Liu
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Ying Han
- Department of HLA Technology, China Bone Marrow Program, Beijing, China
| | - Zhi-Xin Zhang
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
- * E-mail: (ZXZ); (JPC)
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
- Quality control laboratory, China Bone Marrow Program, Beijing, China
- * E-mail: (ZXZ); (JPC)
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Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture. J Hum Genet 2015. [PMID: 26202576 DOI: 10.1038/jhg.2015.90] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The human leukocyte antigen (HLA) region is the most polymorphic region in the human genome. The polymorphic nature of the HLA region is thought to have been shaped from balancing selection. The complex migration events during the Out-of-Africa expansion have influenced geographic patterns of HLA allele frequencies and diversities across present-day human populations. Differences in the HLA allele frequency may contribute geographic differences in the susceptibility to many diseases, such as infectious, autoimmune and metabolic diseases. Here we briefly reviewed characteristics of frequency distribution of HLA alleles and haplotypes in Japanese population. A large part of HLA alleles and haplotypes that are common in Japanese are shared with neighboring Asian populations. The differentiations in HLA alleles and haplotypes across Japanese regional populations may provide clues to model for peopling of Japanese Archipelago and for design of genetic association studies. Finally, we introduce recent topics that new HLA alleles derived from ancient admixtures with Neanderthals and Denisovans are thought to have played an important role in the adaptation of modern humans to local pathogens during Out-of-Africa expansion.
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Yuasa I, Umetsu K, Adachi N, Matsusue A, Nakayashiki N, Fujihara J, Akane A, Harihara S, Jin F, Ishikawa T. Investigation of Japanese-specific alleles: Most are of Jomon lineage. Leg Med (Tokyo) 2015; 17:52-5. [DOI: 10.1016/j.legalmed.2014.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/25/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022]
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Potential and limitation of HLA-based banking of human pluripotent stem cells for cell therapy. J Immunol Res 2014; 2014:518135. [PMID: 25126584 PMCID: PMC4121106 DOI: 10.1155/2014/518135] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/06/2014] [Accepted: 06/18/2014] [Indexed: 12/13/2022] Open
Abstract
Great hopes have been placed on human pluripotent stem (hPS) cells for therapy. Tissues or organs derived from hPS cells could be the best solution to cure many different human diseases, especially those who do not respond to standard medication or drugs, such as neurodegenerative diseases, heart failure, or diabetes. The origin of hPS is critical and the idea of creating a bank of well-characterized hPS cells has emerged, like the one that already exists for cord blood. However, the main obstacle in transplantation is the rejection of tissues or organ by the receiver, due to the three main immunological barriers: the human leukocyte antigen (HLA), the ABO blood group, and minor antigens. The problem could be circumvented by using autologous stem cells, like induced pluripotent stem (iPS) cells, derived directly from the patient. But iPS cells have limitations, especially regarding the disease of the recipient and possible difficulties to handle or prepare autologous iPS cells. Finally, reaching standards of good clinical or manufacturing practices could be challenging. That is why well-characterized and universal hPS cells could be a better solution. In this review, we will discuss the interest and the feasibility to establish hPS cells bank, as well as some economics and ethical issues.
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Klein R, Li X, Kuo JZ, Klein BEK, Cotch MF, Wong TY, Taylor KD, Rotter JI. Associations of candidate genes to age-related macular degeneration among racial/ethnic groups in the multi-ethnic study of atherosclerosis. Am J Ophthalmol 2013; 156:1010-1020.e1. [PMID: 23938121 DOI: 10.1016/j.ajo.2013.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE To describe the relationships of selected candidate genes to the prevalence of early age-related macular degeneration (AMD) in a cohort of whites, blacks, Hispanics, and Chinese Americans. DESIGN Cross-sectional study. METHODS setting: Multicenter study. study population: A total of 2456 persons aged 45-84 years with genotype information and fundus photographs. procedures: Twelve of 2862 single nucleotide polymorphisms (SNPs) from 11 of 233 candidate genes for cardiovascular disease were selected for analysis based on screening with marginal unadjusted P value <.001 within 1 or more racial/ethnic groups. Logistic regression models tested for association in case-control samples. main outcome measure: Prevalence of early AMD. RESULTS Early AMD was present in 4.0% of the cohort and varied from 2.4% in blacks to 6.0% in whites. The odds ratio increased from 2.3 for 1 to 10.0 for 4 risk alleles in a joint effect analysis of Age-Related Maculopathy Susceptibility 2 rs10490924 and Complement Factor H Y402H (P for trend = 4.2×10(-7)). Frequencies of each SNP varied among the racial/ethnic groups. Adjusting for age and other factors, few statistically significant associations of the 12 SNPs with AMD were consistent across all groups. In a multivariate model, most candidate genes did not attenuate the comparatively higher odds of AMD in whites. The higher frequency of risk alleles for several SNPs in Chinese Americans may partially explain their AMD frequency's approaching that of whites. CONCLUSIONS The relationships of 11 candidate genes to early AMD varied among 4 racial/ethnic groups, and partially explained the observed variations in early AMD prevalence among them.
