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Hernández-Doño S, Jakez-Ocampo J, Márquez-García JE, Ruiz D, Acuña-Alonzo V, Lima G, Llorente L, Tovar-Méndez VH, García-Silva R, Granados J, Zúñiga J, Vargas-Alarcón G. Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican. Front Genet 2021; 12:701373. [PMID: 34413879 PMCID: PMC8369992 DOI: 10.3389/fgene.2021.701373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune inflammatory disorder for which Major Histocompatibility Complex (MHC) genes are well identified as risk factors. SLE patients present different clinical phenotypes, which are partly explained by admixture patterns variation among Mexicans. Population genetic has insight into the high genetic variability of Mexicans, mainly described through HLA gene studies with anthropological and biomedical importance. A prospective, case-control study was performed. In this study, we recruited 146 SLE patients, and 234 healthy individuals were included as a control group; both groups were admixed Mexicans from Mexico City. The HLA typing methods were based on Next Generation Sequencing and Sequence-Based Typing (SBT). The data analysis was performed with population genetic programs and statistical packages. The admixture estimations based on HLA-B and -DRB1 revealed that SLE patients have a higher Southwestern European ancestry proportion (48 ± 8%) than healthy individuals (30 ± 7%). In contrast, Mexican Native American components are diminished in SLE patients (44 ± 1%) and augmented in Healthy individuals (63 ± 4%). HLA alleles and haplotypes' frequency analysis found variants previously described in SLE patients from Mexico City. Moreover, a conserved extended haplotype that confers risk to develop SLE was found, the HLA-A∗29:02∼C∗16:01∼B∗44:03∼DRB1∗07:01∼DQB1∗02:02, pC = 0.02, OR = 1.41. Consistent with the admixture estimations, the origin of all risk alleles and haplotypes found in this study are European, while the protection alleles are Mexican Native American. The analysis of genetic distances supported that the SLE patient group is closer to the Southwestern European parental populace and farthest from Mexican Native Americans than healthy individuals. Heterogeneity of genetic admixture determines SLE susceptibility and protection in Mexicans. HLA sequencing is helpful to determine susceptibility alleles and haplotypes restricted to some populations.
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Affiliation(s)
- Susana Hernández-Doño
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan Jakez-Ocampo
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Eduardo Márquez-García
- Molecular Biology Core Facility, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Daniela Ruiz
- Department of Dermatology, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Víctor Acuña-Alonzo
- Laboratory of Physiology, Biochemistry, and Genetics, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Guadalupe Lima
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Luis Llorente
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Víctor Hugo Tovar-Méndez
- Department of Endocrinology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rafael García-Silva
- Department of Internal Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julio Granados
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
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Barton JC, Barton JC, Bertoli LF, Acton RT. HLA-A and -B Type and Haplotype Frequencies in IgG Subclass Deficiency Subgroups. Arch Immunol Ther Exp (Warsz) 2020; 68:14. [PMID: 32307610 DOI: 10.1007/s00005-020-00572-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/05/2020] [Indexed: 01/10/2023]
Abstract
We sought to determine whether HLA-A and -B type and haplotype frequencies differ between subgroups of adults with IgG subclass deficiency (IgGSD). We retrospectively compared type and haplotype frequencies of three subgroups of 269 unrelated adult IgGSD patients (70 subnormal IgG1; 121 subnormal IgG3; 78 subnormal IgG1/IgG3) and controls (1,321 for types; 751 for haplotypes). We selected types and haplotypes because their uncorrected frequencies differed significantly from controls in a previous adult IgGSD/common variable immunodeficiency cohort: A*24; B*14; B*35; B*40; B*49; B*50; B*58; B*62; A*01,B*08; A*02,B*44; A*02,B*60; A*03,B*07; A*03,B*14; A*03,B*44; A*31,B*40; and A*32,B*14. We used χ2 analysis (2 × 4 tables) to identify frequency differences across three subgroups and controls. If the null hypothesis was rejected (p < 0.05), we computed 2 × 2 χ2 tables to compare six combinations of subgroup and control frequencies [Bonferroni p < 0.0083 (< 0.05/6)]. Mean age was 48 ± 13 years; 82.2% were women. B*35 and B*40 frequencies were higher in subnormal IgG1 than subnormal IgG3 patients (0.1000 vs. 0.0248 and 0.0571 vs. 0.0083, respectively; p ≤ 0.0061). B*62 frequencies were lower in three IgGSD subgroups than controls (p < 0.0001, respectively). A*02, B*44 frequency was higher in subnormal IgG1/IgG3 patients than controls (0.1282 vs. 0.0632, respectively; p = 0.0024). A*02, B*60 frequency was lower in subnormal IgG3 patients than controls (0.0 vs. 0.0233, respectively; p = 0.0051). HLA-B*35 and -B*40 frequencies differ significantly between some IgGSD subgroups. B*62, A*02, B*44, and A*02, B*60 frequencies differ significantly between some IgGSD subgroups and controls.
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Affiliation(s)
- James C Barton
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA. .,Southern Iron Disorders Center, Birmingham, AL, USA. .,Department of Medicine, Brookwood Medical Center, Birmingham, AL, USA.
| | | | - Luigi F Bertoli
- Southern Iron Disorders Center, Birmingham, AL, USA.,Department of Medicine, Brookwood Medical Center, Birmingham, AL, USA
| | - Ronald T Acton
- Southern Iron Disorders Center, Birmingham, AL, USA.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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Barquera R, Zuniga J, Flores-Rivera J, Corona T, Penman BS, Hernández-Zaragoza DI, Soler M, Jonapá-Gómez L, Mallempati KC, Yescas P, Ochoa-Morales A, Barsakis K, Aguilar-Vázquez JA, García-Lechuga M, Mindrinos M, Yunis M, Jiménez-Alvarez L, Mena-Hernández L, Ortega E, Cruz-Lagunas A, Tovar-Méndez VH, Granados J, Fernández-Viña M, Yunis E. Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans. Sci Rep 2020; 10:3248. [PMID: 32094421 PMCID: PMC7039995 DOI: 10.1038/s41598-020-58897-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Here we studied HLA blocks and haplotypes in a group of 218 Lacandon Maya Native American using a high-resolution next generation sequencing (NGS) method. We assessed the genetic diversity of HLA class I and class II in this population, and determined the most probable ancestry of Lacandon Maya HLA class I and class II haplotypes. Importantly, this Native American group showed a high degree of both HLA homozygosity and linkage disequilibrium across the HLA region and also lower class II HLA allelic diversity than most previously reported populations (including other Native American groups). Distinctive alleles present in the Lacandon population include HLA-A*24:14 and HLA-B*40:08. Furthermore, in Lacandons we observed a high frequency of haplotypes containing the allele HLA-DRB1*04:11, a relatively frequent allele in comparison with other neighboring indigenous groups. The specific demographic history of the Lacandon population including inbreeding, as well as pathogen selection, may have elevated the frequencies of a small number of HLA class II alleles and DNA blocks. To assess the possible role of different selective pressures in determining Native American HLA diversity, we evaluated the relationship between genetic diversity at HLA-A, HLA-B and HLA-DRB1 and pathogen richness for a global dataset and for Native American populations alone. In keeping with previous studies of such relationships we included distance from Africa as a covariate. After correction for multiple comparisons we did not find any significant relationship between pathogen diversity and HLA genetic diversity (as measured by polymorphism information content) in either our global dataset or the Native American subset of the dataset. We found the expected negative relationship between genetic diversity and distance from Africa in the global dataset, but no relationship between HLA genetic diversity and distance from Africa when Native American populations were considered alone.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
- Laboratory of Molecular Genetics, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Joaquin Zuniga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - José Flores-Rivera
- Clinical Laboratory of Neurodegenerative Diseases, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Teresa Corona
- Clinical Laboratory of Neurodegenerative Diseases, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Bridget S Penman
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Diana Iraíz Hernández-Zaragoza
- Laboratory of Molecular Genetics, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
- Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Manuel Soler
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | | | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
- Biology Department, University of Crete, Heraklion, Greece
| | - Petra Yescas
- Department of Neurogenetics and Molecular Biology, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Adriana Ochoa-Morales
- Department of Neurogenetics and Molecular Biology, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Konstantinos Barsakis
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
- Department of Pathology, Stanford University, CA, USA
| | - José Artemio Aguilar-Vázquez
- Clinical Analysis Laboratory, Unidad Médica Familiar (UMF) No. 23, Instituto Mexicano del Seguro Social (IMSS), Tuxtla Gutiérrez, Chiapas, Mexico
| | - Maricela García-Lechuga
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | | | - María Yunis
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Luis Jiménez-Alvarez
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Lourdes Mena-Hernández
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | - Esteban Ortega
- The William Harvey Research Institute, Barts and London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Víctor Hugo Tovar-Méndez
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMSZ), Mexico City, Mexico.
