1
|
Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
Collapse
Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
| |
Collapse
|
2
|
Arnaiz-Villena A, Juarez I, Palacio-Gruber J, Muñiz E, Campos C, Martinez-Laso J, Nieto J, Lopez-Nares A, Martin-Villa JM, Silvera C. The first free Africans in America: HLA study in San Basilio de Palenque (Colombia). Hum Immunol 2018; 79:585-586. [PMID: 29864459 DOI: 10.1016/j.humimm.2018.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 11/18/2022]
Abstract
Original San Basilio de Palenque population (North Colombia) fled from Spanish traders that carried them as slaves and they funded in nearby Maria Mountains a fortified town (Palenque). They started helping new Africans brought as slaves to flee and join them. Most of them spoke a Bantu-Congo language and nowadays they speak the only one extant Bantu-Spanish Creole language. Spanish Crown was forced to issue a decree declaring them free (1691 CE), more than 100 years before than Haiti Republic existed. HLA-A, -B, -DRB1 and -DQB1 alleles were studied and further computer procedures were performed with Arlequin 3.5 software. No Amerindian or Europeans gene flow to this population was found. However, three specific HLA extended haplotypes are found in this population, which may reflect an isolation from other Africans or Afro-Americans also. This may be due to the maintenance of their own African culture, and even their unique Creole language.
Collapse
Affiliation(s)
- Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain.
| | - Ignacio Juarez
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Jose Palacio-Gruber
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Ester Muñiz
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Cristina Campos
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Jorge Martinez-Laso
- Complejo Hospitalario Universitario Insular, Immunology, Las Palmas, Canary Is, Spain
| | - Jorge Nieto
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Adrian Lopez-Nares
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Jose Manuel Martin-Villa
- Department of Immunology, University Complutense, Medical School, The Madrid Regional Blood Ctr, Madrid, Spain
| | - Carlos Silvera
- Department of Medicina, Ciencias de la Salud, Universidad del Norte, Barranquilla, Colombia
| |
Collapse
|
3
|
|
4
|
Iorio A, De Angelis F, Garzoli A, Battistini A, De Stefano GF. HLA-DQA1 and HLA-DQB1 genes in Tsachilas Indians from Ecuador: new insights in population analysis by Human Leukocyte Antigens. Int J Immunogenet 2014; 41:222-30. [DOI: 10.1111/iji.12116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/11/2014] [Accepted: 02/23/2014] [Indexed: 11/29/2022]
Affiliation(s)
- A. Iorio
- Department of Biology; University of Rome Tor Vergata; Rome Italy
- Clinical Pathophysiology Center; AFaR, “San Giovanni Calibita” Fatebenefratelli Hospital; Rome Italy
| | - F. De Angelis
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - A. Garzoli
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - A. Battistini
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - G. F. De Stefano
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- S J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Yunis JJ, Yunis EJ, Yunis E. MHC Class II haplotypes of Colombian Amerindian tribes. Genet Mol Biol 2013; 36:158-66. [PMID: 23885196 PMCID: PMC3715280 DOI: 10.1590/s1415-47572013005000014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 01/29/2013] [Indexed: 11/21/2022] Open
Abstract
We analyzed 1041 individuals belonging to 17 Amerindian tribes of Colombia, Chimila, Bari and Tunebo (Chibcha linguistic family), Embera, Waunana (Choco linguistic family), Puinave and Nukak (Maku-Puinave linguistic families), Cubeo, Guanano, Tucano, Desano and Piratapuyo (Tukano linguistic family), Guahibo and Guayabero (Guayabero Linguistic Family), Curripaco and Piapoco (Arawak linguistic family) and Yucpa (Karib linguistic family). for MHC class II haplotypes (HLA-DRB1, DQA1, DQB1). Approximately 90% of the MHC class II haplotypes found among these tribes are haplotypes frequently encountered in other Amerindian tribes. Nonetheless, striking differences were observed among Chibcha and non-Chibcha speaking tribes. The DRB1*04:04, DRB1*04:11, DRB1*09:01 carrying haplotypes were frequently found among non-Chibcha speaking tribes, while the DRB1*04:07 haplotype showed significant frequencies among Chibcha speaking tribes, and only marginal frequencies among non-Chibcha speaking tribes. Our results suggest that the differences in MHC class II haplotype frequency found among Chibcha and non-Chibcha speaking tribes could be due to genetic differentiation in Mesoamerica of the ancestral Amerindian population into Chibcha and non-Chibcha speaking populations before they entered into South America.