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Affiliation(s)
- Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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25
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Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 2013; 8:e60793. [PMID: 23577161 PMCID: PMC3618337 DOI: 10.1371/journal.pone.0060793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/03/2013] [Indexed: 01/11/2023] Open
Abstract
The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.
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Ishikawa T, Toyoda Y, Yoshiura KI, Niikawa N. Pharmacogenetics of human ABC transporter ABCC11: new insights into apocrine gland growth and metabolite secretion. Front Genet 2013; 3:306. [PMID: 23316210 PMCID: PMC3539816 DOI: 10.3389/fgene.2012.00306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/11/2012] [Indexed: 11/13/2022] Open
Abstract
Cell secretion is an important physiological process that ensures smooth metabolic activities and tissue repair as well as growth and immunological functions in the body. Apocrine secretion occurs when the secretory process is accomplished with a partial loss of cell cytoplasm. The secretory materials are contained within secretory vesicles and are released during secretion as cytoplasmic fragments into the glandular lumen or interstitial space. The recent finding that the non-synonymous single nucleotide polymorphisms (SNP) 538G > A (rs17822931; Gly180Arg) in the ABCC11 gene determines the type of earwax in humans has shed light on the novel function of this ABC (ATP-binding cassette) transporter in apocrine glands. The wild-type (Gly180) of ABCC11 is associated with wet-type earwax, axillary osmidrosis, and colostrum secretion from the mammary gland as well as the potential risk of mastopathy. Furthermore, the SNP (538G > A) in the ABCC11 gene is suggested to be a clinical biomarker for the prediction of chemotherapeutic efficacy. The aim of this review article is to provide an overview on the discovery and characterization of genetic polymorphisms in the human ABCC11 gene and to explain the impact of ABCC11 538G > A on the apocrine phenotype as well as the anthropological aspect of this SNP in the ABCC11 gene and patients’ response to nucleoside-based chemotherapy.
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Affiliation(s)
- Toshihisa Ishikawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology Yokohama, Japan ; Omics Science Center, RIKEN Yokohama Institute Yokohama, Japan
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KUDAKA MASATOMI, FUKASE HITOSHI, KIMURA RYOSUKE, HANIHARA TSUNEHIKO, MATSUMURA HIROFUMI, SASO AIKO, FUKUMINE TADAHIKO, ISHIDA HAJIME. Metric characteristics of human limb bones in Asian and Japanese populations. ANTHROPOL SCI 2013. [DOI: 10.1537/ase.121125] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- MASATOMI KUDAKA
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HITOSHI FUKASE
- Division of Human Evolution Studies, Graduate School of Medicine, Hokkaido University, Sapporo
| | - RYOSUKE KIMURA
- Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Nishihara
| | - TSUNEHIKO HANIHARA
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara
| | | | - AIKO SASO
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo
| | - TADAHIKO FUKUMINE
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
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Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, Tanabe H, Mano S, Suto Y, Kaname T, Naritomi K, Yanagi K, Niikawa N, Omoto K, Tokunaga K, Saitou N. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J Hum Genet 2012; 57:787-95. [PMID: 23135232 DOI: 10.1038/jhg.2012.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.
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Haimila K, Penttilä A, Arvola A, Auvinen MK, Korhonen M. Analysis of the adequate size of a cord blood bank and comparison of HLA haplotype distributions between four populations. Hum Immunol 2012; 74:189-95. [PMID: 23137880 DOI: 10.1016/j.humimm.2012.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 10/22/2012] [Accepted: 10/26/2012] [Indexed: 11/17/2022]
Abstract
The number of units and especially the number of different HLA haplotypes present in a cord blood (CB) bank is a crucial determinant of its usefulness. We generated data relevant to the development of our national CB in Finland. The HLA haplotype distribution was examined between specific populations. We developed graphical ways of data presentation that enable easy visualization of differences. First, we estimated the optimal size of a CB bank for Finland and found that approximately 1700 units are needed to provide a 5/6 HLA-matched donor for 80% of Finnish patients. Secondly, we evaluated HLA haplotype distributions between four locations, Finland, Japan, Sweden and Belgium. Our results showed that the Japanese Tokyo Cord Blood Bank differs in both the frequency and distribution of haplotypes from the European banks. The European banks (Finnish Cord Blood Registry, The Swedish National Cord Blood Bank, and Marrow Donor Program-Belgium) have similar frequencies of common haplotypes, but 26% of the haplotypes in the Finnish CB bank are unique, which justifies the existence of a national bank. The tendency to a homogenous HLA haplotype distribution in banks underlines the need for targeting recruitment at the poorly represented minority populations.
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Affiliation(s)
- Katri Haimila
- Finnish Red Cross Blood Service, Kivihaantie 7, FI-00310 Helsinki, Finland.
