RESUMEN
The importance of the HLA gene system in haematopoietic cell transplant outcomes was established early on and advances in both fields have led to ever increasing success of this clinical therapy. In large part, improvements in the understanding of HLA have been driven by the advancement in typing technologies. Each iteration of typing technology has improved the resolution of HLA typing, and often enabled the identification of polymorphism within the HLA loci. The discovery of the enormous amount of variation in the HLA genes, and the need to be able to characterise this for clinical HLA typing, has often resulted in a move away from one typing method to another more suited to typing of this complexity. Today, the gold standard for HLA typing are methods that can produce definitive HLA typing results.
Asunto(s)
Antígenos HLA , Trasplante de Células Madre Hematopoyéticas , Prueba de Histocompatibilidad , Humanos , Prueba de Histocompatibilidad/métodos , Antígenos HLA/genética , Antígenos HLA/inmunología , Polimorfismo GenéticoRESUMEN
A total of 43 novel HLA alleles detected in haematopoietic cell donors using single molecule real-time DNA sequencing.
Asunto(s)
Alelos , Antígenos HLA , Prueba de Histocompatibilidad , Donantes de Tejidos , Humanos , Antígenos HLA/genética , Prueba de Histocompatibilidad/métodos , Análisis de Secuencia de ADN/métodos , Trasplante de Células Madre Hematopoyéticas , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Células Madre Hematopoyéticas/metabolismoRESUMEN
Sequence confirmations of 175 HLA class I and II alleles in the IPD-IMGT/HLA Database.
Asunto(s)
Alelos , Bases de Datos Genéticas , Antígenos de Histocompatibilidad Clase II , Antígenos de Histocompatibilidad Clase I , Humanos , Antígenos de Histocompatibilidad Clase II/genética , Antígenos de Histocompatibilidad Clase II/inmunología , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/inmunología , Análisis de Secuencia de ADN , Prueba de HistocompatibilidadRESUMEN
Two novel alleles, HLA-G*01:04:09 and HLA-DPB1*04:01:01:136, were identified in a single healthy individual.
Asunto(s)
Genes MHC Clase I , Antígenos HLA-G , Humanos , Alelos , Cadenas beta de HLA-DP/genéticaRESUMEN
HLA-DPB1 is the classical HLA class II genes with the least recorded variation on the IPD-IMGT/HLA Database, suggesting the full extent of its diversity is perhaps yet to be characterized. Here, a full-gene typing strategy was employed to genotype a UK cohort of 1470 HCT recipients (n = 744) and donors (n = 726). In total, 2940 full-length HLA-DPB1 sequences were generated, comprising 193 distinct alleles. Of these, 107 sequences contained novel variation, totaling 49 unique intronic HLA-DPB1 alleles, and one coding variant (HLA-DPB1*1188:01). Full-gene sequencing resulted in zygosity changes for 129 individuals by identifying two distinct intronic variants of the same coding allele. We verified the existence of nine unconfirmed alleles and extended the sequence of two existing alleles on the IPD-IMGT/HLA Database.
Asunto(s)
Donante no Emparentado , Humanos , Alelos , Cadenas beta de HLA-DP/genética , Genotipo , Reino UnidoRESUMEN
Two novel non-classical HLA class I alleles have been characterized, HLA-F*01:16 and -F*01:17.
Asunto(s)
Genes MHC Clase I , Donantes de Tejidos , Humanos , AlelosRESUMEN
Until recently the number of alleles of the nonclassical HLA class I gene HLA-E documented in the IPD-IMGT/HLA Database was small and as a result, the gene was often not considered to be notably polymorphic. Here, we describe our work in identifying and submitting 86 novel HLA-E alleles after full-gene single-molecule real-time (SMRT) DNA sequencing of 6227 DNA samples. These samples were comprised of 2468 patients undergoing hematopoietic cell transplantation and 3759 unrelated potential donors. A total of 111 unique HLA-E alleles were detected in this cohort. The majority of novel alleles (79.1%) contained polymorphisms in intronic regions, highlighting the significant undiscovered variation present in the noncoding regions of the HLA-E gene.
Asunto(s)
Trasplante de Células Madre Hematopoyéticas , Humanos , Alelos , Antígenos HLA-ERESUMEN
Two novel HLA class II alleles were characterized, HLA-DRB1*03:01:01:05 and HLA-DPB1*04:02:01:21.