| | | | - Edmond Yunis
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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Dutra VDF, Bub CB, Costa TH, Santos LD, Bastos EP, Aravechia MG, Kutner JM. Allele and haplotype frequencies of human platelet and leukocyte antigens in platelet donors. EINSTEIN-SAO PAULO 2019; 17:eAO4477. [PMID: 30758400 PMCID: PMC6438674 DOI: 10.31744/einstein_journal/2019ao4477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/13/2018] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To described the allele and haplotype frequencies of human leukocyte antigen genes at the -A, -B loci and human platelet antigen genes for human platelet antigen systems 1 to 9, 11 and 15 in blood. METHODS We included 867 healthy unrelated volunteer donors who donated platelets between January 2011 and December 2014. Microarray genotyping was performed using a BeadChip microarray. Medium resolution typing of the human leukocyte antigen at loci A and B was carried out using sequence-specific oligonucleotide probe hybridization. We used multivariate analysis and our human leukocyte antigen population was compared to data from the United States national bone marrow donor program. Human platelet antigen results were compared to a literature review and data from around the world. RESULTS Our human leukocyte antigen haplotype results were more similar to those of hispanics, followed by caucasians. Likewise, our human platelet antigen sample is more similar to those of Argentina, Rio Grande do Sul and Italy. CONCLUSION This was the first article that discusses human platelet antigen and human leukocyte antigen data together. Rare genotypes or antibody associations can make patient management difficult. A blood bank with genotyped donors allows for optimal transfusion and can contribute to better results. Our information can serve as basis for a database of platelet antigen polymorphisms.
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Du QS, Wang SQ, Xie NZ, Wang QY, Huang RB, Chou KC. 2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications. Oncotarget 2017; 8:70564-70578. [PMID: 29050302 PMCID: PMC5642577 DOI: 10.18632/oncotarget.19757] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/30/2017] [Indexed: 01/25/2023] Open
Abstract
A two-level principal component predictor (2L-PCA) was proposed based on the principal component analysis (PCA) approach. It can be used to quantitatively analyze various compounds and peptides about their functions or potentials to become useful drugs. One level is for dealing with the physicochemical properties of drug molecules, while the other level is for dealing with their structural fragments. The predictor has the self-learning and feedback features to automatically improve its accuracy. It is anticipated that 2L-PCA will become a very useful tool for timely providing various useful clues during the process of drug development.
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Affiliation(s)
- Qi-Shi Du
- State Key Laboratory of China for Biomass Energy Enzyme Technology, National Engineering Research Center of China for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
- Gordon Life Science Institute, Boston, MA 02478, USA
| | - Shu-Qing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Neng-Zhong Xie
- State Key Laboratory of China for Biomass Energy Enzyme Technology, National Engineering Research Center of China for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Qing-Yan Wang
- State Key Laboratory of China for Biomass Energy Enzyme Technology, National Engineering Research Center of China for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Ri-Bo Huang
- State Key Laboratory of China for Biomass Energy Enzyme Technology, National Engineering Research Center of China for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Gordon Life Science Institute, Boston, MA 02478, USA
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Hernández EG, Granados J, Partida-Rodríguez O, Valenzuela O, Rascón E, Magaña U, Escamilla-Tilch M, López-Reyes A, Nieves-Ramírez M, González E, Morán P, Rojas L, Valadez A, Luna A, Estrada FJ, Maldonado C, Ximénez C. Prevalent HLA Class II Alleles in Mexico City Appear to Confer Resistance to the Development of Amebic Liver Abscess. PLoS One 2015; 10:e0126195. [PMID: 25938667 PMCID: PMC4418702 DOI: 10.1371/journal.pone.0126195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/30/2015] [Indexed: 11/19/2022] Open
Abstract
Amebiasis is an endemic disease and a public health problem throughout Mexico, although the incidence rates of amebic liver abscess (ALA) vary among the geographic regions of the country. Notably, incidence rates are high in the northwestern states (especially Sonora with a rate of 12.57/100,000 inhabitants) compared with the central region (Mexico City with a rate of 0.69/100,000 inhabitants). These data may be related to host genetic factors that are partially responsible for resistance or susceptibility. Therefore, we studied the association of the HLA-DRB1 and HLA-DQB1 alleles with resistance or susceptibility to ALA in two Mexican populations, one each from Mexico City and Sonora. Ninety ALA patients were clinically diagnosed by serology and sonography. Genomic DNA was extracted from peripheral blood mononuclear cells. To establish the genetic identity of both populations, 15 short tandem repeats (STRs) were analyzed with multiplexed PCR, and the allelic frequencies of HLA were studied by PCR-SSO using LUMINEX technology. The allele frequencies obtained were compared to an ethnically matched healthy control group (146 individuals). We observed that both affected populations differed genetically from the control group. We also found interesting trends in the population from Mexico City. HLA-DQB1*02 allele frequencies were higher in ALA patients compared to the control group (0.127 vs 0.047; p= 0.01; pc= NS; OR= 2.9, 95% CI= 1.09-8.3). The less frequent alleles in ALA patients were HLA-DRB1*08 (0.118 vs 0.238 in controls; p= 0.01; pc= NS; OR= 0.42, 95% CI= 0.19-0.87) and HLA-DQB1*04 (0.109 vs 0.214; p= 0.02; pc= NS; OR= 0.40, 95% CI= 0.20-0.94). The haplotype HLA-DRB1*08/-DQB1*04 also demonstrated a protective trend against the development of this disease (0.081 vs. 0.178; p=0.02; pc=NS; OR= 0.40, 95% CI= 0.16-0.93). These trends suggest that the prevalent alleles in the population of Mexico City may be associated with protection against the development of ALA.