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Kulski JK, Shigenari A, Inoko H. Genetic variation and hitchhiking between structurally polymorphic Alu insertions and HLA-A, -B, and -C alleles and other retroelements within the MHC class I region. ACTA ACUST UNITED AC 2012; 78:359-77. [PMID: 21988723 DOI: 10.1111/j.1399-0039.2011.01776.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We investigated structurally polymorphic Alu insertions (POALINs) at five loci in the major histocompatibility complex (MHC) class I genomic region to determine their allele and haplotype frequencies and associations with the human leukocyte antigen (HLA)-A, -B, and -C genes in three populations, the Australian Caucasians, Japanese, and African Americans. The POALINs varied in allelic frequency between 0% and 42.3% with significant differences between populations at three of the five loci. The linkage disequilibrium (LD) between Alu insertions and the HLA-A, -B, or -C alleles and previously published polymorphic retroelements (four SVA and human endogenous retrovirus type 9 (HERVK9) loci) within the class I region of the MHC were calculated in pairwise analyses of haplotypes to show strong allelic associations and possible crossing-over events between some loci. Each POALIN was in significant LD with a variety of HLA-A, -B, or -C two-digit alleles probably as a result of hitchhiking. The POALINs helped to further stratify the HLA-A:B:C haplotypes into different POALIN:HLA-A:B:C haplotype frequencies. Of the multilocus haplotype analyses, the seven- and eight-locus haplotypes showed the largest number of differences between the populations, and fewer matched haplotypes between populations that ranged, for example, from 49% for HLA-B:HLA-A haplotypes to 7% for AluMICB:HLA-B:HLA-C:AluTF:AluHJ:HLA-A:AluHG:AluTF haplotypes in the Japanese. This comparative study of multilocus POALINs in the HLA class I region of three ethnic populations shows that POALINs alone or together with the HLA class I alleles and other retroelements are informative ancestral markers for assessing the interrelationship of HLA class I haplotype lineages, LD, and genetic diversity within the same and/or different populations.
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Affiliation(s)
- J K Kulski
- Centre for Forensic Science, The University of Western Australia, Nedlands, WA 6008, Australia.
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31
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Chiang HL, Lee-Chen GJ, Chen CM, Chen YC, Lee CM, Liao MH, Wu YR. Genetic analysis of HLA-DRA region variation in Taiwanese Parkinson’s disease. Parkinsonism Relat Disord 2012; 18:391-3. [DOI: 10.1016/j.parkreldis.2011.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/26/2011] [Accepted: 12/28/2011] [Indexed: 12/09/2022]
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Gu Y, Zhang M, Chen H, Wang Z, Xing C, Yang H, Xu X, Liu Y, Zhou Z, Yu L, Hutton J, Eisenbarth G, Yang T. Discordant association of islet autoantibodies with high-risk HLA genes in Chinese type 1 diabetes. Diabetes Metab Res Rev 2011; 27:899-905. [PMID: 22069282 DOI: 10.1002/dmrr.1270] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND To reveal the aetiology of diabetes, the relationships between the islet autoantibodies, human leukocyte antigen (HLA)-A and DRB1 genotypes in the Chinese patients with type l diabetes (T1D) were investigated in our study. METHODS In the cross-sectional and case-control study, peripheral blood samples were collected from 600 T1D patients and 102 healthy controls. The genetic polymorphisms of HLA-A and DRB1 are examined with polymerase chain reaction-sequence oligonucleotide probe method. The zinc transporter 8 antibody (ZnT8A), glutamic acid decarboxylase antibody (GADA) and protein-tyrosine-phosphatase-2 autoantibody (IA2A) were detected by radioligand assay. RESULTS The A*2402, DRB1*0301, DRB1*0405 and DRB1*0901 alleles, and A*1101-DRB1*0901, A*2402-DRB1*0405 and A*2402-DRB1*0901 haplotypes were associated with T1D (all p<0.05). The positive rates of ZnT8A in patients carried DRB1*0901, IA2A in patients carried DRB1*0405 and A*1101-DRB1*0901 and GADA in patients carried DRB1*0901 and A*2402-DRB1*0901 were significantly higher than those not carried (p<0.05). HLA-DRB1*0901 was the independent risk factor of positive antibody in T1D patients. In addition, higher body mass index is also related with the loss of islet function besides high-risk HLA gene and islet autoantibody (p<0.05). CONCLUSIONS The discordant association of autoantibodies with high-risk HLA gene may indicate the different immunology mechanisms of those autoantibodies. And metabolic burden resulting from overweight may accelerate apoptosis of beta cells.
