Reviews in immunogenetics最新文献

The IMGT/HLA sequence database. IMGT/HLA序列数据库。

Reviews in immunogenetics Pub Date : 2000-01-01

J Robinson, S G Marsh

{"title":"The IMGT/HLA sequence database.","authors":"J Robinson, S G Marsh","doi":"","DOIUrl":"","url":null,"abstract":"The IMGT/HLA database (wwwebi.ac.uk/imgt/hla/) specialises in sequences of the polymorphic genes of the HLA system, the humanmajor histocompatibility complex (MHC). This complex is located within the 6p213 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes, which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis. These include allele reports, alignment tools, and detailed descriptions of the source cells. The online submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee. The latest version (release 1.10.0 April 2001) contains 1329 HLA alleles, 61 HLA related sequences, derived from around 3350 component sequences from the EMBL/ GenBank/DDBJ databases. The IMGT/HLA database provides a model that will be extended to provide specialist databases for polymorphic MHC genes of other species.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Approaches to managing volunteer marrow donor registry HLA data. Algorithms for directing donor center-initiated HLA-DR typing of selected donors. 管理志愿骨髓供者HLA数据的方法。指导供体中心发起的选定供体HLA-DR分型的算法。

Reviews in immunogenetics Pub Date : 2000-01-01

U Schuler, C Rutt, D Baier, J V Keller, A Stahr, A Grathwohl, G Ehninger

引用次数: 0

Natural killer cell recognition of HLA class I molecules. 自然杀伤细胞识别 HLA I 类分子。

Reviews in immunogenetics Pub Date : 2000-01-01

A G Brooks, J C Boyington, P D Sun

{"title":"Natural killer cell recognition of HLA class I molecules.","authors":"A G Brooks, J C Boyington, P D Sun","doi":"","DOIUrl":"","url":null,"abstract":"Human NK cells express multiple receptors that interact with HLA class I molecules. These receptors belong to one of two major protein superfamilies, the immunoglobulin superfamily or the C type lectin superfamily. The killer cell immunoglobulin-like receptor (KIR) family predominantly recognise classical HLA class I molecules and different family members interact with discrete HLA class I allotypes. The solution of the crystal structure of KIR2DL2 in complex with its ligand, HLA-Cw3 has provided the molecular details of a KIR/class I interaction. The interaction site spans both the alpha1 and alpha2 helices of class I and the KIR makes direct contact with peptide residues 7 and 8. The allotype specificity of KIR2DL2 for HLA-Cw3 is the result of a single hydrogen bond from Lys44 of the KIR to Asn80 of HLA-C as all other HLA-C residues that contact KIR are conserved. The lectin-like CD94/NKG2 receptors specifically interact with the non-classical class I molecule, HLA-E. Cell surface expression of HLA-E is dependent on the expression of other class I molecules as they are the major source of HLA-E binding peptides in normal cells. Consequently recognition of HLA-E by the CD94/NKG2 receptors allows NK cells to indirectly monitor the expression of a broad array of class I molecules. While the molecular interactions underlying ligand recognition by both KIR and CD94/NKG2 receptors are likely to be distinct, recognition of class I by both families of receptors appears peptide dependent. This suggest that cells that lack class I and also those that are impaired in their ability to load class I molecules with peptide will become targets for NK-mediated destruction.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138815477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Storage and utilization of HLA genomic data--new approaches to HLA typing. HLA基因组数据的存储和利用——HLA分型的新方法。