Collapse
Affiliation(s)
- Juan J Yunis
- Departamento de Patología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia . ; Grupo de Identificación Humana e Inmunogenética, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia . ; Instituto de Genética, Servicios Médicos Yunis Turbay y Cia, Bogotá, Colombia
| | | | | |
Collapse
|
7
|
Black patients of African descent and HLA-DRB1*15:03 frequency overrepresented in epidermolysis bullosa acquisita. J Invest Dermatol 2011; 131:2386-93. [PMID: 21833018 DOI: 10.1038/jid.2011.231] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Epidermolysis bullosa acquisita (EBA) is a rare autoimmune bullous disease (AIBD). However, higher EBA incidence and predisposing genetic factor(s) involving an HLA haplotype have been suspected in some populations. This retrospective study assessed the overrepresentation of black patients with EBA, its link with HLA-DRB1*15:03, and their clinical and immunological characteristics. Between 2005 and 2009, 7/13 (54%) EBA and 6/183 (3%) other-AIBD patients seen consecutively in our department were black (P=10(-6)); moreover 7/13 (54%) black patients and 6/183 (3%) white patients had EBA (P=10(-6)). In addition, between 1983 and 2005, 12 black patients had EBA. Finally, among the 19 black EBA patients, most of them had very atypical clinical presentations, 9 were natives of sub-Saharan Africa, 1 from Reunion Island, 7 from the West Indies, and 2 were of mixed ancestry. HLA-DRB1*15:03 allelic frequencies were 50% for African patients, significantly higher than the control population (P<10(-3)), and 21% for the West Indians (nonsignificant). High EBA frequencies have already been reported in American blacks significantly associated with the HLA-DR2. In conclusion, black-skinned patients developing EBA seem to have a genetic predisposition, and EBA should be suspected systematically for every AIBD seen in this population.
Collapse
|
8
|
Silvera C, Vargas-Alarcon G, Areces C, Rey D, Parga-Lozano C, Gomez-Prieto P, Barbolla L, Martinez-Laso J, Arnaiz-Villena A. HLA genes in Wayu Amerindians from Colombia. Immunol Invest 2010; 40:92-100. [PMID: 20923327 DOI: 10.3109/08820139.2010.517390] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Amerindians origins and prehistory are still debated. HLA profile is different to all other World populations, although they have particular alleles in common with Asians, Australians and Pacific Islanders. In the present work, HLA-A, -B, -DRB1, -DQB1 alleles have been studied in Wayu Amerindians from Colombia. HLA alleles haplotypes, genetic distances and NJ dendrograms were calculated by Arlequin and DISPAN software. Only a few both class I and class II alleles have been observed. Most common extended haplotypes include: A*24-B*51-DRB1*0403-DQB1*0302, A*2-B*15-DRB1*1602-DQB1*0301, A*2-B*35-DRB1*0407-DQB1*0302, but also A*68-B*15-DRB1*0403-DQB1*0302. No trace of Caucasoid or Negroid admixture is detected. The Wayu HLA profile is typical from Amerindians and shows how languages and genes do not correlated particularly in this case (i.e., Wayu closest HLA genetic group is North Argentinian Guarani group). Results obtained in this work may be useful for future transplant programs and also for HLA linked diseases and individualized pharmacogenetics.
Collapse
Affiliation(s)
- Carlos Silvera
- Department of Genetics, Universidad del Norte, Barranquilla, Colombia
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Maria L Parolín
- Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Facultad de Filosofía y Letras, Universidad de Buenos Aires, Buenos Aires Argentina
| | | |
Collapse
|
10
|
Frecuencias alélicas, genotípicas y haplotípicas HLA-A, HLA-B, HLA-DRB1 en donantes fallecidos, Medellín, Colombia. BIOMEDICA 2007. [DOI: 10.7705/biomedica.v27i4.172] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Alves-Leon SV, Papais-Alvarenga R, Magalhães M, Alvarenga M, Thuler LCS, Fernández y Fernandez O. Ethnicity-dependent association of HLA DRB1-DQA1-DQB1 alleles in Brazilian multiple sclerosis patients. Acta Neurol Scand 2007; 115:306-11. [PMID: 17489940 DOI: 10.1111/j.1600-0404.2006.00750.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The present study focused on human leukocyte antigen (HLA) DQB1, DQA1 and DRB1 allelic variation according to ethnicity and analyzed whether susceptibility to multiple sclerosis (MS) depends on population characteristics. METHODS Eighty-eight healthy African-Brazilians and 92 healthy white Brazilians living in Rio de Janeiro City were selected and the HLA phenotype between the two ethnic groups was compared with 44 MS patients of African descent and 40 patients of European descent. HLA class II genes were performed using polymerase chain reaction (PCR) and PCR-sequence-specific primer amplification. RESULTS DQA1*0201-0301 alleles were associated with the white Brazilian population (P < 0.001). The DRB*1501 allele was present in White Brazilians (P=0.003), and DRB1*03-1503 in African-Brazilians. The DRB1*1501 allele confers an ethnicity-dependent MS susceptibility in White patients and the DQB1*0602 allele confers genetic susceptibility regardless of ethnicity. CONCLUSION Heterogeneous phenotypes occur in both Brazilian ethnic groups. Taking into account that the response to immunomodulator drugs for MS treatment changes according to the DRB1*1501 allele and African-American MS patients presented poor response to the interferons, phenotype heterogeneity of HLA loci found in this study could influence therapeutic decisions in the Brazilian MS population.