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Affiliation(s)
- Yong Gu
- Department of Endocrinology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Dai CY, Chuang WL, Hsieh MY, Huang JF, Lin YY, Chu PY, Hou NJ, Lin ZY, Chen SC, Hsieh MY, Wang LY, Yu ML. Human leukocyte antigen alleles and the response to pegylated interferon/ribavirin therapy in chronic hepatitis C patients. Antiviral Res 2010; 85:396-402. [PMID: 19931565 DOI: 10.1016/j.antiviral.2009.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 10/30/2009] [Accepted: 11/16/2009] [Indexed: 12/12/2022]
Abstract
Human leukocyte antigens (HLAs) may play a role in the clinical evolution of hepatitis C virus (HCV) infection. The present study was aimed at elucidating the association between the HLA loci and responses to combination therapy with pegylated interferon-alpha 2a (PEG-IFN) and ribavirin in Taiwanese. We enrolled a total of 208 treatment-naïve Taiwanese chronic hepatitis C (CHC) patients treated with combination therapy. Patients with sustained virological response (SVR) had a significantly higher frequency of genotype non-1b infection, lower pretreatment HCV RNA levels and a higher frequency of mild hepatic fibrosis (fibrosis score: F: 0-2). The HLA A24 and B40 alleles were significantly associated with SVR after adjusted for the other three confounding factors including HCV genotype, hepatic fibrosis and pretreatment serum HCV RNA levels. Haplotypes (B40-DRB1*3, B46- DRB1*9, Cw1- DQB1*3, and Cw1- DRB1*9) were significantly associated with SVR to combination therapy. For 167 patients with genotype 1b infection and viral load < or =5.6 logIU/ml or genotype non-1b infection, the B46 was significantly associated with sustained response with OR (odds ratio) [95% CI (confidence interval) of 0.047 (0.168-0.988)]. Haplotypes B40-DRB1*3, B46- DRB1*9, Cw1- DQB1*3, Cw1- DRB1*9 and DQB1*3- DRB1*9 were found to be associated with SVR to PEG-IFN/ribavirin therapy with OR (95% CI) of 0.179 (0.032-0.989), 0.313 (0.107-0.918), 0.350 (0.145-0.845), 0.282 (0.105-0.759) and 0.412 (0.174-0.978), respectively. We concluded that the virological and the host immunogenetic factors may possibly predict the response to combination therapy in CHC patients.
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Affiliation(s)
- Chia-Yen Dai
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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Parolín ML, Carnese FR. HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay. Genet Mol Biol 2009; 32:212-9. [PMID: 21637670 PMCID: PMC3036916 DOI: 10.1590/s1415-47572009000200002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 09/05/2008] [Indexed: 12/01/2022] Open
Abstract
The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied.
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Affiliation(s)
- Maria L Parolín
- Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires Argentina
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Yuliwulandari R, Kashiwase K, Nakajima H, Uddin J, Susmiarsih TP, Sofro ASM, Tokunaga K. Polymorphisms of HLA genes in Western Javanese (Indonesia): close affinities to Southeast Asian populations. ACTA ACUST UNITED AC 2009; 73:46-53. [PMID: 19140832 DOI: 10.1111/j.1399-0039.2008.01178.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Identification of human leukocyte antigen (HLA) antigens that are known as the highest polymorphic genes has become a valuable tool for tissue transplantation, platelet transfusion, disease susceptibility or resistance, and forensic and anthropological studies. In the present study, the allele and haplotype frequencies of HLA-A, HLA-B, and HLA-DRB1 were studied in 237 unrelated healthy Western Javanese (Indonesia) by the high-resolution polymerase chain reaction-Luminex method. A total of 18 A, 40 B, and 20 DRB1 alleles were identified. The most frequent HLA-A, -B, and -DRB1 alleles were HLA-A*2407 (21.6%), HLA-B*1502 (11.6%) and HLA-B*1513 (11.2%), and DRB1*1202 (37.8%), respectively. The most frequent two-locus haplotypes were HLA-A*2407-B*3505 (7%) and HLA-B*1513-DRB1*1202 (9.2%), and three-locus haplotypes were HLA-A*3401-B*1521-DRB1*150201 (4.6%), HLA-A*2407-B*3505-DRB1*1202 (4.3%), and HLA-A*330301-B*440302-DRB1*070101 (4.2%). HLA allele and haplotype frequencies in addition to phylogenetic tree and principal component analyses based on the four-digit sequence-level allele frequencies for HLA-A, HLA-B, and HLA-DRB1 showed that Western Javanese (Indonesia) was closest to Southeast Asian populations.