Asunto(s)
Antígenos HLA-DQ , Leucemia , Alelos , Frecuencia de los Genes , Antígenos HLA-DQ/genética , Cadenas beta de HLA-DQ , Cadenas HLA-DRB1/genética , Humanos , Leucemia/genética , Leucemia/terapia , Polimorfismo GenéticoRESUMEN
HLA-E*01:03:02:25 sequenced from blood and buccal samples of an ALL patient.
Asunto(s)
Antígenos de Histocompatibilidad Clase I , Leucemia-Linfoma Linfoblástico de Células Precursoras , Alelos , Antígenos de Histocompatibilidad Clase I/genética , Prueba de Histocompatibilidad , Humanos , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/terapia , Antígenos HLA-ERESUMEN
Pacific Biosciences SMRT sequencing used to identify the novel allele, HLA-A*02:01:02:206.
Asunto(s)
Antígenos HLA-A , Población Blanca , Alelos , Antígenos HLA-A/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Análisis de Secuencia de ADNRESUMEN
As the primary genetic determinant of immune recognition of self and non-self, the hyperpolymorphic HLA genes play key roles in disease association and transplantation. The large, variably sized HLA class II genes have historically been less well characterized than the shorter HLA class I genes. Here, we have used Pacific Biosciences Single Molecule Real-Time (SMRT®) DNA sequencing to perform four-field resolution HLA typing of HLA-DRB1/3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 from a panel of 181 B-lymphoblastoid cell lines from the International HLA and Immunogenetics Workshops. By interrogating all exons, introns, and the untranslated regions of these important reference cells, we have improved their HLA typing resolution on the IPD-IMGT/HLA database. We observed widespread non-coding polymorphism, with over twice as many unique genomic sequences identified compared with coding sequences (CDS). We submitted 263 unique sequences to the IPD-IMGT/HLA Database, often from multiple cell lines, including 114 confirmations of existing alleles, of which 30 were also extensions to full-length genomic sequences where only CDS was available previously. A total of 149 novel alleles were identified, largely differing from their closest reference allele sequences by a single nucleotide polymorphism (SNP). However, some highly divergent alleles were deemed to be recombinants, only detectable by full-length sequencing with long, phased reads. The fourth-field variation we observed allowed fine mapping of linkage disequilibrium patterns and haplotypes to particular ancestries. This study has highlighted the under-appreciated non-coding diversity in HLA class II genes, with potential implications for population genetic and clinical studies.
Asunto(s)
Genes MHC Clase II , Inmunogenética , Alelos , Línea Celular , Frecuencia de los Genes , Haplotipos , HumanosRESUMEN
PURPOSE: Ultrahigh resolution (UHR) HLA matching is reported to result in better outcomes following unrelated donor hematopoietic cell transplantation, improving survival and reducing post-transplant complications. However, most studies included relatively small numbers of patients. Here we report the findings from a large, multicenter validation study. METHODS: UHR HLA typing was available on 5,140 conventionally 10 out of 10 HLA-matched patients with malignant disease transplanted between 2008 and 2017. RESULTS: After UHR HLA typing, 82% of pairs remained 10 out of 10 UHR-matched; 12.3% of patients were 12 out of 12 UHR HLA-matched. Compared with 12 out of 12 UHR-matched patients, probabilities of grade 2-4 acute graft-versus-host disease (aGVHD) were significantly increased with UHR mismatches (overall P = .0019) and in those patients who were HLA-DPB1 T-cell epitope permissively mismatched or nonpermissively mismatched (overall P = .0011). In the T-cell-depleted subset, the degree of UHR HLA mismatch was only associated with increased transplant-related mortality (TRM) (overall P = .0068). In the T-cell-replete subset, UHR HLA matching was associated with a lower probability of aGVHD (overall P = .0020); 12 out of 12 UHR matching was associated with reduced TRM risk when compared with HLA-DPB1 T-cell epitope permissively mismatched patients, whereas nonpermissive mismatching resulted in a greater risk (overall P = .0003). CONCLUSION: This study did not confirm that UHR 12 out of 12 HLA matching increases the probability of overall survival but does demonstrate that aGVHD risk, and in certain settings TRM, is lowest in UHR HLA-matched pairs and thus warrants consideration when multiple 10 out of 10 HLA-matched donors of equivalent age are available.
Asunto(s)
Trasplante de Células Madre Hematopoyéticas/métodos , Prueba de Histocompatibilidad/métodos , Acondicionamiento Pretrasplante/métodos , Adolescente , Adulto , Niño , Preescolar , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Donante no Emparentado , Adulto JovenRESUMEN
A novel variant of HLA-C*03:04:01:47 was identified using Pacific Biosciences SMRT sequencing platform.