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Affiliation(s)
- Eric G. Hernández
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Julio Granados
- División de Inmunogenética, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), SSa, Mexico City, México
| | - Oswaldo Partida-Rodríguez
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Olivia Valenzuela
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Edgar Rascón
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Ulises Magaña
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Mónica Escamilla-Tilch
- División de Inmunogenética, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), SSa, Mexico City, México
| | - Alberto López-Reyes
- Laboratorio de Sinovioanálisis Molecular, Instituto Nacional de Rehabilitación, SSa, Mexico City, México
| | - Miriam Nieves-Ramírez
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Enrique González
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Patricia Morán
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Liliana Rojas
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Alicia Valadez
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
| | - Alexandra Luna
- Laboratorio de Biología Molecular, Escuela de Medicina, Universidad Panamericana, Mexico City, México
| | - Francisco J. Estrada
- Laboratorio de Biología Molecular, Escuela de Medicina, Universidad Panamericana, Mexico City, México
| | - Carmen Maldonado
- Laboratorio de Investigación en Inmunología y proteómica, Hospital Infantil de México Federico Gómez, SSa, Mexico City, México
| | - Cecilia Ximénez
- Laboratorio de Inmunología, Departamento de Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, México
- * E-mail:
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Fionnuala W, Derek M. HLA-A, -B, -C, and -DRB1 genotyping of 1000 Northern Irish individuals from Belfast, Northern Ireland in the United Kingdom. Hum Immunol 2015; 76:395-6. [PMID: 25797202 DOI: 10.1016/j.humimm.2015.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
One thousand individuals from Belfast, Northern Ireland were genotyped at the HLA-A, -B, -C and -DRB1 loci using sequence-specific oligonucleotide probe methods. HLA-A locus genotypes display a minor Hardy-Weinberg (HW) deviation (p=0.0375); HLA-B, -C and -DRB1 genotypes are consistent with expected HW proportions. These genotype data are available in the Allele Frequencies Net Database under identifier AFND 1243.
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Affiliation(s)
- Williams Fionnuala
- Northern Ireland Histocompatibility and Immunogenetics Laboratory, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Middleton Derek
- Transplant Immunology, Royal Liverpool Hospital, Liverpool, UK.
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Macêdo MB, Tsuneto LT, Teixeira RADO, Oliveira MDSBD, Moita Neto JM, Silva ASD, Sousa LCDDM, Carvalho MG, Sales HLA, Barroso JRPDM, Araújo ADS, Monte SJHD. Rio Grande do Norte, Brazil, voluntary bone marrow donors registry analysis. Rev Assoc Med Bras (1992) 2015; 61:23-9. [DOI: 10.1590/1806-9282.61.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/03/2014] [Indexed: 11/21/2022] Open
Abstract
Objective: this study aimed to report the allele and haplotype frequencies of volunteer bone marrow donors (VBMD) from the state of Rio Grande do Norte (RN) who were enrolled in the Brazilian Volunteer Bone Marrow Donor Registry (REDOME). Methods: the sample comprised 12,973 VBMD who had their allele and haplotype frequencies calculated by Arlequin 3.5.1.2. A multivariate analysis of the data was obtained through a principal component analysis (PCA) and hierarchical cluster analysis (HCA) performed with SPSS 8.0. Results: the most frequent allelic group was HLA-A*02, followed by -DRB1*13, -DRB1*04, -DRB1*07, -B*44, -B*35, -A*24 and -DRB1*01. Of the 2,701 haplotypes observed, the three most frequent were HLA-A*01 B*08 DRB1*03 (1.62%), -A*29 B*44 DRB1*07 (1.56%) and -A*02 B*44 DRB1*04 (1.29%). These haplotypes were in linkage disequilibrium. RN allele and haplotype frequencies were very similar to those in other Brazilian states in which similar studies have been performed. The PCA revealed that RN is highly genetically similar to Caucasian populations, especially those from Iberian countries, which strongly influenced the state’s ethnic composition. Africans and Amerindians also influenced the RN population structure, to a lesser extent. Conclusion: the HCA reinforced the conclusion that, despite its highly admixed profile, the RN population is genetically similar to European and European-descended populations. The PCA also showed that RN cities do not contribute to the same extent to REDOME, with less populous cities being underrepresented, indicating the need to enroll more VBMD from these smaller cities to faithfully depict the state’s population structure in the database.
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Samandary S, Kridane-Miledi H, Sandoval JS, Choudhury Z, Langa-Vives F, Spencer D, Chentoufi AA, Lemonnier FA, BenMohamed L. Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine. Hum Immunol 2014; 75:715-29. [PMID: 24798939 DOI: 10.1016/j.humimm.2014.04.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 02/01/2023]
Abstract
A significant portion of the world's population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) over a half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A(∗)24, HLA-B(∗)27, HLA-B(∗)53 and HLA-B(∗)58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B(∗)44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy.
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Affiliation(s)
- Sarah Samandary
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Hédia Kridane-Miledi
- UNITE INSERM 1016, Institut Cochin, Hôpital Saint-Vincent-de-Paul, 82, Avenue Denfert-Rochereau, 75674 Paris Cedex 14, France
| | - Jacqueline S Sandoval
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Zareen Choudhury
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Francina Langa-Vives
- Plate-Forme Technologique, Centre d'Ingénierie Génétique Murine, Département de Biologie du Développement, Institut Pasteur, 75015 Paris, France
| | - Doran Spencer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Aziz A Chentoufi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - François A Lemonnier
- UNITE INSERM 1016, Institut Cochin, Hôpital Saint-Vincent-de-Paul, 82, Avenue Denfert-Rochereau, 75674 Paris Cedex 14, France
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92697, USA.
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10
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Grubic Z, Burek Kamenaric M, Mikulic M, Stingl Jankovic K, Maskalan M, Zunec R. HLA-A, HLA-B and HLA-DRB1 allele and haplotype diversity among volunteer bone marrow donors from Croatia. Int J Immunogenet 2014; 41:211-21. [PMID: 24762167 DOI: 10.1111/iji.12117] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 02/09/2014] [Accepted: 02/23/2014] [Indexed: 01/01/2023]
Abstract
The determination of human leucocyte antigen (HLA)-A, HLA-B and HLA-DRB1 alleles in the routine procedure of a volunteer hematopoietic stem cell (HSC) donor's registration in the Croatian Bone Marrow Donor Registry (CBMDR) is performed to enhance the odds of finding a suitable HLA compatible donor for patients in need of a HSC transplantation worldwide. However, besides its original purpose, it also provides valuable information about the HLA polymorphism among Croats. The aim of the present study was to analyse the HLA allele and haplotype frequencies in a sample of 4000 donors from CBMDR. The distribution of HLA-A, HLA-B and HLA-DRB1 alleles did not demonstrate significant differences from the data reported for other European populations. The higher frequency of B*40:02 allele in comparison with B*40:01 and DRB1*11:04 in comparison with DRB1*11:01 is interesting because it represents a difference in comparison with the Western and Northern European populations which are a main source of donors for Croatian patients. The haplotype frequencies show a greater variation and difference in comparison with data from other registries and populations; however, due to a lack of high-resolution haplotype data, comparison was possible only with a very limited number of other populations.