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Affiliation(s)
- R Yuliwulandari
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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36
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ISHIDA HAJIME, HANIHARA TSUNEHIKO, KONDO OSAMU, FUKUMINE TADAHIKO. Craniometric divergence history of the Japanese populations. ANTHROPOL SCI 2009. [DOI: 10.1537/ase.081219] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HAJIME ISHIDA
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara
| | - TSUNEHIKO HANIHARA
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara
| | - OSAMU KONDO
- Department of Biological Sciences, The University of Tokyo, Tokyo
| | - TADAHIKO FUKUMINE
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara
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Sohn EH, Kim HS, Lee AY, Fukuda T, Sugie H, Kim DS. A novel PYGM mutation in a Korean patient with McArdle disease: the role of nonsense-mediated mRNA decay. Neuromuscul Disord 2008; 18:886-9. [PMID: 18667317 DOI: 10.1016/j.nmd.2008.06.384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/04/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
Abstract
We have identified a compound heterozygous mutation of PYGM in a Korean patient with McArdle disease, which is composed of a novel single codon deletion (p.779delE) and a common nonsense mutation (p.R50X). Our study also showed an evidence of nonsense-mediated mRNA decay (NMD) caused by p.R50X mutation, supporting the importance of RNA processing defects in the molecular pathology of McArdle disease.
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Affiliation(s)
- Eun Hee Sohn
- Department of Neurology, Chungnam University Hospital, Daejeon, Republic of Korea
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KOMESU ATSUKO, HANIHARA TSUNEHIKO, AMANO TETSUYA, ONO HIROKO, YONEDA MINORU, DODO YUKIO, FUKUMINE TADAHIKO, ISHIDA HAJIME. Nonmetric cranial variation in human skeletal remains associated with Okhotsk culture. ANTHROPOL SCI 2008. [DOI: 10.1537/ase.070323] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- ATSUKO KOMESU
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus
| | | | | | - HIROKO ONO
- Hokkaido University Museum, Hokkaido University
| | - MINORU YONEDA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
| | - YUKIO DODO
- Department of Nursing, Faculty of Human Science, Hokkaido Bunkyo University
| | - TADAHIKO FUKUMINE
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus
| | - HAJIME ISHIDA
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus
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Shi L, Ogata S, Yu JK, Ohashi J, Yu L, Shi L, Sun H, Lin K, Huang XQ, Matsushita M, Horai S, Muramatsu M, Chu JY, Tokunaga K. Distribution of HLA alleles and haplotypes in Jinuo and Wa populations in Southwest China. Hum Immunol 2007; 69:58-65. [PMID: 18295677 DOI: 10.1016/j.humimm.2007.11.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 11/26/2007] [Accepted: 11/28/2007] [Indexed: 11/30/2022]
Abstract
The frequencies of human leukocyte antigen (HLA) alleles HLA-A, -B, and -DRB1 alleles and A-B-DRB1, A-B, and B-DRB1 haplotypes were studied in Jinuo and Wa populations in Southwest China using the polymerase chain reaction-Luminex (PCR-Luminex) typing method. A total of 12 A, 22 B, and 16 DRB1 alleles were found in the Jinuo population, and 10 A, 28 B, and 18 DRB1 alleles were found in the Wa population. The A*110101-B*1502-DRB1*120201 was the predominant haplotype in both the Jinuo and Wa populations; A*110101-B*1301-DRB1*120201 and A*24020101-B*1502-DRB1*120201 were common in the Jinuo population, whereas A*110101-B*1532-DRB1*1504 and A*110101-B*350101-DRB1*1404 were common in the Wa population. Phylogenetic tree and principal component analyses based on HLA-A, -B, and -DRB1 allele frequencies suggested that both the Jinuo and Wa populations belong to the Southeast Asian group, whereas Wa population is still maintaining its original genetic character and a great distance from other populations because of a founder effect and subsequent geographic isolation. A close relationship among Jinuo, Wa, Thai, and Vietnamese was also suggested.
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Affiliation(s)
- Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China
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40
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Paradisi I, Hernández A, Arias S. Huntington disease mutation in Venezuela: age of onset, haplotype analyses and geographic aggregation. J Hum Genet 2007; 53:127-135. [PMID: 18157708 DOI: 10.1007/s10038-007-0227-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 11/09/2007] [Indexed: 11/29/2022]
Abstract
The aggregation of patients with Huntington's disease (HD) around Lake Maracaibo, Zulia State, Venezuela, is widely recognized, but the epidemiology of HD in the whole country is relatively unstudied. We have examined 279 individuals from 60 unrelated affected families residing in various areas of Venezuela for the presence of CAG repeats and other features associated with HD. The number of expanded repeats in 139 carriers varied from 35 to 112. Based on our examination of 71 symptomatic individuals, we developed a log-transformed regression equation, y= -0.0238x + 2.6616, to enable the prediction of age of onset in asymptomatic carriers. Intragenic haplotypes were constructed with two VNTRs (variable number of tandem repeats) and two SNPs (single nucleotide polymorphisms) in the promoter region as well as CCG repeat and Delta2642 polymorphisms to assess kinship between families. In 43 of 45 tested families, the haplotype on the mutated chromosome was 1;G;C;7;(A). The other haplotypes observed, 1;G;C;7;(B) and 4;G;C;7;(A), were of Peruvian and French origins, respectively. The geographic source of the first affected ancestor was assessed in 54 families from 15 different states. Residents of the states of Miranda, Lara and Táchira, excluding those of Zulia, had a mutated allele prevalence five- to ninefold higher than that of other areas. A low (approx. 1/200,000) prevalence, a wide-spread distribution with aggregation in some states and a likely remote European Caucasoid origin are defining epidemiologic features of HD in Venezuela.
