- Email: [email protected]
123-P The IPD-MHC NHP database: New nomenclature for the non-human primate MHC alleles
S100
Abstracts
123-P
THE IPD-MHC NHP DATABASE: NEW NOMENCLATURE FOR THE NON-HUMAN PRIMATE MHC ALLELES. Natasja G. de Groot,1 Nel Otting,1 James Robinson,2 Steven G.E. Marsh,2 Ronald E. Bontrop.1 1 Comparative Gentics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands; 2Royal Free Hospital, Anthony Nolan Research Institute, London, United Kingdom. Aim: The IPD-MHC NHP database (www.ebi.ac.uk/ipd/mhc/nhp) is a specialized database for the major histocompatibility complex (MHC) genes of non-human primates (NHP). It is part of the Immuno Polymorphism database (IPD) that comprises data from sources related to the study of polymorphic genes in the immune system. The NHP-database covers Apes, Old and New World monkeys, and comprises at present approximately 3600 sequences of 42 different species. The first version was released online in March 2002. In April 2010 the WHO Nomenclature Committee for the Factors of the HLA system launched a new nomenclature protocol. For the designation of the NHP MHC alleles we aimed to follow these rules. Besides we aimed to revise the macaque MHC class I nomenclature. Methods: Phylogenetic and sequence comparison of the different macaque MHC class I alleles were used to adapt the nomenclature. Results: The new nomenclature protocol for the NHP MHC alleles comprises the incorporation of colons in the designations of the alleles. This update is incorporated in the database-release from November 2010. In addition this release includes the streamlining of the designations of the macaque MHC class I alleles in which the rhesus macaque lineage numbers were taken as consensus. Conclusions: The more consistent macaque allele designations and the adaptation of the NHP-MHC nomenclature to the WHO defined nomenclature rules strengthen the quality of the IPD-MHC NHP database and provides the investigators in the field of biomedical, evolution and conservation research a convenient platform to compare NHP-MHC data with the HLA-database.
124-P
HLA-E IN THE BRAZILIAN POPULATION: DIVERSITY OF CODING REGION AND NEW VARIATION SITES. Luciana C. Veiga-Castelli,1 Erick C. Castelli,2 Celso T. Mendes, Jr,3 Wilson A. Silva, Jr,4 Marie-Claude Faucher,5 Karine Beauchemin,5 Michel Roger,5 Phillipe Moreau,6 Eduardo A. Donadi.1 1 Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; 2Laboratório de Genética Molecular e Citogenética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, University of Goias, Goiânia, Goias, Brazil; 3 Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; 4Departamento de Genética, Faculdade de Medicina de Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil; 5Départment de Microbiologie et Immunologie, Centre Hospitalier de L’Université de Montréal, Université de Montréal, Montreal, QC, Canada; 6 Commissariat à l’EnergieAtomique/DSV/I2BM/Service de Recherches en Hémato-Immunologie, IUH, Hôpital Saint-Louis, Paris, France. Aim: The non-classical HLA class I genes HLA-E, HLA-F and HLA-G present very low rate of variation. So far, only ten HLA-E coding alleles encoding three different proteins have been described (E*01:01, *01:03 and *01:04), but only the first two are frequently found in worldwide population. Due to its historical admixed background, Brazilians are very suitable for population genetics studies. We aimed to evaluate the HLA-E sequence searching for variation and assessing the haplotype structure of this region. Methods: A hundred and four blood marrow donors from Southeast Brazil were evaluated for HLA-E exons 1 to 4 segment by polymerase chain reaction (PCR) methodology resulting in a 2041-bp product. HLAE variation was evaluated by direct sequencing of PCR products. Results: Sevenvariation sites were found, including two previously recognized SNPs at positions ⫹424 (codon 77) and ⫹756 (codon 107) and five new SNPs at positions ⫹170 (intron 1), ⫹1294 (intron 3) and positions ⫹1625, ⫹1645 and ⫹1857 (exon 4). Of those, only 3 reached polymorphic frequencies (⫹424, ⫹756 and ⫹1645) and one was close to reach such frequency (⫹1857). Three previously described variation sites were not found in the present series (positions ⫹887, ⫹906 and ⫹1691). Haplotyping analysis did reveal 8 different haplotypes, 3 of them known as E*01:01:01, E*01:03:01 and E*01:03:02:01. The five remaining haplotypes were in fact new alleles, each one carrying one of the new variation sites. The HLA-E*01:01:01 allele was the predominant haplotype (62.50%), followed by E*01:03:02:01 (24.52%) and E*01:03:01 (9.13%). Conclusions: Although few studies have evaluated the variability of the HLA-E locus, the low HLA-E variability found in worldwide populations is a consistent data. In conclusion, even in an admixed population such Brazilians, the HLA-E locus is very conserved presenting few polymorphic SNPs in the coding region.
