ABSTRACT
A review of the British Society for Histocompatibility and Immunogenetics (BSHI) "Guideline for selection and HLA matching of related, adult unrelated donors and umbilical cord units for haematopoietic progenitor cell transplantation" was undertaken by a BSHI appointed writing committee. Literature searches were performed, and the data extracted were presented as recommendations according to the GRADE nomenclature.
Subject(s)
HLA Antigens/immunology , Hematopoietic Stem Cell Transplantation/methods , Histocompatibility Testing/methods , Immunogenetics/methods , Adult , Donor Selection , Fetal Blood , HLA Antigens/genetics , Humans , Tissue DonorsABSTRACT
The new HLA-A*02:06:01:02 allele differs from HLA-A*02:06:01 by a CâG substitution in Intron 1.
Subject(s)
Genes, MHC Class II , HLA-A2 Antigen/isolation & purification , Alleles , Base Sequence , HLA-A2 Antigen/genetics , Histocompatibility Testing , Humans , Molecular Sequence Data , Real-Time Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology, Nucleic AcidABSTRACT
The genomic sequence of the novel HLA-B*44:220 allele identified in a British Caucasoid male.
Subject(s)
Alleles , Amino Acid Substitution , HLA-B44 Antigen/genetics , Polymorphism, Single Nucleotide , Base Sequence , Codon , Exons , Gene Expression , HLA-B44 Antigen/immunology , Histocompatibility Testing , Humans , Male , Molecular Sequence Data , Sequence Alignment , United Kingdom , White PeopleABSTRACT
Genomic sequencing of HLA-A*30:02:01:03, an intronic variant, and HLA-C*08:113, an exonic variant.
Subject(s)
Alleles , HLA-A Antigens/genetics , HLA-C Antigens/genetics , Mutation , Registries , Amino Acid Substitution , Base Sequence , Bone Marrow Transplantation , Exons , Genotype , HLA-A Antigens/immunology , HLA-C Antigens/immunology , Histocompatibility Testing , Humans , Introns , Molecular Sequence Data , Polymerase Chain Reaction , Sequence Alignment , Sequence Analysis, DNA , South Africa , Tissue DonorsABSTRACT
Genomic sequence of HLA-A*02:95 identified in an Anthony Nolan volunteer donor.
Subject(s)
Alleles , Exons/genetics , HLA-A Antigens/genetics , Base Sequence , Cloning, Molecular , Genome , Histocompatibility Testing , Humans , Molecular Sequence Data , Mutation/genetics , Sequence Analysis, DNA , United KingdomABSTRACT
The new HLA-A*74:23 allele differs from the closest allele A*74:01 by a nucleotide change in exon 3 at codon 97.
Subject(s)
Alleles , HLA-A Antigens/genetics , Costa Rica , Humans , MaleABSTRACT
Theory indicates that landscape composition affects transmission of vector-borne crop diseases, but few empirical studies have investigated how landscape composition affects plant disease epidemiology. Since 2006, Bemisia tabaci (Gennadius) has vectored the cucurbit yellow stunting disorder virus (CYSDV) to cantaloupe and honeydew melons (Cucumis melo L.) in the southwestern United States and northern Mexico, causing significant reductions in yield of fall melons and increased use of insecticides. Here, we show that a landscape-based approach allowing simultaneous assessment of impacts of local (i.e., planting date) and regional (i.e., landscape composition) factors provides valuable insights on how to reduce crop disease risks. Specifically, we found that planting fall melon fields early in the growing season, eliminating plants germinating from seeds produced by spring melons after harvest, and planting fall melon fields away from cotton and spring melon fields may significantly reduce the incidence of CYSDV infection in fall melons. Because the largest scale of significance of the positive association between abundance of cotton and spring melon fields and CYSDV incidence was 1,750 and 3,000 m, respectively, reducing areas of cotton and spring melon fields within these distances from fall melon fields may decrease CYSDV incidence. Our results indicate that landscape-based studies will be fruitful to alleviate limitations imposed on crop production by vector-borne diseases.
Subject(s)
Crops, Agricultural/virology , Cucumis melo/virology , Hemiptera/virology , Insect Vectors/virology , Plant Diseases/virology , Animals , Arizona , GeographyABSTRACT
The new DRB1*11:129 allele differs from the closest matching allele HLA-DRB1*11:06:01 by one nucleotide substitution in exon 3 at position 623 (GâA).