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Affiliation(s)
- Irene Paradisi
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela
| | - Alba Hernández
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela
| | - Sergio Arias
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela.
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Barros Kanzaki LI, Casseb J. Unusual finding of HTLV-I infection among Amazonian Amerindians. Arch Med Res 2007; 38:897-900. [PMID: 17923274 DOI: 10.1016/j.arcmed.2007.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Human T-cell lymphotropic virus type II is a retrovirus endemic in Amerindian communities throughout the American continent, although some Amerindian groups that apparently emerged from the same ethnic root as HTLV-II carriers do not secrete antibodies against the virus and show very low prevalence for human T-cell lymphotropic virus type I. In this study, sera from 487 Amazonian amerinds were screened for HTLV type I and II antibody by the gelatin particle agglutination assay and ELISA and confirmed by Western blot and indirect immunofluorescence assay. None was positive for HTLV type II. One young healthy male of Waiãpi ethnicity was reactive with HTLV-I and was confirmed by Western blot assay and indirect immunofluorescence test. The absence of HTLV type II infection among these Amerindian communities would suggest a behavior pattern distinct from other groups in the American continent. Also, the very low prevalence of HTLV type I infection among these ethnic groups probably indicates contamination by blood transfusion (external transmission route).
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Affiliation(s)
- Luis Isamu Barros Kanzaki
- Laboratory of Molecular Pharmacology, Faculty of Health Sciences, University of Brasilia, Brasilia, DF, Brazil.
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Vicente J, Sinues B, Fanlo A, Vasquez P, Medina JC, Martinez-Jarreta B. Polymorphism C3435T of the MDR1 gene in Central Americans and Spaniards. Mol Biol Rep 2007; 35:473-8. [PMID: 17577681 DOI: 10.1007/s11033-007-9109-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 05/31/2007] [Indexed: 01/11/2023]
Abstract
The human multidrug resistance gene (MDR1) encodes for P-glycoprotein (P-gp) which is a transmembrane transporter protein that acts as an efflux pump for a number of lypophilic compounds. It plays a protective role for cells against DNA damage. The wobble C3435T polymorphism at exon 26 has been associated with different expression levels and activity. Differences in allele frequency of the C3435T polymorphism have been demonstrated between distinct ethnic groups. In our study we examined these polymorphisms in 433 healthy individuals. From these, 229 were Central American mestizos from Nicaragua (n = 117) and El Salvador (n = 112) to be compared with a group of 204 North Spaniards, with the aim of detecting potential genotypic differences between these populations. The genotypes were determined by PCR-RFLP. The frequencies of the C allele were very similar among Central Americans (0.53) and Spaniards (0.52), which is consistent with the ethnic origin of Central American individuals (Amerindians and European Caucasians). In comparison to other previously studied populations, the C allele frequency in Central Americans was significantly lower than that found in African populations and higher than that observed in the Indian and Southwest Asian populations. These data may be relevant for dose recommendation of P-gp substrate drugs and also for studies of allele disease association in the Central American population.
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Affiliation(s)
- J Vicente
- Department of Pharmacology, Medicine School, University of Zaragoza, Domingo Miral s/n, Zaragoza, Spain
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43
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Hu SP, Luan JA, Li B, Chen JX, Cai KL, Huang LQ, Xu XY. Genetic link between Chaoshan and other Chinese Han populations: Evidence from HLA-A and HLA-B allele frequency distribution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:140-50. [PMID: 16883565 DOI: 10.1002/ajpa.20460] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The genetic polymorphism of HLA-A and HLA-B loci was investigated in 505 Chaoshanese using PCR-SSP method. Among the HLA-A alleles detected, A*11 (35.64%) was most frequent, followed by A*02 (31.78%). Of 34 HLA-B alleles tested, 30 were observed, in which B*60 (21.68%), B*46 (14.46%), and B*58 (10.69%) were highly predominant. Comparison was made with other nine Chinese Han ethnic groups covering the Mainland China, Taiwan, Hong Kong, and Singapore. The high frequent alleles found in Chaoshanese were also common in other Chinese groups compared though the frequency levels varied from group to group. The phylogenic tree analysis based on the HLA-A and -B allele frequencies of all the 10 Chinese ethnic groups revealed that Chaoshanese, while clustering in general with the southern China-related Han Chinese, had the highest affinity to the Mainland Minnanese, but separated distinctively from the northern Han Chinese. The study, however, was yet to confirm the hypothesis of the Central Plains Han origin of Chaoshanese. Interestingly, the alleles (B*46, B*38, and B*58) and the related haplotypes (A*02-B*46 and A*33-B*58) that are positively associated with nasopharyngeal carcinoma (NPC), a disease prevailing predominantly among southern Chinese, were always at much higher frequencies among southern Chinese than among northern Chinese, whereas A*31 and B*13, the two alleles with highly protective effects for NPC, and the associated haplotype A*30-B*13 were predominantly high in northern Chinese. The different genetic background between northern and southern China may explain, at least partially, the prevalence of NPC among southern Chinese.
