ABSTRACT
Full-length KIR2DL1 allele sequence extensions characterised by single molecule real-time (SMRT) DNA sequencing.
Subject(s)
Genotype , Introns/genetics , Receptors, KIR2DL1/genetics , Alleles , Cohort Studies , High-Throughput Nucleotide Sequencing , Humans , Polymorphism, Single Nucleotide , United Kingdom , World Health OrganizationABSTRACT
The novel KIR2DL1*037 allele discovered and characterised by single molecule real-time (SMRT) DNA sequencing.
Subject(s)
Genotype , Killer Cells, Natural/physiology , Receptors, KIR2DL1/genetics , White People , Alleles , Cell Line , Consanguinity , High-Throughput Nucleotide Sequencing , Histocompatibility Testing , Homozygote , Humans , Polymorphism, Genetic , Sequence Alignment , World Health OrganizationABSTRACT
The hyperpolymorphic HLA genes play important roles in disease and transplantation and act as genetic markers of migration and evolution. A panel of 107 B-lymphoblastoid cell lines (B-LCLs) was established in 1987 at the 10th International Histocompatibility Workshop as a resource for the immunogenetics community. These B-LCLs are well characterised and represent diverse ethnicities and HLA haplotypes. Here we have applied Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing to HLA type 126 B-LCL, including the 107 International HLA and Immunogenetics Workshop (IHIW) cells, to ultra-high resolution. Amplicon sequencing of full-length HLA class I genes (HLA-A, -B and -C) and partial length HLA class II genes (HLA-DRB1, -DQB1 and -DPB1) was performed. We typed a total of 931 HLA alleles, 895 (96%) of which were consistent with the typing in the IPD-IMGT/HLA Database (Release 3.27.0, January 20, 2017), with 595 (64%) typed at a higher resolution. Discrepant types, including novel alleles (n = 10) and changes in zygosity (n = 13), as well as previously unreported types (n = 34) were observed. In addition, patterns of linkage disequilibrium were distinguished by four-field resolution typing of HLA-B and HLA-C. By improving and standardising the HLA typing of these B-LCLs, we have ensured their continued usefulness as a resource for the immunogenetics community in the age of next generation DNA sequencing.
Subject(s)
Computer Systems , HLA Antigens/genetics , Immunogenetics , Internationality , Sequence Analysis, DNA , Single Molecule Imaging , Alleles , Cell Line , Humans , Linkage Disequilibrium/geneticsABSTRACT
Improving haematopoietic cell transplantation outcomes by selection of an HLA-matched unrelated donor is best practice; however, donor selection by secondary characteristics is controversial. We studied 1271 recipients with haematological malignancies who underwent T-cell-depleted allografts and had complete data on HLA-matching status for six loci (HLA-A, -B, -C, -DRB1, -DQB1, -DPB1) and clinical outcome data. Five-year overall survival was 40.6%. HLA mismatching (at HLA-A, -B, -C, -DRB1, -DQB1) relative risk (RR) 1.22, 95% confidence interval (CI) 1.2-1.5, P=0.033 for 1 mismatch and RR 1.46, 95% CI 1.1-1.9, P=0.009 for >1 mismatch) and CMV mismatching (RR 1.37, 95% CI 1.2-1.6, P<0.001) were significantly associated with inferior survival. Donors aged <30 years showed a trend towards better survival. The multivariate model for mortality, combining CMV and HLA-match status, found an RR of 1.36 (95% CI 1.1-1.7, P=0.003) for HLA matched/CMV mismatched, an RR of 1.22 (95% CI 0.99-1.5, P=0.062) for HLA mismatched/CMV matched and an RR of 1.81 (95% CI 1.4-2.3, P=<0.001) for HLA/ CMV mismatched, compared with the HLA/CMV-matched recipients. These data suggest that HLA and CMV matching status should be considered when selecting unrelated donors and that CMV matching may abrogate the effect of an HLA mismatch.
Subject(s)
Cytomegalovirus/immunology , HLA Antigens/immunology , Hematologic Neoplasms/therapy , Hematopoietic Stem Cell Transplantation/methods , Unrelated Donors/supply & distribution , Adolescent , Adult , Aged , Child , Child, Preschool , Female , Histocompatibility , Humans , Lymphocyte Depletion , Male , Middle Aged , Risk Factors , Serologic Tests , Survival Analysis , Young AdultABSTRACT
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 sequence of HLA-A*02:95 identified in an Anthony Nolan volunteer donor.