Reviews in immunogenetics Pub Date : 2000-01-01

W Helmberg

引用次数: 0

NCBI genetic resources supporting immunogenetic research. 支持免疫遗传学研究的NCBI遗传资源。

Reviews in immunogenetics Pub Date : 2000-01-01

M Feolo, W Helmberg, S Sherry, D R Maglott

{"title":"NCBI genetic resources supporting immunogenetic research.","authors":"M Feolo, W Helmberg, S Sherry, D R Maglott","doi":"","DOIUrl":"","url":null,"abstract":"The NCBI creates and maintains a set of integrated bibliographic, sequence, map, structure and other database resources to promote the efficient retrieval of information and the discovery of novel relationships. The connections made between elements of these resources permit researchers to start a search from a wide spectrum of entry points. These multiple dimensions of data can be roughly categorized by primary content as text or bibliographic (PubMed, PubMedCentral, OMIM, LocusLink), sequence (GenBank, Reference Sequence Project (RefSeq), dbSNP, MMDB), protein structure (MMDB) or map position (MapView). They can also becategorized by level of expert curation, which may range from validation of submissions from external groups (GenBank, PubMed, PubMedCentral,), to automatic computation (HomoloGene, UniGene), and to highly reviewed and corrected (LocusLink, MMDB, OMIM, RefSeq). Searches can be made by words (in an article title, key words, sequence annotation, database value, author) by sequence (BLAST or e-PCR against multiple sequence databases), or by map coordinates. By computing or curating bi-directional links between related objects, NCBI can represent content on the genetics, molecular biology, and clinical considerations of interest to immunogeneticists. There is also an emerging resource developed by the NCBI in collaboration with the IHWG devoted to the presentation of MHC data (dbMHC). How dbMHC will augment existing resources at the NCBI is described.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Data acquisition, data storage, and data presentation in a modern genetics laboratory. 现代遗传学实验室的数据采集、数据存储和数据呈现。

Reviews in immunogenetics Pub Date : 2000-01-01

D E Geraghty, S Fortelny, B Guthrie, M Irving, H Pham, R Wang, R Daza, B Nelson, J Stonehocker, L Williams, Q Vu

{"title":"Data acquisition, data storage, and data presentation in a modern genetics laboratory.","authors":"D E Geraghty, S Fortelny, B Guthrie, M Irving, H Pham, R Wang, R Daza, B Nelson, J Stonehocker, L Williams, Q Vu","doi":"","DOIUrl":"","url":null,"abstract":"Modern genetic analysis can be divided into three main areas of investigation. The first is data acquisition, in the form of genomic sequence and the cataloguing of polymorphism data of the single nucleotide polymorphism variety (so called SNPs). Once identified, such genetic information can be adapted into high throughput tests to examine genetic information in large populations, making the analysis of sufficiently large numbers both cost and time effective so that relatively low-penetrant genetic effects can be accurately detected. The third step is correlating variation with phenotype (e.g. disease susceptibility or resistance) for a variety of disorders is paramount in our motivation and indeed is a common goal of modern human genetic analysis. While the technology to acquire vast amounts of genetic data is now well established and continues to expand, the ability to deal with such data, from the process of acquisition, storage, and analysis depends fundamentally on a solid informatics infrastructure as an essential component. Indeed, most of the major gains in productivity in this field are to be realized on the informatics front, and involve automating data acquisition, defining and sorting data in databases for quality control and analysis and facilitating access to data for the large variety of data analyses. Informatics-related issues including those relating to data acquisition, database structure, and analysis tools are summarized here in an effort to define some of the issues relevant to establishing informatics infrastructure in a small genetics laboratory focused on resequencing human immune response genes. From inherited diseases to drug efficacy to the specific genetic changes occurring during tumor development, this new field of medical genetics promises a profound impact on the state of human health. Ultimately, any and all advances in this field will continue to depend on major investments in informatics.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.". 从基因组和蛋白质组学信息中鉴定细胞毒性T细胞表位:“人类MHC计划”。

Reviews in immunogenetics Pub Date : 2000-01-01

S L Lauemøller, C Kesmir, S L Corbet, A Fomsgaard, A Holm, M H Claesson, S Brunak, S Buus

{"title":"Identifying cytotoxic T cell epitopes from genomic and proteomic information: \"The human MHC project.\".","authors":"S L Lauemøller, C Kesmir, S L Corbet, A Fomsgaard, A Holm, M H Claesson, S Brunak, S Buus","doi":"","DOIUrl":"","url":null,"abstract":"Complete genomes of many species including pathogenic microorganisms are rapidly becoming available and with them the encoded proteins, or proteomes. Proteomes are extremely diverse and constitute unique imprints of the originating organisms allowing positive identification and accurate discrimination, even at the peptide level. It is not surprising that peptides are key targets of the immune system. It follows that proteomes can be translated into immunogens once it is known how the immune system generates and handles peptides. Recent advances have identified many of the basic principles involved. The single most selective event is that of peptide binding to MHC, making it particularly important to establish accurate descriptions and predictions of peptide binding for the most common MHC variants. These predictions should be integrated with those of other steps involved in antigen processing, as these become available. The ability to translate the accumulating primary sequence databases in terms of immune recognition should enable scientists and clinicians to analyze any protein of interest for the presence of potentially immunogenic epitopes. The computational tools to scan entire proteomes should also be developed, as this would enable a rational approach to vaccine development and immunotherapy. Thus, candidate vaccine epitopes might be predicted from the various microbial genome projects, tumor vaccine candidates from mRNA expression profiling of tumors (\"transcriptomes\") and auto-antigens from the human genome.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