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Affiliation(s)
- Sheng-Ping Hu
- Center for Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, Guangdong 515031, People's Republic of China.
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Nakajima F, Tokunaga K, Nakatsuji N. Human leukocyte antigen matching estimations in a hypothetical bank of human embryonic stem cell lines in the Japanese population for use in cell transplantation therapy. Stem Cells 2006; 25:983-5. [PMID: 17185611 DOI: 10.1634/stemcells.2006-0566] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human embryonic stem (hES) cell lines are of great potential in cell transplantation therapy. However, recipients of such allogeneic transplants probably need treatment with immunosuppressants. Recently, Taylor et al. [Lancet 2005;366:2019-2025] proposed banking of hES cell lines and estimated the required number of hES cell lines for beneficial human leukocyte antigen (HLA) matching in the U.K. population. Here, we carried out such an estimation in the Japanese population. We calculated the proportion of patients who can find at least one HLA-matched donor at three loci of HLA-A, -B, and -DR. With a bank of hES cell lines from 170 randomly selected donated embryos, 80% of patients were expected to find at least one hES cell line with a single mismatch at one HLA locus or a better match. Furthermore, 80% of patients are expected to find at least one donor with complete matching at the three HLA loci if parthenogenetic homozygous hES cell lines are established from 55 randomly selected donated oocytes. The relatively low ethnic diversity of the Japanese population may have resulted in a high success rate in beneficial matching. Moreover, parthenogenetic hES cell lines can greatly reduce the number required for a higher degree of HLA matching.
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Affiliation(s)
- Fumiaki Nakajima
- Research and Development Department, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
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45
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Yoshiura KI, Kinoshita A, Ishida T, Ninokata A, Ishikawa T, Kaname T, Bannai M, Tokunaga K, Sonoda S, Komaki R, Ihara M, Saenko VA, Alipov GK, Sekine I, Komatsu K, Takahashi H, Nakashima M, Sosonkina N, Mapendano CK, Ghadami M, Nomura M, Liang DS, Miwa N, Kim DK, Garidkhuu A, Natsume N, Ohta T, Tomita H, Kaneko A, Kikuchi M, Russomando G, Hirayama K, Ishibashi M, Takahashi A, Saitou N, Murray JC, Saito S, Nakamura Y, Niikawa N. A SNP in the ABCC11 gene is the determinant of human earwax type. Nat Genet 2006; 38:324-30. [PMID: 16444273 DOI: 10.1038/ng1733] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 12/13/2005] [Indexed: 11/09/2022]
Abstract
Human earwax consists of wet and dry types. Dry earwax is frequent in East Asians, whereas wet earwax is common in other populations. Here we show that a SNP, 538G --> A (rs17822931), in the ABCC11 gene is responsible for determination of earwax type. The AA genotype corresponds to dry earwax, and GA and GG to wet type. A 27-bp deletion in ABCC11 exon 29 was also found in a few individuals of Asian ancestry. A functional assay demonstrated that cells with allele A show a lower excretory activity for cGMP than those with allele G. The allele A frequency shows a north-south and east-west downward geographical gradient; worldwide, it is highest in Chinese and Koreans, and a common dry-type haplotype is retained among various ethnic populations. These suggest that the allele A arose in northeast Asia and thereafter spread through the world. The 538G --> A SNP is the first example of DNA polymorphism determining a visible genetic trait.
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Affiliation(s)
- Koh-ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
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Amos W, Manica A. Global genetic positioning: evidence for early human population centers in coastal habitats. Proc Natl Acad Sci U S A 2006; 103:820-4. [PMID: 16407146 PMCID: PMC1334655 DOI: 10.1073/pnas.0507991103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For an alternative perspective on relationships among human populations, we combined genetic and geographic information, using allele frequency gradients to place populations and individuals on the globe. Reanalyzing published data on 51 worldwide populations [Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivitovsky, L. A. & Feldman, M. W. (2002) Science 298, 2381-2385] reveals five geographic clusters lying in plausible sites either of early agricultural innovation or on ancient migration routes. Also, the inferred sites show significant association with coastlines, suggesting that most early humans lived near large bodies of water. Our approach is flexible, and developments should prove useful both for exploring historical demography and for the identification of likely origin for unknown forensic samples.