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Affiliation(s)
- Z Grubic
- Tissue Typing Center, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
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11
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Wennerström A, Vlachopoulou E, Lahtela LE, Paakkanen R, Eronen KT, Seppänen M, Lokki ML. Diversity of extended HLA-DRB1 haplotypes in the Finnish population. PLoS One 2013; 8:e79690. [PMID: 24278156 PMCID: PMC3836878 DOI: 10.1371/journal.pone.0079690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022] Open
Abstract
The Major Histocompatibility Complex (MHC, 6p21) codes for traditional HLA and other host response related genes. The polymorphic HLA-DRB1 gene in MHC Class II has been associated with several complex diseases. In this study we focus on MHC haplotype structures in the Finnish population. We explore the variability of extended HLA-DRB1 haplotypes in relation to the other traditional HLA genes and a selected group of MHC class III genes. A total of 150 healthy Finnish individuals were included in the study. Subjects were genotyped for HLA alleles (HLA-A, -B, -DRB1, -DQB1, and -DPB1). The polymorphism of TNF, LTA, C4, BTNL2 and HLA-DRA genes was studied with 74 SNPs (single nucleotide polymorphism). The C4A and C4B gene copy numbers and a 2-bp silencing insertion at exon 29 in C4A gene were analysed with quantitative genomic realtime-PCR. The allele frequencies for each locus were calculated and haplotypes were constructed using both the traditional HLA alleles and SNP blocks. The most frequent Finnish A∼B∼DR -haplotype, uncommon in elsewhere in Europe, was A*03∼B*35∼DRB1*01∶01. The second most common haplotype was a common European ancestral haplotype AH 8.1 (A*01∼B*08∼DRB1*03∶01). Extended haplotypes containing HLA-B, TNF block, C4 and HLA-DPB1 strongly increased the number of HLA-DRB1 haplotypes showing variability in the extended HLA-DRB1 haplotype structures. On the contrary, BTNL2 block and HLA-DQB1 were more conserved showing linkage with the HLA-DRB1 alleles. We show that the use of HLA-DRB1 haplotypes rather than single HLA-DRB1 alleles is advantageous when studying the polymorphisms and LD patters of the MHC region. For disease association studies the HLA-DRB1 haplotypes with various MHC markers allows us to cluster haplotypes with functionally important gene variants such as C4 deficiency and cytokines TNF and LTA, and provides hypotheses for further assessment. Our study corroborates the importance of studying population-specific MHC haplotypes.
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Affiliation(s)
- Annika Wennerström
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
- * E-mail:
| | | | - L. Elisa Lahtela
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Riitta Paakkanen
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Katja T. Eronen
- Transplantation Laboratory, Haartman Institute, Helsinki, Finland
| | - Mikko Seppänen
- Division of Infectious Diseases, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
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12
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Zúñiga J, Yu N, Barquera R, Alosco S, Ohashi M, Lebedeva T, Acuña-Alonzo V, Yunis M, Granados-Montiel J, Cruz-Lagunas A, Vargas-Alarcón G, Rodríguez-Reyna TS, Fernandez-Viña M, Granados J, Yunis EJ. HLA class I and class II conserved extended haplotypes and their fragments or blocks in Mexicans: implications for the study of genetic diversity in admixed populations. PLoS One 2013; 8:e74442. [PMID: 24086347 PMCID: PMC3781075 DOI: 10.1371/journal.pone.0074442] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/03/2023] Open
Abstract
Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations.
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Affiliation(s)
- Joaquín Zúñiga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Neng Yu
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Sharon Alosco
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Marina Ohashi
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Tatiana Lebedeva
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - María Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julio Granados-Montiel
- Tissue Engineering, Cell Therapy and Regenerative Medicine Research Unit, Instituto Nacional de Rehabilitación, Mexico City, Mexico
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Gilberto Vargas-Alarcón
- Laboratory of Genomics, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City, Mexico
| | - Tatiana S. Rodríguez-Reyna
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- * E-mail: (EJY); (JG)
| | - Edmond J. Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (EJY); (JG)
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13
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Mack SJ, Cano P, Hollenbach JA, He J, Hurley CK, Middleton D, Moraes ME, Pereira SE, Kempenich JH, Reed EF, Setterholm M, Smith AG, Tilanus MG, Torres M, Varney MD, Voorter CEM, Fischer GF, Fleischhauer K, Goodridge D, Klitz W, Little AM, Maiers M, Marsh SGE, Müller CR, Noreen H, Rozemuller EH, Sanchez-Mazas A, Senitzer D, Trachtenberg E, Fernandez-Vina M. Common and well-documented HLA alleles: 2012 update to the CWD catalogue. ACTA ACUST UNITED AC 2013; 81:194-203. [PMID: 23510415 DOI: 10.1111/tan.12093] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 11/26/2022]
Abstract
We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages.
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Affiliation(s)
- S J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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14
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Pan Q, Fan S, Wang X, Zhao X, Pan M, Wang C, Shen J. The distribution of HLA-A, -B, and -DRB1 alleles and haplotypes in inhabitants of Guizhou Province of China. J Biomed Res 2013; 25:328-34. [PMID: 23554708 PMCID: PMC3596729 DOI: 10.1016/s1674-8301(11)60044-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/30/2010] [Accepted: 03/23/2011] [Indexed: 12/04/2022] Open
Abstract
The present study was aimed to analyze the frequencies of human leukocyte antigen (HLA)-A, -B, and -DRB1 alleles and A-B-DRB1, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence specific oligonucleotide probe (PCR-rSSOP) method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A*11(30.72%) and A*02(30.65%), B*40(16.27%) and B*46(16.27%), and DRB1*09(15.91%) and DRB1*15(13.51%), respectively. The most common haplotype was A*02-B*46-DRB1*09(5.59%) in A-B-DRB1, A*02-B*46(11.73%) in A-B, B*46-DRB1*09(7.49%) in B-DRB1, and A*02-DRB1*09(8.08%) in A-DRB1. Some haplotypes with strong linkage disequilibrium (LD) were found not only in the common haplotypes, such as A*33-B*58, B*30-DRB1*07, and B*33-DRB1*03, but also in the rare haplotypes, such as A*01-B*37, B*37-DRB1*10, and A*01-DRB1*10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.
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Affiliation(s)
- Qinqin Pan
- HLA Laboratory, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Sun C, Wei L, Luo F, Li Y, Li J, Zhu F, Kang P, Xu R, Xiao L, Liu Z, Xu P. HLA-DRB1 alleles are associated with the susceptibility to sporadic Parkinson's disease in Chinese Han population. PLoS One 2012; 7:e48594. [PMID: 23139797 PMCID: PMC3490875 DOI: 10.1371/journal.pone.0048594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/26/2012] [Indexed: 12/19/2022] Open
Abstract
Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The χ(2) test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate.
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Affiliation(s)
- Congcong Sun
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lei Wei
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Feifei Luo
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third People’s Hospital of Chengdu, Chengdu, People’s Republic of China
| | - Yi Li
- Department of Neurology, Department of Neurology, Red-Cross Hospital in Guangzhou, Guangzhou, People’s Republic of China
| | - Jiaobiao Li
- Department of Neurology, HeYuan City Hospital, Guangdong, People’s Republic of China
| | - Feiqi Zhu
- Department of Neurology, Yuebei People's Hospital of Shantou University Medical College, Guangdong, People’s Republic of China
| | - Ping Kang
- Department of Neurology, The First People’s Hospital of Shaoguan, Guangdong, People’s Republic of China
| | - Rensi Xu
- Department of Neurology, The First Affiliated Hospital of NanChang University, NanChang, People’s Republic of China
| | - LuLu Xiao
- Department of Tissue Typing Center, Nanfang Hospital of Southern Medical University, Guangzhou, People’s Republic of China
| | - Zhuolin Liu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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16
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Winchester R, Minevich G, Steshenko V, Kirby B, Kane D, Greenberg DA, FitzGerald O. HLA associations reveal genetic heterogeneity in psoriatic arthritis and in the psoriasis phenotype. ACTA ACUST UNITED AC 2011; 64:1134-44. [PMID: 22006066 DOI: 10.1002/art.33415] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Rigorously ascertained cases of psoriatic arthritis in subjects presenting to a rheumatology unit were compared with cases of psoriasis in subjects presenting to a dermatology unit, where subjects with musculoskeletal features were excluded, to address 1) the extent to which the contribution of the major histocompatibility complex (MHC) to psoriatic arthritis susceptibility resembles that in psoriasis, and 2) whether MHC genes determine quantitative traits within the psoriatic arthritis phenotype. METHODS Separate discovery and validation subcohorts of patients recruited from a relatively homogeneous population were studied by sequence-based HLA typing, in which frequencies of the HLA-B and HLA-C alleles and haplotypes were compared. RESULTS In patients with psoriatic arthritis, the frequency of C*06:02 was lower than that in patients with psoriasis (28.7% versus 57.5%; P = 9.9 × 10(-12) ). Three haplotypes containing B*27:05 or B*39:01 were significantly increased in frequency in patients with psoriatic arthritis, but not in those with psoriasis. The structurally related B*39:06 allele was not increased in frequency. B*27 was associated with an interval of 0.98 years between skin and musculoskeletal disease (P = 2.05 × 10(-6) ), compared with an interval of 10.14 years for C*06. Preliminary evidence suggested that B*38:01 and B*08 may be associated with psoriatic arthritis susceptibility, and that allotypes encoding P2 pockets that bind side chains opposite in charge from those encoded by the B*27 and B*39 molecules may exert a protective role. CONCLUSION These findings suggest that the psoriasis phenotype results from two patterns of MHC effect. The first involves the classic psoriasis susceptibility gene C*06, which confers more penetrant skin disease with less prevalent and more time-dependent musculoskeletal phenotype development. The second pattern appears to be mediated by HLA-B alleles, notably B*27, and includes temporally more coincident musculoskeletal involvement that is nearly equivalent in penetrance to that of the skin disease.