Collapse
Affiliation(s)
- S V Alves-Leon
- Neurology Department, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, Brazil.
| | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Pedro Cano
- University of Texas M. D. Anderson Cancer Center, HLA Typing Laboratory, Houston, Texas 77054, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Suárez A, Valbuena MC, Rey M, de Porras Quintana L. Association of HLA subtype DRB1*0407 in Colombian patients with actinic prurigo. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2006; 22:55-8. [PMID: 16606409 DOI: 10.1111/j.1600-0781.2006.00205.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Human leukocyte antigen (HLA) DRB1*0407 had been associated with actinic prurigo in different populations. This class II HLA-DR subtype had not been studied in Colombia. OBJECTIVE The objective of this study was to establish whether there was an association of actinic prurigo with HLA DR in a Colombian population. MATERIALS AND METHODS Forty patients with a clinical diagnosis of actinic prurigo and 40 healthy subjects, paired by age, sex and birthplace, were studied. HLA typing for HLA DRB1 and DRB1*04, if necessary, was performed by the PCR-SSP method using blood samples. RESULTS A high frequency of HLA DRB1*0407 was found in the patients (97.5% vs. 30%; P<0.00001). The allelic frequency of HLA DRB1*0407 was 63.8% in the case group, and 14.5% in the controls (P<0.00001). In the control group, there was a higher frequency of the alleles DRB1*01 (14.5% vs. 1.25%; P=0.0027) and DRB1*13 (23.7% vs. 2.5%; P=0.00013). LIMITATIONS The small number of controls does not allow us to drive conclusions about other HLA alleles. CONCLUSIONS HLA subtype DRB1*0407, found in actinic prurigo patients in studies conducted in England, Scotland, Ireland and Mexico, was also associated in Colombian patients. This finding, concordant in patients from different ethnic groups, could be helpful in the diagnosis of this disease and probably important in its pathogenesis. DRB1*01 and DRB1*13 alleles were more frequent in controls than in patients; we do not know whether they play any role in the resistance to the disease.
Collapse
Affiliation(s)
- Alfonso Suárez
- Centro Dermatológico Federico Lleras Acosta, E.S.E. Bogota, Colombia
| | | | | | | |
Collapse
|
14
|
Wong RC, Steele RH, Reeves GE, Wilson RJ, Pink A, Adelstein S. Antibody and genetic testing in coeliac disease. Pathology 2003. [DOI: 10.1080/0031302031000150542] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
15
|
Carrington CVF, Kondeatis E, Ramdath DD, Norman PJ, Vaughan RW, Stephens HAF. A comparison of HLA-DR and -DQ allele and haplotype frequencies in Trinidadian populations of African, South Asian, and mixed ancestry. Hum Immunol 2002; 63:1045-54. [PMID: 12392858 DOI: 10.1016/s0198-8859(02)00437-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Using polymerase chain reaction-sequence-specific primer (PCR-SSP) typing, this study determined the frequency of human leukocyte antigen (HLA) DR- and -DQ alleles and haplotypes in individuals of African (n = 75), South Asian (n = 98), and mixed (n = 102) ancestry from the Caribbean island of Trinidad. We detected 19 different haplotypes containing DRB3, 8 containing DRB4, 6 containing DRB5, and 6 different haplotypes without DRB3/4/5 genes. Twenty-nine haplotypes were identified in Africans, 24 in the South Asians, and 32 in the mixed group. We detected significant differences between the populations, principally at the DQA1 and DQB1 loci, although the allele frequency for DRB1*0901 was highest in the Africans (p(c) < 0.05). Trinidad African and mixed groups were generally more diverse than the South Asians and displayed a wider range of DRB1-DQB1 associations; DQB1*02 and DQB1*0301 each associated with five to six different DRB1 alleles in the Africans and mixed group but only two in South Asians. In the Africans and the mixed group, DQB1*04 was found with DRB1*0302 and DRB1*04, but only with DRB1*08 in the South Asians. Trinidad Africans revealed consistencies with populations in Western, Central, and Northern Africa, but differed considerably from individual populations on the African continent. Trinidad South Asians displayed similar allele frequencies and associations to other populations from Northern India.