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Affiliation(s)
- William Amos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
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Shi L, Xu SB, Ohashi J, Sun H, Yu JK, Huang XQ, Tao YF, Yu L, Horai S, Chu JY, Tokunaga K. HLA-A, HLA-B, and HLA-DRB1 alleles and haplotypes in Naxi and Han populations in southwestern China (Yunnan province). ACTA ACUST UNITED AC 2006; 67:38-44. [PMID: 16451199 DOI: 10.1111/j.1399-0039.2005.00526.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The frequencies of the human leukocyte antigen alleles HLA-A, HLA-B, and HLA-DRB1 and the A-B-DRB1, A-B, and B-DRB1 haplotypes were studied in Naxi and Yunnan Han populations using polymerase chain reaction (PCR)-sequence-specific amplification for alleles A and B and a PCR-microtiter plate hybridization method for the DRB1 allele. A total of 8 A, 19 B, and 30 DRB1 alleles were found in the Naxi population, and 15 A, 21 B, and 36 DRB1 alleles were found in Yunnan Han population. The common A-B-DRB1 haplotypes in the Naxi population were A*24-B*15-DRB1*1202, A*11-B*15-DRB1*0405, A*11-B*15-DRB1*1202, A*11-B*38-DRB1*08032, and A*11-B*55-DRB1*0405; the common A-B haplotypes were A*11-B*15, A*11-B*38, and A*24-B*15; and the common B-DRB1 haplotypes were B*15-DRB1*1202, B*38-DRB1*08032, and B*48-DRB1*1201. In the Yunnan Han population, the common A-B-DRB1 haplotypes were A*24-B*15-DRB1*1501, A*24-B*46-DRB1*08032, and A*24-B*15-DRB1*1201; the common A-B haplotypes were A*24-B*15, A*24-B*46, and A*34-B*46; and the common B-DRB1 haplotypes were B*15-DRB1*1501, B*46-DRB1*09012, and B*46-DRB1*1401. Phylogenetic tree and principal component analyzes based on HLA-A, HLA-B, and DRB1 allele frequencies suggested that the Naxi ethnic group belongs to the southern Chinese groups, while the Yunnan Han population is a characteristic population located intermediate between northern and southern Chinese groups, although they live in the southwest of China.
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Affiliation(s)
- L Shi
- Institute of Medical Biology, Chinese Academy of Medical Science, Kunming, China
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FUKUMINE TADAHIKO, HANIHARA TSUNEHIKO, NISHIME AKIRA, ISHIDA HAJIME. Nonmetric cranial variation of early modern human skeletal remains from Kumejima, Okinawa and the peopling of the Ryukyu Islands. ANTHROPOL SCI 2006. [DOI: 10.1537/ase.050606] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- TADAHIKO FUKUMINE
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus
| | | | | | - HAJIME ISHIDA
- Department of Anatomy, Faculty of Medicine, University of the Ryukyus
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Barton JC, Acton RT, Lovato L, Speechley MR, McLaren CE, Harris EL, Reboussin DM, Adams PC, Dawkins FW, Gordeuk VR, Walker AP. Initial screening transferrin saturation values, serum ferritin concentrations, and HFE genotypes in Native Americans and whites in the Hemochromatosis and Iron Overload Screening Study. Clin Genet 2005; 69:48-57. [PMID: 16451136 DOI: 10.1111/j.1399-0004.2006.00553.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We compared initial screening transferrin saturation (TfSat) and serum ferritin (SF) phenotypes and HFE C282Y and H63D genotypes of 645 Native American and 43,453 white Hemochromatosis and Iron Overload Screening Study participants who did not report a previous diagnosis of hemochromatosis or iron overload. Elevated measurements were defined as TfSat >50% in men and >45% in women and SF >300 ng/ml in men and >200 ng/ml in women. Mean TfSat was 31% in Native American men and 32% in white men (p = 0.0337) and 25% in Native American women and 27% in white women (p < 0.0001). Mean SF was 153 microg/l in Native American and 151 microg/l in white men (p = 0.8256); mean SF was 55 microg/l in Native American women and 63 microg/l in white women (p = 0.0015). The C282Y allele frequency was 0.0340 in Native Americans and 0.0683 in whites (p < 0.0001). The H63D allele frequency was 0.1150 in Native Americans and 0.1532 in whites (p = 0.0001). We conclude that the screening TfSat and SF phenotypes of Native Americans are similar to those of whites. The allele frequencies of HFE C282Y and H63D are significantly lower in Native Americans than in whites.
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Affiliation(s)
- J C Barton
- Southern Iron Disorders Center, University of Alabama at Birmingham Birmingham, AL 35209, USA.
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50
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Li SL, Yamamoto T, Yoshimoto T, Uchihi R, Mizutani M, Kurimoto Y, Tokunaga K, Jin F, Katsumata Y, Saitou N. Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci. Hum Genet 2005; 118:695-707. [PMID: 16315063 DOI: 10.1007/s00439-005-0106-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 11/01/2005] [Indexed: 10/25/2022]
Abstract
We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K> or =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.
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Affiliation(s)
- Shi-Lin Li
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
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