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17
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Chang CC, Too CL, Murad S, Hussein SH. Association of HLA-B*1502 allele with carbamazepine-induced toxic epidermal necrolysis and Stevens-Johnson syndrome in the multi-ethnic Malaysian population. Int J Dermatol 2011; 50:221-4. [PMID: 21244392 DOI: 10.1111/j.1365-4632.2010.04745.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Carbamazepine (CBZ), a frequently used anticonvulsant drug, is one of the most common causes of life-threatening cutaneous adverse drug reactions such as toxic epidermal necrolysis (TEN) and Stevens-Johnson syndrome (SJS). Recent studies have revealed a strong association between HLA-B*1502 and CBZ-induced TEN/SJS in the Taiwan Han Chinese population. OBJECTIVES This study is aimed to investigate the association between human leucocyte antigens (HLA) and CBZ-induced TEN/SJS in the multi-ethnic Malaysian population. METHODS A sample of 21 unrelated patients with CBZ-induced TEN/SJS and 300 race-matched, healthy controls were genotyped for HLA-A, -B and -DR using polymerase chain reaction (PCR). Allele frequencies were compared. RESULTS HLA-B*1502 was present in 75.0% (12/16) of Malay patients with CBZ-induced TEN/SJS but in only 15.7% (47/300) of normal controls (odds ratio 16.15, 95% confidence interval 4.57-62.4; corrected P-value = 7.87 × 10(-6) ), which suggests a strong association between HLA and CBZ-induced TEN/SJS. Additionally, HLA-B*1502 was found in all three Chinese and two Indian patients. Existing data show that frequencies of the HLA-B*1502 allele are generally much higher in Asian populations than in White European populations, which explains the higher incidences of SJS and TEN in Asian countries. CONCLUSIONS HLA-B*1502 is strongly associated with CBZ-induced TEN/SJS in the Malay population in Malaysia, as has been seen in Han Chinese in Taiwan. This indicates that the genetic association apparent in the incidence of CBZ-induced TEN/SJS is linked with the presence of HLA-B*1502, irrespective of racial origin. Screening of patients for this genetic marker can help to prevent the occurrence of TEN/SJS.
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Affiliation(s)
- Choong-Chor Chang
- Department of Dermatology, Kuala Lumpur Hospital Allergy and Immunology Research Center, Kuala Lumpur, Malaysia.
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18
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Stevenson R, Fatehullah A, Jagan I, Deevi RK, Bingham V, Irvine AE, Armstrong M, Morrison PJ, Dimmick I, Stewart R, Campbell FC. Enhanced lymphocyte interferon (IFN)-γ responses in a PTEN mutation-negative Cowden disease kindred. Clin Exp Immunol 2011; 164:202-10. [PMID: 21361912 DOI: 10.1111/j.1365-2249.2011.04336.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Identification of immune modifiers of inherited cancer syndromes may provide a rationale for preventive therapy. Cowden disease (CD) is a genetically heterogeneous inherited cancer syndrome that arises predominantly from germline phosphatase and tensin homologue deleted on chromosome 10 (PTEN) mutation and increased phosphoinositide 3-kinase/mammalian target of rapamycin (PI3K/mTOR) signalling. However, many patients with classic CD diagnostic features are mutation-negative for PTEN (PTEN M-Neg). Interferon (IFN)-γ can modulate the PI3K/mTOR pathway, but its association with PTEN M-Neg CD remains unclear. This study assessed IFN-γ secretion by multi-colour flow cytometry in a CD kindred that was mutation-negative for PTEN and other known susceptibility genes. Because IFN-γ responses may be regulated by killer cell immunoglobulin-like receptors (KIR) and respective human leucocyte antigen (HLA) ligands, KIR/HLA genotypes were also assessed. Activating treatments induced greater IFN-γ secretion in PTEN M-Neg CD peripheral blood lymphocytes versus healthy controls. Increased frequency of activating KIR genes, potentially activating KIR/HLA compound genotypes and reduced frequency of inhibitory genotypes, were found in the PTEN M-Neg CD kindred. Differences of IFN-γ secretion were observed among PTEN M-Neg CD patients with distinct KIR/HLA compound genotypes. Taken together, these findings show enhanced lymphocyte secretion of IFN-γ that may influence the PI3K/mTOR CD causal molecular pathway in a PTEN mutation-negative CD kindred.
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Affiliation(s)
- R Stevenson
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, UK
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19
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Kongmaroeng C, Romphruk A, Ruangwerayut R, Paupairoj C, Leelayuwat C, Inoko H, Romphruk A. HLA-B*15 subtypes in Burmese population by sequence-based typing. ACTA ACUST UNITED AC 2009; 74:164-7. [PMID: 19497038 DOI: 10.1111/j.1399-0039.2009.01281.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA)-B*15 encompasses an increasing number of subtypes of more than 150. Frequency studies and a strong genetic association between HLA subtypes and susceptibility to drug hypersensitivity have been reported in different ethnic populations. To identify HLA-B*15 subtypes in Burmese using sequence-based typing (SBT) method, we selected 65 HLA-B*15-positive samples from 170 unrelated healthy Burmese who were genotyped HLA-B* by polymerase chain reaction with the sequence-specific primer method. The frequency of HLA-B*15 in Burmese was found to be 38.2%. By the SBT method, results showed 10 alleles of HLA-B*15 subtypes. Four common alleles, B*1502 (45.2%), B*1532 (16.4%), B*1525 (12.3%), and B*1501 (8.2%), were found in 82.1% of HLA-B*15-positive Burmese. Whereas the B*1501 was the highest in the Caucasians, Koreans, and Japanese, the highest frequency of HLA-B*15 alleles in Burmese was B*1502 (45.2%) that is similar to the frequency found in northeastern Thais and Vietnamese. This study is the first report of HLA-B*15 subtypes in Burmese. These results will provide the basic data in the further study in transplantations, genetic association with diseases, and drug hypersensitivity.
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Affiliation(s)
- C Kongmaroeng
- PhD Program in Biomedical Science, Faculty of Graduate School, Khon Kaen University, Khon Kaen, Thailand.