Collapse
Affiliation(s)
- Christine V F Carrington
- Department of Pre-Clinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad.
| | | | | | | | | | | |
Collapse
|
16
|
Abstract
A review was made in relation to the molecular variability present in North, Central, and South American Indian populations. It involved results from ancient DNA, mitochondrial DNA in extant populations, HLA and other autosomal markers, X and Y chromosome variation, as well as data from parasitic viruses which could show coevolutionary changes. The questions considered were their origin, ways in which the early colonization of the continent took place, types and levels of the variability which developed, peculiarities of the Amerindian evolutionary processes, and eventual genetic heterogeneity which evolved in different geographical areas. Although much information is already available, it is highly heterogeneous in relation to populations and types of genetic systems investigated. Unfortunately, the present trend of favoring essentially applied research suggest that the situation will not basically improve in the future.
Collapse
Affiliation(s)
- Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS.
| |
Collapse
|
17
|
Benitez O, Loiseau P, Busson M, Dehay C, Hors J, Calvo F, Durand Mura M, Charron D. Hispano-Indian admixture in Paraguay studied by analysis of HLA-DRB1 polymorphism. PATHOLOGIE-BIOLOGIE 2002; 50:25-9. [PMID: 11873625 DOI: 10.1016/s0369-8114(01)00263-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic polymorphism of the Paraguayan population results from the admixture between South American Indians named Guaranis and Spaniards. In order to evaluate the genetic predominance in the Paraguayan population, we typed 50 healthy Paraguayans for HLA-DRB1 by molecular biology and compared their HLA-DRB1 polymorphism to that of the Guaranis and of two Spanish populations. Six significant differences of alleles frequencies were observed between Paraguayans and Guaranis--DRB1*01, 06 (13, 14), 15, 16, 07--whereas only one difference was observed with the Spaniards (DRB1*14). The DRB1*14 frequency was higher in Paraguayan than in the Spanish populations essentially due to the presence of DRB1*1402 related alleles (1402,06,13). These alleles are extremely rare in the Spanish populations whereas frequent in the Guaranis from Brazil and in South American Indian tribes living in the lymitrophe regions of Paraguay (Toba, Wichi and Terena). Thus, the presence of the DRB1*1402 related alleles (6%) in the Paraguayan population constitutes the major Indian contribution to the HLA-DR polymorphism of the Paraguayan population. The genetic distances between Paraguayans and the two Spanish populations were closer (.494 and .415) than that between Paraguayans and Guaranis (.958). Altogether these results suggest the predominance of the Spanish genetic in the Paraguayan population. Historical events are discussed to explain this predominance.
Collapse
Affiliation(s)
- O Benitez
- Laboratoire d'histocompatibilité, hôpital Saint-Louis, 1, avenue Claude Vellefeaux, 75475 Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Chen JJ, Hollenbach JA, Trachtenberg EA, Just JJ, Carrington M, Rønningen KS, Begovich A, King MC, McWeeney S, Mack SJ, Erlich HA, Thomson G. Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups. TISSUE ANTIGENS 1999; 54:533-42. [PMID: 10674966 DOI: 10.1034/j.1399-0039.1999.540601.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Testing the fit of population data to Hardy-Weinberg proportions is crucial in the validation of many current approaches in population genetic studies. In this paper, we tested fit to Hardy-Weinberg proportions using exact approaches for both the overall and individual heterozygote genotype data of four HLA Class II loci: DRB1, DQA1, DQB1, and DPB1, from 26 human populations. Eighty of 99 overall tests fit the Hardy-Weinberg expectation (73% for DRB1, 89% for DQA1, 81% for DQB1 and 81% for DPB1). Deviations from Hardy-Weinberg proportions were both locus and group specific. Although we could not rule out other mechanisms at work, the individual test results indicated that the departure was possibly partly due to recent admixture. Evidence for selection and other sources of deviation are also discussed.