Abstracts
123-P
THE IPD-MHC NHP DATABASE: NEW NOMENCLATURE FOR THE NON-HUMAN PRIMATE MHC ALLELES. Natasja G. de Groot,1 Nel Otting,1 James Robinson,2 Steven G.E. Marsh,2 Ronald E. Bontrop.1 1 Comparative Gentics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands; 2Royal Free Hospital, Anthony Nolan Research Institute, London, United Kingdom. Aim: The IPD-MHC NHP database (www.ebi.ac.uk/ipd/mhc/nhp) is a specialized database for the major histocompatibility complex (MHC) genes of non-human primates (NHP). It is part of the Immuno Polymorphism database (IPD) that comprises data from sources related to the study of polymorphic genes in the immune system. The NHP-database covers Apes, Old and New World monkeys, and comprises at present approximately 3600 sequences of 42 different species. The first version was released online in March 2002. In April 2010 the WHO Nomenclature Committee for the Factors of the HLA system launched a new nomenclature protocol. For the designation of the NHP MHC alleles we aimed to follow these rules. Besides we aimed to revise the macaque MHC class I nomenclature. Methods: Phylogenetic and sequence comparison of the different macaque MHC class I alleles were used to adapt the nomenclature. Results: The new nomenclature protocol for the NHP MHC alleles comprises the incorporation of colons in the designations of the alleles. This update is incorporated in the database-release from November 2010. In addition this release includes the streamlining of the designations of the macaque MHC class I alleles in which the rhesus macaque lineage numbers were taken as consensus. Conclusions: The more consistent macaque allele designations and the adaptation of the NHP-MHC nomenclature to the WHO defined nomenclature rules strengthen the quality of the IPD-MHC NHP database and provides the investigators in the field of biomedical, evolution and conservation research a convenient platform to compare NHP-MHC data with the HLA-database.
124-P
HLA-E IN THE BRAZILIAN POPULATION: DIVERSITY OF CODING REGION AND NEW VARIATION SITES. Luciana C. Veiga-Castelli,1 Erick C. Castelli,2 Celso T. Mendes, Jr,3 Wilson A. Silva, Jr,4 Marie-Claude Faucher,5 Karine Beauchemin,5 Michel Roger,5 Phillipe Moreau,6 Eduardo A. Donadi.1 1 Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; 2Laboratório de Genética Molecular e Citogenética, Departamento de Biologia Geral, Instituto de Ciências Biológicas, University of Goias, Goiânia, Goias, Brazil; 3 Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil; 4Departamento de Genética, Faculdade de Medicina de Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil; 5Départment de Microbiologie et Immunologie, Centre Hospitalier de L’Université de Montréal, Université de Montréal, Montreal, QC, Canada; 6 Commissariat à l’EnergieAtomique/DSV/I2BM/Service de Recherches en Hémato-Immunologie, IUH, Hôpital Saint-Louis, Paris, France. Aim: The non-classical HLA class I genes HLA-E, HLA-F and HLA-G present very low rate of variation. So far, only ten HLA-E coding alleles encoding three different proteins have been described (E*01:01, *01:03 and *01:04), but only the first two are frequently found in worldwide population. Due to its historical admixed background, Brazilians are very suitable for population genetics studies. We aimed to evaluate the HLA-E sequence searching for variation and assessing the haplotype structure of this region. Methods: A hundred and four blood marrow donors from Southeast Brazil were evaluated for HLA-E exons 1 to 4 segment by polymerase chain reaction (PCR) methodology resulting in a 2041-bp product. HLAE variation was evaluated by direct sequencing of PCR products. Results: Sevenvariation sites were found, including two previously recognized SNPs at positions ⫹424 (codon 77) and ⫹756 (codon 107) and five new SNPs at positions ⫹170 (intron 1), ⫹1294 (intron 3) and positions ⫹1625, ⫹1645 and ⫹1857 (exon 4). Of those, only 3 reached polymorphic frequencies (⫹424, ⫹756 and ⫹1645) and one was close to reach such frequency (⫹1857). Three previously described variation sites were not found in the present series (positions ⫹887, ⫹906 and ⫹1691). Haplotyping analysis did reveal 8 different haplotypes, 3 of them known as E*01:01:01, E*01:03:01 and E*01:03:02:01. The five remaining haplotypes were in fact new alleles, each one carrying one of the new variation sites. The HLA-E*01:01:01 allele was the predominant haplotype (62.50%), followed by E*01:03:02:01 (24.52%) and E*01:03:01 (9.13%). Conclusions: Although few studies have evaluated the variability of the HLA-E locus, the low HLA-E variability found in worldwide populations is a consistent data. In conclusion, even in an admixed population such Brazilians, the HLA-E locus is very conserved presenting few polymorphic SNPs in the coding region.