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20
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Abdeen H, McErlean C, Moraes ME, Romero M, Marques SB, Goncales AC, Guariento EG, Middleton D. Identification of two novel alleles HLA-B*3569 and -B*4450 and confirmation of HLA-A*2631 in the Brazilian population. ACTA ACUST UNITED AC 2007; 69:273-6. [PMID: 17493154 DOI: 10.1111/j.1399-0039.2006.00788.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two novel alleles, human leukocyte antigen (HLA)-B*3569, -B*4450 and a confirmatory sequence of HLA-A*2631 were identified during a routine typing for the Brazilian Bone Marrow Donor Registry. Sequence analysis of coding exons 2 and 3 revealed a single nucleotide substitution in HLA-B*3569 and two single nucleotide substitutions in HLA-B*4450, compared with closely related alleles. At the protein level, these substitutions result in a change of a single amino acid residue in each of HLA-B*3569 and -B*4450 at positions 74 (Arg > Pro) and 80 (Thr > Ile), respectively. These variations are located in the highly polymorphic region at the end of the alpha(1) domain of the HLA molecule. It appears that HLA-B*3569 arose from the analogous HLA-B*3510 through a point mutation. However, HLA-B*4450 may have arisen from HLA-B*440301 and -B*4425 by gene conversion.
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Affiliation(s)
- H Abdeen
- Northern Ireland Histocompatibility and Immunogenetics Laboratory, Belfast City Hospital, Belfast, UK.
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21
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Badger SA, Soong CV, O'Donnell ME, Middleton D. The role of human leukocyte antigen genes in the formation of abdominal aortic aneurysms. J Vasc Surg 2007; 45:475-80. [PMID: 17321339 DOI: 10.1016/j.jvs.2006.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 09/19/2006] [Indexed: 12/20/2022]
Abstract
BACKGROUND Increasing evidence suggests an autoimmune component to abdominal aortic aneurysm (AAA) formation. This study was conducted to determine if a difference exists in human leukocyte antigen (HLA) allele distribution between patients with AAA and population controls, and between patients with small and large AAA. METHODS Patients with known AAA attending the vascular unit were consented for recruitment. HLA-A, HLA-B and HLA-DR was determined by polymerase chain reaction and sequence-specific oligonucleotide probes. The distribution of these alleles in the Northern Ireland general population was obtained from the histocompatibility and immunogenetics database. The chi(2) test was used for statistical analysis with Bonferroni correction. RESULTS A total of 241 AAA patients were recruited, with a wide range of aneurysm size. In class I, the most frequent allele families were HLA-A*02 and *01 and HLA-B*07, *08, and *44. In class II, HLA-DRB1*03, *04, *07, and *15 were the most frequent. HLA-A*11 was lower in AAA cases (10.4% vs 15.0%; P = .08), whereas HLA-B*08 was lower in the controls (29.8% vs 36.5%; P = .05) and HLA-DRB1*11 was lower in cases (4.2% vs 8.1%; P = .05). After Bonferroni correction, however, the proportion of allele families was not significantly different in AAA patients compared with the proportion seen in controls. HLA-DRB1*11 and *14 had a lower prevalence in large AAAs (0.9% vs 6.7% [P = .05]; 0.0% vs 5.9% [P = .03]). HLA-A*68 was also lower in large AAA (1.9% vs 11.9%; P = .0075). After Bonferroni correction, however, no difference was demonstrated between small and large aneurysms. CONCLUSION This study provides more definitive results on this important subject and has failed to demonstrate the risk association between AAA and these alleles as reported by others. Therefore, the role of these particular genes and the autoimmune component in AAA etiology does not appear to be as crucial as previously proposed.
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Affiliation(s)
- Stephen A Badger
- Vascular and Endovascular Surgery Centre, Belfast City Hospital, Belfast, United Kingdom.
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22
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Cano P, Klitz W, Mack SJ, Maiers M, Marsh SGE, Noreen H, Reed EF, Senitzer D, Setterholm M, Smith A, Fernández-Viña M. Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. Hum Immunol 2007; 68:392-417. [PMID: 17462507 DOI: 10.1016/j.humimm.2007.01.014] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
In histocompatibility testing some genotype ambiguities are almost always resolved into the genotype with the most common alleles. To achieve unambiguous assignments additional unwieldy tests are performed. The American Society for Histocompatibility and Immunogenetics formed a committee to define what human leukocyte antigen (HLA) genotypes do not need to be resolved in external proficiency testing. The tasks included detailed analysis of large datasets of high-resolution typing and thorough review of the pertinent scientific literature. Strict criteria were used to create a catalogue of common and well-documented (CWD) alleles. In total, 130, 245, 81, and 143 of the highly polymorphic HLA-A, -B, -C, and DRB1 loci fell into the CWD category; these represent 27%-30% of all alleles recognized. For the loci DRB3/4/5, DQA1, DQB1, and DPB1, a total of 29, 16, 26, and 52 CWD alleles were identified. A recommendation indicated that an acceptable report should only include one possible genotype; multiple genotypes can only be reported if only one of these includes two alleles of the CWD group. Exceptions in which resolution is not necessary are ambiguities involving functional alleles with identical sequences in the antigen recognition site. The criteria were established for proficiency testing, which could be a valuable tool when making clinical histocompatibility decisions.
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Affiliation(s)
- Pedro Cano
- University of Texas M. D. Anderson Cancer Center, HLA Typing Laboratory, Houston, Texas 77054, USA
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23
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Leal CA, Mendoza-Carrera F, Rivas F, Rodriguez-Reynoso S, Portilla-de Buen E. HLA-A and HLA-B allele frequencies in a mestizo population from Guadalajara, Mexico, determined by sequence-based typing. ACTA ACUST UNITED AC 2006; 66:666-73. [PMID: 16305683 DOI: 10.1111/j.1399-0039.2005.00495.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
HLA-A and HLA-B genes were typed by DNA sequencing in a mestizo population from Guadalajara, Jalisco, Mexico. Thirty-seven HLA-A and 51 HLA-B alleles were observed in 103 samples. The common typical Amerindian alleles (>5%) and haplotypes (>or=2.0%) found were A*02010101, *24020101, *310102, B*350101, and *4002, and A*310102-B*4002, A*240201-B*350101, and the typical European alleles were A*010101, *29010101, B*1402, B*180101, and A*020101-B*1402, A*020101-B*510101, and A*3002-B*180101. This reflects the blending of the two main parental populations of mestizos: Amerindian and Iberian. Mexicans were found to be relatively closer to the Portuguese than to Spaniards. This proximity may indicate a larger Portuguese influence in Mexicans than previously considered. Present data contribute to the understanding of the genetic structure in Mexico.
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Affiliation(s)
- C A Leal
- Surgical Research Division, Centro de Investigación Biomédica de Occidente, IMSS, Guadalajara, Jalisco, C.P. 44340 México.
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24
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Middleton D, Hawkins BR, Williams F, Meenagh A, Moscoso J, Zamora J, Arnaiz-Villena A. HLA class I allele distribution of a Hong Kong Chinese population based on high-resolution PCR-SSOP typing. ACTA ACUST UNITED AC 2005; 63:555-61. [PMID: 15140031 DOI: 10.1111/j.0001-2815.2004.00234.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A stem cell registry population from Hong Kong, of Chinese ethnicity, was examined for HLA-A and HLA-B alleles using a two-stage sequence-specific oligonucleotide probe system. Comparison of the HLA-A and HLA-B frequencies with different populations showed a close relationship with a Chinese population from Singapore, although there were several differences in the presence/absence of alleles at the HLA-B locus. Having the data available on these registry donors will influence the search strategy and the ongoing compilation of new donors to the registry. In addition, knowing which alleles do/do not occur in this population will aid in the distinction of ambiguities which result from the use of many of the typing kits available.