Collapse
Affiliation(s)
- J J Chen
- School of Public Health, Saint Louis University, Missouri 63108, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Fleischhauer K, Agostino A, Zino E, Mazzi B, Benazzi E, Arevalo-Herrera M, Herrera S, Bordignon C, Romero P. Molecular characterization of HLA class I in Colombians carrying HLA-A2: high allelic diversity and frequency of heterozygotes at the HLA-B locus. TISSUE ANTIGENS 1999; 53:519-26. [PMID: 10395101 DOI: 10.1034/j.1399-0039.1999.530601.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP) typing was used to analyze HLA class I A, B and C alleles in three different Colombian populations. Fifty-nine samples were from Hispano-American Mestizos living in the urban areas of Cali (referred to here as Aso population). Forty-four and thirty samples were from the African Black populations of Zacarias (Zac) and Punta Soldado (PS), respectively. Samples were selected for expression of HLA-A2 by monoclonal antibody staining and allele-specific hybridization, and their HLA-A2 subtype distribution has been reported previously. Although only a limited number of samples was analyzed, the data suggest the existence of a remarkable degree of HLA class I polymorphism in the populations studied, with representatives of most serological classes. Despite their common African origin, the populations Zac and PS, both resident in malaria endemic regions, showed some striking differences in allelic distribution for all three class I loci. Furthermore, the samples from Aso and PS, but not Zac, showed a low percentage of blank alleles at the HLA-B locus (0 and 0.4%, respectively), suggesting the possibility of a heterozygote advantage for HLA-B alleles in Colombian populations.
Collapse
Affiliation(s)
- K Fleischhauer
- Tissue Typing Laboratory, Istituto Scientifico H.S. Raffaele, Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Mullighan CG, Bunce M, Welsh KI. High-resolution HLA-DQB1 typing using the polymerase chain reaction and sequence-specific primers. TISSUE ANTIGENS 1997; 50:688-92. [PMID: 9458131 DOI: 10.1111/j.1399-0039.1997.tb02936.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Polymorphism at HLA-DQB1 is known to influence tissue compatibility and disease susceptibility; however, current DQB1 typing methods are unable to distinguish the 32 currently recognized DQB1 alleles. We have developed a 32-reaction PCR-SSP method capable of differentiating all DQB1 alleles that differ in amino acid sequence. This method can resolve all heterozygous combinations of DQB1 alleles, with the exception of several combinations involving alleles not thus far detected in Caucasoid populations.
Collapse
Affiliation(s)
- C G Mullighan
- Oxford Transplant Centre, Nuffield Department of Surgery, Churchill Hospital, United Kingdom.
| | | | | |
Collapse
|
21
|
Bodmer JG, Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Charron D, Dupont B, Erlich HA, Fauchet R, Mach B, Mayr WR, Parham P, Sasazuki T, Schreuder GMT, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for Factors of the HLA System, 1996. Vox Sang 1997. [DOI: 10.1046/j.1423-0410.1997.7320105.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
22
|
Dufossé F, Guignier F, Cracco P, Becuwe D, Huart JJ. A novel HLA DRB1 allele (DRB1*0309). TISSUE ANTIGENS 1997; 49:523-5. [PMID: 9174149 DOI: 10.1111/j.1399-0039.1997.tb02791.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- F Dufossé
- Laboratoire d'Histocompatibilité, Etablissement de Transfusion Sanguine, Lille, France
| | | | | | | | | |
Collapse
|
23
|
Bodmer JG, Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Charron D, Dupont B, Erlich HA, Fauchet R, Mach B, Mayr WR, Parham P, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA System, 1996. Hum Immunol 1997; 53:98-128. [PMID: 9127153 DOI: 10.1016/s0198-8859(97)00031-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J G Bodmer
- ICRF Cancer and Immunogenetics Laboratory, Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Bodmer JG, Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Charron D, Dupont B, Erlich HA, Fauchet R, Mach B, Mayr WR, Parham P, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 1996. TISSUE ANTIGENS 1997; 49:297-321. [PMID: 9098945 DOI: 10.1111/j.1399-0039.1997.tb02759.x] [Citation(s) in RCA: 257] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J G Bodmer
- ICRF Cancer and Immunogenetics Laboratory, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
|