B cell tolerance and autoimmunity. B细胞耐受性和自身免疫。

Reviews in immunogenetics Pub Date : 2000-01-01 DOI: 10.1201/9781482283723-9

T. Tsubata, T. Honjo

引用次数: 0

Maintaining updated DNA-based HLA assignments in the National Marrow Donor Program Bone Marrow Registry. 在国家骨髓捐献计划骨髓登记处保持更新的基于dna的HLA分配。

Reviews in immunogenetics Pub Date : 2000-01-01

M Maiers, C K Hurley, L Perlee, M Fernandez-Vina, J Baisch, D Cook, P Fraser, U Heine, S Hsu, M S Leffell, D Mauer, H Noreen, T Tang, M Trucco, S Y Yang, R J Hartzman, M Setterholm, T Winden, D Shepherd, J Hegland

{"title":"Maintaining updated DNA-based HLA assignments in the National Marrow Donor Program Bone Marrow Registry.","authors":"M Maiers, C K Hurley, L Perlee, M Fernandez-Vina, J Baisch, D Cook, P Fraser, U Heine, S Hsu, M S Leffell, D Mauer, H Noreen, T Tang, M Trucco, S Y Yang, R J Hartzman, M Setterholm, T Winden, D Shepherd, J Hegland","doi":"","DOIUrl":"","url":null,"abstract":"The National Marrow Donor Program (NMDP) has instituted an approach to address the impact of new alleles on the DNA-based HLA assignments obtained during volunteer donor typing. This approach was applied to the DRB typing results from 371,187 donors received from 14 laboratories in 1999. Samples were tested with a standardized set of sequence specific oligonucleotide reagents and the positive and negative hybridization results transmitted electronically to the NMDP. A software program interpreted the primary data into HLA assignments and rejected assignments which did not produce a result at the specified level of resolution. Comparison of the HLA assignments derived by the NMDP software to the assignments made by the laboratories using several local software prograins showed 90.5% of the assignments to be identical. Differences in assignments were explained by varying levels of typing resolution, variation in the inclusion of the second expressed DRB loci, disparity arising when alternative assignments were summarized, and failure to submit correct information. When the primary data collected in 1999 were interpreted into HLA assignments using the set of alleles defined in July 2000, 74% of the HLA-DRB assignments were altered by the description of new alleles, justifying the development of this software.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bioinformatics: analysis of HLA sequence data. 生物信息学:HLA序列数据分析。

Reviews in immunogenetics Pub Date : 2000-01-01

E H Rozemuller, M G Tilanus

{"title":"Bioinformatics: analysis of HLA sequence data.","authors":"E H Rozemuller, M G Tilanus","doi":"","DOIUrl":"","url":null,"abstract":"High resolution HLA typing is a requirement for the selection of matched donors in hematopoietic cell transplantation. The high resolution typing method that provides the most accurate and complete identification of HLA genotypes is sequencing-based typing (SBT). For each sample being tested, SBT defines the exact nucleotide sequence of the coding regions of both alleles at a given HLA locus. Identification of the underlying genotype of the sample can then be made by computerized sequence comparison with all possible HLA allele combinations at that locus. The use of SBT to identify the complete nucleotide sequence of a given HLA gene also enables the direct detection of previously undefined alleles. Since different HLA alleles may differ by a single nucleotide, the accurate assignment of an HLA genotype by SBT is absolutely dependent on the correct identification of the nucleotide at each position for a given sample. However, automated sequence analysis of heterozygous samples may result in the ambiguous assignment of nucleotides at a given position. In addition, ambiguous assignments may result from the sequencing of two different samples that express different HLA alleles but whose sequence profiles appear exactly the same. Both of these ambiguous situations can be resolved by the application of the multi-sequence analysis (MSA) method described here.","PeriodicalId":82484,"journal":{"name":"Reviews in immunogenetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22049257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0