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Affiliation(s)
- D Middleton
- Northern Ireland Histocompatibility and Immunogenetics Laboratory, Blood Transfusion Building, City Hospital, Belfast, UK.
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25
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McKiernan SM, Hagan R, Curry M, McDonald GSA, Kelly A, Nolan N, Walsh A, Hegarty J, Lawlor E, Kelleher D. Distinct MHC class I and II alleles are associated with hepatitis C viral clearance, originating from a single source. Hepatology 2004; 40:108-14. [PMID: 15239092 DOI: 10.1002/hep.20261] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The role of cytotoxic T lymphocyte responses, restricted by human leukocyte antigen (HLA) class I alleles, is recognized as highly significant in the successful clearance of hepatitis C virus (HCV). The frequency of class I alleles in females inoculated with HCV genotype 1b from a single source was examined for an association with outcome. Class I typing was performed using polymerase chain reaction sequence-specific primers in 227 female subjects: 141 had chronic infection and 86 had viral clearance. Statistical analysis included chi(2) testing and multiple logistic regression analysis. A*03, B*27, and Cw*01 occurred more frequently in those with viral clearance (39.5%, 14%, and 9.3%, respectively) compared with those with chronic infection (19.1%, 2.1%, and 1.4%, respectively; P < or = .005). B*08 occurred more often in those with chronic infection compared with viral clearance (39.7% vs. 19.8%; P =.002). In combination with previously reported class II allele associations, over 75% that successfully eliminate HCV carry either A*03, DRB1*0101, or *0401, compared with only 37% of those with chronic infection (P <.0001). The haplotypes A*03-B*07-DRB1*15-DQB1*0602 and A*02-B*27-Cw*01-DRB1*0101-DQB1*0501 are associated with viral clearance (P =.004 and.01, respectively). By multiple logistic regression analysis, the alleles A*03, B*27, DRB1*0101, *0401, and *15 are associated with viral clearance, and B*27 has the strongest association (odds ratio [OR] 7.99). The haplotype A*01-B*08-Cw*07-DRB1*03011-DQB1*0201 is associated with chronic infection (P =.002), being independent for DQB1*0201 (OR 0.27). In conclusion, certain class I alleles are associated with outcome in this homogeneous cohort. More significantly, either HLA-A*03, -DRB1*0101, or -*0401 are carried by an overwhelming majority of those subjects who successfully clear HCV.
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Affiliation(s)
- Susan M McKiernan
- Hepatology Center, St. James's Hospital and Trinity College, Dublin, Ireland.
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26
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Cao K, Moormann AM, Lyke KE, Masaberg C, Sumba OP, Doumbo OK, Koech D, Lancaster A, Nelson M, Meyer D, Single R, Hartzman RJ, Plowe CV, Kazura J, Mann DL, Sztein MB, Thomson G, Fernández-Viña MA. Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. ACTA ACUST UNITED AC 2004; 63:293-325. [PMID: 15009803 DOI: 10.1111/j.0001-2815.2004.00192.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 subjects from five sub-Saharan populations from Kenya (Nandi and Luo), Mali (Dogon), Uganda, and Zambia. Distributions of genotypes at all loci and in all populations fit Hardy-Weinberg equilibrium expectations. There was not a single allele predominant at any of the loci in these populations, with the exception of A*3002 [allele frequency (AF) = 0.233] in Zambians and Cw*1601 (AF = 0.283) in Malians. This distribution was consistent with balancing selection for all class I loci in all populations, which was evidenced by the homozygosity F statistic that was less than that expected under neutrality. Only in the A locus in Zambians and the C locus in Malians, the AF distribution was very close to neutrality expectations. There were six instances in which there were significant deviations of allele distributions from neutrality in the direction of balancing selection. All allelic lineages from each of the class I loci were found in all the African populations. Several alleles of these loci have intermediate frequencies (AF = 0.020-0.150) and seem to appear only in the African populations. Most of these alleles are widely distributed in the African continent and their origin may predate the separation of linguistic groups. In contrast to native American and other populations, the African populations do not seem to show extensive allelic diversification within lineages, with the exception of the groups of alleles A*02, A*30, B*57, and B*58. The alleles of human leukocyte antigen (HLA)-B are in strong linkage disequilibrium (LD) with alleles of the C locus, and the sets of B/C haplotypes are found in several populations. The associations between A alleles with C-blocks are weaker, and only a few A/B/C haplotypes (A*0201-B*4501-Cw*1601; A*2301-B*1503-Cw*0202; A*7401-B* 1503-Cw*0202; A*2902-B*4201-Cw*1701; A*3001-B*4201-Cw*1701; and A*3601-B*5301-Cw*0401) are found in multiple populations with intermediate frequencies [haplotype frequency (HF) = 0.010-0.100]. The strength of the LD associations between alleles of HLA-A and HLA-B loci and those of HLA-B and HLA-C loci was on average of the same or higher magnitude as those observed in other non-African populations for the same pairs of loci. Comparison of the genetic distances measured by the distribution of alleles at the HLA class I loci in the sub-Saharan populations included in this and other studies indicate that the Luo population from western Kenya has the closest distance with virtually all sub-Saharan population so far studied for HLA-A, a finding consistent with the putative origin of modern humans in East Africa. In all African populations, the genetic distances between each other are greater than those observed between European populations. The remarkable current allelic and haplotypic diversity in the HLA system as well as their variable distribution in different sub-Saharan populations is probably the result of evolutionary forces and environments that have acted on each individual population or in their ancestors. In this regard, the genetic diversity of the HLA system in African populations poses practical challenges for the design of T-cell vaccines and for the transplantation medical community to find HLA-matched unrelated donors for patients in need of an allogeneic transplant.
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Affiliation(s)
- K Cao
- Department of Oncology, Georgetown University, Washington, DC, USA
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27
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Williams F, Meenagh A, Single R, McNally M, Kelly P, Nelson MP, Meyer D, Lancaster A, Thomson G, Middleton D. High resolution HLA-DRB1 identification of a caucasian population. Hum Immunol 2004; 65:66-77. [PMID: 14700598 DOI: 10.1016/j.humimm.2003.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polymerase chain reaction-sequence-specific oligonucleotide probes typing methods have been applied to 1000 individuals from the Northern Ireland population to give human leukocyte antigen DRB1 (HLA-DRB1) allele assignment. HLA-DRB1 allele frequencies and four-locus haplotypes (A/B/C/DR) for this Caucasian population, based on HLA class I and class II allele assignment, are now presented. No significant deviations from Hardy-Weinberg proportions were observed. The HLA-C locus exhibited marginal evidence of selection (p<0.03, uncorrected one-sided test) in the direction of balancing selection; the HLA-A, -B, and -DRB1 allele frequency distributions were compatible with expectations under a neutral model (which does not mean that selection is not operating). Evidence for selection was seen on haplotypes HLA-A*010101-B*0801-DRB1*030101 and HLA-A*290201-B*440301-DRB1*070101 based on their patterns of linkage disequilibrium.
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Affiliation(s)
- Fionnuala Williams
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast, Northern Ireland.
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28
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Middleton D, Menchaca L, Rood H, Komerofsky R. New allele frequency database: http://www.allelefrequencies.net. TISSUE ANTIGENS 2003; 61:403-7. [PMID: 12753660 DOI: 10.1034/j.1399-0039.2003.00062.x] [Citation(s) in RCA: 334] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A new website (http://www.allelefrequencies.net) has been compiled to execute the frequency of alleles at various polymorphic regions of different populations in the field of histocompatibility and immunogenetics. Data for HLA alleles has been added but this will be extended to include frequency data of polymorphisms in other immunogenetic regions, e.g. cytokines, KIR receptors, MIC.