Subject(s)
Alleles , HLA-DRB1 Chains/genetics , Point Mutation , Asian People/genetics , Base Sequence , Exons , HLA-DRB1 Chains/immunology , Histocompatibility Testing , Humans , Molecular Sequence Data , Polymerase Chain ReactionABSTRACT
Identification of the antigen presenting molecule HLA-DRB1*03:49 by group-specific sequence-based typing.
Subject(s)
Alleles , HLA-DRB1 Chains/genetics , Histocompatibility Testing , Base Sequence , Europe , Exons/genetics , Humans , Molecular Sequence Data , Sequence AlignmentABSTRACT
HLA-DRB1*03:85 differs from HLA-DRB1*03:06 by two nucleotides, position 257 A>T and position 258T>C, resulting in Valine at codon 57.
Subject(s)
Alleles , HLA-DRB1 Chains/genetics , Base Sequence , Exons/genetics , Humans , Molecular Sequence Data , Sequence AlignmentABSTRACT
Estimation of human leukocyte antigen (HLA) haplotype frequencies from unrelated stem cell donor registries presents a challenge because of large sample sizes and heterogeneity of HLA typing data. For the 14th International HLA and Immunogenetics Workshop, five bioinformatics groups initiated the 'Registry Diversity Component' aiming to cross-validate and improve current haplotype estimation tools. Five datasets were derived from different donor registries and then used as input for five different computer programs for haplotype frequency estimation. Because of issues related to heterogeneity and complexity of HLA typing data identified in the initial phase, the same five implementations, and two new ones, were used on simulated datasets in a controlled experiment where the correct results were known a priori. These datasets contained various fractions of missing HLA-DR modeled after European haplotype frequencies. We measured the contribution of sampling fluctuation and estimation error to the deviation of the frequencies from their true values, finding equivalent contributions of each for the chosen samples. Because of patient-directed activities, selective prospective typing strategies and the variety and evolution of typing technology, some donors have more complete and better HLA data. In this setting, we show that restricting estimation to fully typed individuals introduces biases that could be overcome by including all donors in frequency estimation. Our study underlines the importance of critical review and validation of tools in registry-related activity and provides a sustainable framework for validating the computational tools used. Accurate frequencies are essential for match prediction to improve registry operations and to help more patients identify suitably matched donors.
Subject(s)
HLA Antigens/immunology , Haplotypes/immunology , Histocompatibility Testing/standards , Models, Statistical , Registries , Software/standards , Stem Cell Transplantation , Gene Frequency , HLA Antigens/genetics , Histocompatibility Testing/methods , Histocompatibility Testing/statistics & numerical data , Humans , Unrelated Donors/statistics & numerical dataABSTRACT
Knowledge of an individual's human leukocyte antigen (HLA) genotype is essential for modern medical genetics, and is crucial for hematopoietic stem cell and solid-organ transplantation. However, the high levels of polymorphism known for the HLA genes make it difficult to generate an HLA genotype that unambiguously identifies the alleles that are present at a given HLA locus in an individual. For the last 20 years, the histocompatibility and immunogenetics community has recorded this HLA genotyping ambiguity using allele codes developed by the National Marrow Donor Program (NMDP). While these allele codes may have been effective for recording an HLA genotyping result when initially developed, their use today results in increased ambiguity in an HLA genotype, and they are no longer suitable in the era of rapid allele discovery and ultra-high allele polymorphism. Here, we present a text string format capable of fully representing HLA genotyping results. This Genotype List (GL) String format is an extension of a proposed standard for reporting killer-cell immunoglobulin-like receptor (KIR) genotype data that can be applied to any genetic data that use a standard nomenclature for identifying variants. The GL String format uses a hierarchical set of operators to describe the relationships between alleles, lists of possible alleles, phased alleles, genotypes, lists of possible genotypes, and multilocus unphased genotypes, without losing typing information or increasing typing ambiguity. When used in concert with appropriate tools to create, exchange, and parse these strings, we anticipate that GL Strings will replace NMDP allele codes for reporting HLA genotypes.
Subject(s)
Algorithms , Genotyping Techniques/standards , HLA Antigens/immunology , Hematopoietic Stem Cell Transplantation , Histocompatibility Testing/standards , Organ Transplantation , Receptors, KIR/immunology , Alleles , Gene Frequency , Genotype , Genotyping Techniques/statistics & numerical data , HLA Antigens/genetics , Histocompatibility Testing/statistics & numerical data , Humans , Polymorphism, Genetic , Receptors, KIR/genetics , Sequence Analysis, DNA , Terminology as Topic , Unrelated DonorsABSTRACT
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.