Asunto(s)
Antígenos HLA-C , Secuenciación de Nucleótidos de Alto Rendimiento , Alelos , Genes MHC Clase I , Antígenos HLA-C/genética , Humanos , Análisis de Secuencia de ADNRESUMEN
We have developed a genotyping assay that produces fully phased, unambiguous HLA-E genotyping using Pacific Biosciences' single molecule real-time DNA sequencing. In total 212 cell lines were genotyped, including the panel of 107 established at the 10th International Histocompatibility Workshop. Our results matched the previously known HLA-E genotype in 94 (44.3%) cell lines, in all cases either improving or equalling previous genotyping resolution. Three (1.4%) cells had discrepant HLA-E genotyping data and 115 (54.2%) had no previous HLA-E data. The HLA-E genotypes for four (1.9%) cell lines resulted in a change of zygosity by identifying two distinct haplotypes. We discovered eight novel HLA-E alleles, extended the known reference sequence of seven and confirmed the existence of a further 10.
Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Antígenos de Histocompatibilidad Clase II , Alelos , Línea Celular , Genotipo , Antígenos HLA , Antígenos de Histocompatibilidad Clase II/genética , Prueba de Histocompatibilidad , Análisis de Secuencia de ADNRESUMEN
The reported influence of donor Killer-cell Immunoglobulin-like Receptor (KIR) genes on the outcomes of haematopoietic cell transplantation (HCT) are contradictory, in part due to diversity of disease, donor sources, era and conditioning regimens within and between different studies. Here, we describe the results of a retrospective clinical analysis establishing the effect of donor KIR motifs on the outcomes of 119 HLA-matched, unrelated donor HCT for adult acute myeloid leukaemia (AML) using myeloablative conditioning (MAC) in a predominantly T-cell deplete (TCD) cohort. We observed that HCT involving donors with at least one KIR B haplotype were more likely to result in non-relapse mortality (NRM) than HCT involving donors with two KIR A haplotypes (p = 0.019). Upon separation of KIR haplotypes into their centromeric (Cen) and telomeric (Tel) motif structures, we demonstrated that the Cen-B motif was largely responsible for this effect (p = 0.001). When the cause of NRM was investigated further, infection was the dominant cause of death (p = 0.006). No evidence correlating donor KIR B haplotype with relapse risk was observed. The results from this analysis confirm previous findings in the unrelated, TCD, MAC transplant setting and imply a protective role for donor-encoded Cen-A motifs against infection in allogeneic HCT recipients.
Asunto(s)
Trasplante de Células Madre Hematopoyéticas , Leucemia Mieloide Aguda , Receptores KIR , Adulto , Antígenos HLA , Humanos , Leucemia Mieloide Aguda/terapia , Recurrencia Local de Neoplasia , Receptores KIR/genética , Estudios Retrospectivos , Linfocitos TRESUMEN
The assignment of an HLA allele name to a sequence requires a comparison between the generated target sequence and a reference sequence on the IPD-IMGT/HLA database. Absence of a full-length reference sequence can result in the inability of HLA typing software to accurately compare and assign the sequence. We sequenced the most frequently seen HLA class I alleles on the Anthony Nolan register present in the database with only a partial genomic sequence, with the aim of increasing the number of complete reference sequences. We successfully extended 95 full-length HLA class I sequences and identified 13 novel variants. Increasing the number of full-length HLA class I reference sequences in the database has aided accuracy of HLA analysis tools for all histocompatibility and immunogenetics laboratories.
Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Antígenos de Histocompatibilidad Clase I/genética , Alelos , Genómica , Humanos , Análisis de Secuencia de ADNRESUMEN
The novel allele, HLA-C*07:01:01:30 differs by one nucleotide substitution with HLA-C*07:01:01:01 at gDNA 627.
Asunto(s)
Antígenos HLA-C/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN/métodos , Alelos , Sustitución de Aminoácidos , Secuencia de Bases , Humanos , Homología de SecuenciaRESUMEN
Pacific Biosciences' SMRT sequencing method was used to extend the sequence of HLA-A*02:13.
Asunto(s)
Genómica/métodos , Antígeno HLA-A2/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Alelos , HumanosRESUMEN
HLA-DRB1*01:01:01:02 is the first reported intronic variant of DRB1*01:01:01, differing by a single nucleotide substitution.