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Affiliation(s)
- D Middleton
- Northern Ireland Histocompatibility and Immunogenetics Laboratory, Belfast, Northern Ireland.
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29
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Estefanía E, Gómez-Lozano N, de Pablo R, Moreno ME, Vilches C. Complementary DNA sequence of the HLA-B*3924 allele. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 2003; 30:11-2. [PMID: 12558815 DOI: 10.1046/j.1365-2370.2003.00362.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have isolated the complete coding region of HLA-B*39 from a Spanish Caucasoid, using a new PCR primer for its 5' untranslated region. The cDNA matched partial genomic sequences of B*3924, an allele whose distribution appears to be restricted to Mediterranean and Arabian Caucasoids. A single amino acid change exclusive to B*3924 (threonine-98) distinguishes it from B*3903.
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Affiliation(s)
- E Estefanía
- Servicio de Immunología, Hospital Universitario Puerta de Hierro, Madrid, Spain
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30
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Meenagh A, Williams F, Ross OA, Patterson C, Gorodezky C, Hammond M, Leheny WA, Middleton D. Frequency of cytokine polymorphisms in populations from western Europe, Africa, Asia, the Middle East and South America. Hum Immunol 2002; 63:1055-61. [PMID: 12392859 DOI: 10.1016/s0198-8859(02)00440-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PCR-SSOP identification procedures for IL-2, IL-6, IL-10, TNF-alpha and TNF-beta cytokine polymorphisms have been developed. Application of the procedures to a range of diverse geographically distributed populations has identified ethnic differences within the groups studied. Five populations were investigated, Northern Ireland, South African Zulu, Omani, Singapore Chinese and Mexican Mestizos.
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Affiliation(s)
- Ashley Meenagh
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast, Northern Ireland
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31
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Abstract
Natural killer (NK) cells have been known for a long time to be a very important component of the innate immune system. However, it is only during the last 10 years that knowledge of their receptors has emerged. Described in the present review are those receptor families killer inhibitory receptor (KIR) (belonging to the immunoglobulin superfamily), and killer lectin like receptor (KLR) CD94/NKG2, that both use HLA as a ligand and have inhibiting and activating types of receptors, and natural cytotoxic receptors (NCR) which do not associate with HLA. Association of the receptor gives rise to either an inhibiting or activating signal leading to either failure or success in lysing a target cell. The KIR receptors are very polymorphic both in the number of genes expressed in an individual and the alleles present for a gene. They would appear to have had a rapid evolution compared to the CD94/NKG2 receptors. The roles that NK cells and their receptors have with various facets of transplantation, disease, pregnancy and control of virus infection in humans are described.
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MESH Headings
- Animals
- Antigens, CD/immunology
- Autoimmune Diseases/immunology
- Chromosomes, Human, Pair 19/genetics
- Cytotoxicity, Immunologic
- Evolution, Molecular
- Female
- HLA Antigens/immunology
- Histocompatibility Antigens Class I/immunology
- Humans
- Killer Cells, Lymphokine-Activated/immunology
- Killer Cells, Natural/immunology
- Lectins, C-Type/immunology
- Ligands
- Lymphocyte Activation
- Mice
- Models, Molecular
- NK Cell Lectin-Like Receptor Subfamily C
- NK Cell Lectin-Like Receptor Subfamily D
- Pregnancy
- Protein Conformation
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Receptors, KIR
- Receptors, Natural Killer Cell
- Transplantation Immunology
- HLA-E Antigens
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Affiliation(s)
- Derek Middleton
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, Belfast City Hospital, Belfast, UK.
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32
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Williams F, Meenagh A, Patterson C, Middleton D. Molecular diversity of the HLA-C gene identified in a caucasian population. Hum Immunol 2002; 63:602-13. [PMID: 12072195 DOI: 10.1016/s0198-8859(02)00408-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A DNA typing procedure, based on a two stage polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing strategy, has been developed and applied to DNA from 1000 healthy individuals from the Northern Ireland region. The two-stage procedure involves human leukocyte antigen (HLA-C) identification through the use of a medium resolution PCR-SSOP system, followed by four secondary group specific PCR-SSOP systems, to enable allele resolution. The PCR-SSOP systems were designed for the identification of HLA-Cw alleles with possible discrimination within exons 2 and 3 of the HLA-C gene, i.e., HLA-Cw*01-Cw*16. PCR-SSP tests were designed for the resolution of HLA-Cw*17 and -Cw*18 alleles. The systems can also be used independently of each other if selective allele resolution is required. HLA-Cw allele frequencies occurring within the Northern Ireland population have been compiled, along with estimations of HLA-B/Cw haplotype frequencies.
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Affiliation(s)
- Fionnuala Williams
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Northern, Belfast, Ireland.
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33
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Cao K, Hollenbach J, Shi X, Shi W, Chopek M, Fernández-Viña MA. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum Immunol 2001; 62:1009-30. [PMID: 11543903 DOI: 10.1016/s0198-8859(01)00298-1] [Citation(s) in RCA: 357] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The HLA system is the most polymorphic of all human genetic systems. The frequency of HLA class I alleles and their linkage disequilibrium patterns differ significantly among human populations as shown in studies using serologic methods. Many DNA-defined alleles with identical serotypes may have variable frequencies in different populations. We typed HLA-A, B, and C loci at the allele level by PCR-based methods in 1,296 unrelated subjects from five major outbred groups living in the U.S.A (African, AFAM; Caucasians, CAU; Asian, ORI; Hispanic, HIS, and North American Natives, NAI). We detected 46, 100 and 32 HLA-A, B, and C alleles, respectively. ORI and HIS presented more alleles at each of these loci. There was lack of correlation between the levels of heterozygosity and the number of alleles detected in each population. In AFAM, heterozygosity (>90%) is maximized at all class I loci. HLA-A had the lowest heterozygosity in all populations but CAU. Tight LD was observed between HLA-B and C alleles. AFAM had weaker or nonexistent associations between alleles of HLA-A and B than other populations. Analysis of the genetic distances between these and other populations showed a close relationship between specific US populations and a population from their original continents. ORI exhibited the largest genetic distance with all the other U.S. groups and were closer to NAI. Evidence of admixture with CAU was observed for AFAM and HIS. HIS also had significant frequencies of AFAM and Mexican Indian alleles. Differences in both LD and heterozygosity levels suggest distinct evolutionary histories of the HLA loci in the geographical regions from where the U.S. populations originated.
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Affiliation(s)
- K Cao
- American Red Cross National Histocompatibility Laboratory, Baltimore, Maryland, USA
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34
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Williams F, Meenagh A, Darke C, Acosta A, Daar AS, Gorodezky C, Hammond M, Nascimento E, Middleton D. Analysis of the distribution of HLA-B alleles in populations from five continents. Hum Immunol 2001; 62:645-50. [PMID: 11390040 DOI: 10.1016/s0198-8859(01)00247-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A two stage PCR-SSOP typing procedure, that permitted HLA-B allele assignment, was applied to DNA samples obtained from six diverse populations -Brazilian, Mexican (Series and Mestizos), Cuban (Caucasoid and Mulatto), South African Zulu, Omani, and Singapore Chinese. HLA-B allele frequencies and HLA-A/B two locus haplotype frequencies were compiled for each population.
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Affiliation(s)
- F Williams
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast, Northern Ireland
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