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The document provides an update on the nomenclature for factors of the HLA system, listing newly assigned sequences and confirmations of previously reported sequences. Authors are encouraged to submit new sequences directly to the WHO Nomenclature Committee for Factors of the HLA System. Accession numbers are provided for retrieving sequence files from data libraries. The document includes a comprehensive list of newly assigned sequences and their submitting authors from various countries, reflecting the global nature of genetic research and collaboration among international institutions in the field of immunogenetics. [Extracted from the article]

The given text is a list of references from a research article or document. It includes various authors and their corresponding publications, which likely pertain to a specific topic of study. The purpose of this list is to provide readers with a comprehensive list of sources that can be consulted for further research. [Extracted from the article]

HLA antigens were historically defined according to the unique reactivity pattern of cells expressing HLA molecules with distinctive clusters of allo‐antisera and/or monoclonal antibodies. Subsequently, amino acid residues determining epitopes (DEP) in the HLA molecule were correlated with reactivity patterns. In current clinical practice, the presence of allo‐antibodies is assessed using Luminex‐based solid phase single antigen bead (SAB) assays for transplantation. Recently, novel antigens were proposed for HLA molecules with DEP patterns that do not match any serologically defined antigens recognised by the WHO Nomenclature Committee. To validate the antigens, mean fluorescence intensity values of SABs tested on >13,000 patients' sera were extracted from clinical databases and analysed by scatter plots using a linear regression model. We found that when two proteins were considered as the same antigen in the original study, for example, HLA‐A*02:01 and ‐A*02:06, their correlation ranked among the highest values at each locus. In contrast, discrete asymmetric outliers were observed when there were different antigens, for example, HLA‐A*30:01 and ‐A*30:02, allowing validation and confirmation of 20 novel antigens for HLA‐A, ‐B, ‐C and ‐DR. The outliers were confirmed to be true or false by flow cytometric crossmatches. In addition to the previously defined residues for antigen assignments, findings suggest that further distinction should be made for common antigens by including the substitutions at residue 67 of HLA‐B, 67 and 74 of ‐DR. These serologic analyses can be applied systematically to identify and confirm novel antigens. These developments will lead to designing optimal SAB panels and further improving virtual donor‐specific antibodies assessment. [ABSTRACT FROM AUTHOR]

The document titled "Nomenclature for factors of the HLA system, update January, February and March 2024" provides a list of newly assigned sequences and confirmations of previously reported sequences for the HLA system. The sequences have been submitted to the Nomenclature Committee and assigned official allele designations. Accession numbers are provided for each sequence, which can be used to retrieve the sequence files from data libraries. The document also mentions additional information and recent publications related to new HLA sequences. [Extracted from the article]

A total of 43 novel HLA alleles detected in haematopoietic cell donors using single molecule real‐time DNA sequencing. [ABSTRACT FROM AUTHOR]

Sequence confirmations of 175 HLA class I and II alleles in the IPD‐IMGT/HLA Database. [ABSTRACT FROM AUTHOR]

Twenty‐five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD‐IMGT/HLA Database has provided a stable, highly accessible, user‐friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high‐resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD‐IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic. [ABSTRACT FROM AUTHOR]

The document titled "Nomenclature for factors of the HLA system, update October, November and December 2023" provides a list of newly assigned sequences and confirmations of previously reported sequences for the Human Leucocyte Antigen (HLA) system. It includes accession numbers for each sequence, recent publications on new HLA sequences, and a list of individuals and organizations associated with specific genetic markers It also provides information on genetic codes, genetic samples, and genetic markers associated with immune response genes. The document includes researchers and locations from various countries, promoting diverse perspectives in genetic research. [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

Amalia Tejeda Velarde, Salamanca, SpainB*44:03:01:57AN300841OY496742Anthony Nolan Research Institute, London, UKB*44:03:01:59AN302699OY496948Anthony Nolan Research Institute, London, UKB*47:13HG00051326, HG00051327OR371952, OR371953Histogenetics, Ossining, NY, USAB*49:115430901620OR418347Dr. Renata Zunec, Zagreb, CroatiaC*07:01:01:131AN302868OY497138Anthony Nolan Research Institute, London, UKC*07:01:01:132AN302700OY496949Anthony Nolan Research Institute, London, UKC*07:01:01:133AN302809OY497076Anthony Nolan Research Institute, London, UKC*07:01:120RP-272456OR237968Dr. Adele Dhuyser, Vandoeuvre Les Nancy, FranceB*39:01:01:30AN302614OY496855Anthony Nolan Research Institute, London, UKB*39:06:02:09AN300835, AN300836OY496740, OY496741Anthony Nolan Research Institute, London, UKB*39:06:02:10AN302607OY496848Anthony Nolan Research Institute, London, UKB*39:06:092301629OR470754Dr. Francesc Rudilla, Barcelona, SpainA*26:01:01:55AN301228OY496808Anthony Nolan Research Institute, London, UKA*26:239HG00051169OR101686Histogenetics, Ossining, NY, USAA*26:240NHG00050479OP429147Histogenetics, Ossining, NY, USAA*26:241148272428OR388072Dr. [Extracted from the article]

An additional 122 alleles were recently published but have not been included in Table 3 due to space considerations.[3] In addition, the alleles A*02:03:12, A*03:01:96, A*11:01:98, A*30:02:25, A*34:01:06, A*68:01:59, DRB1*10:38Q, and DRB1*11:01:01:12Q have had suffix changes and have been renamed A*02:03:12Q, A*03:01:96Q, A*11:01:98Q, A*30:02:25Q, A*34:01:06Q, A*68:01:59Q, DRB1*10:38, and DRB1*11:01:01:12N respectively. The following sequences have been submitted to the Nomenclature Committee since the January, February and March 2023 nomenclature update[1] and, following agreed policy, have been assigned official allele designations.[2] Full details of all sequences will be published in a forthcoming report. 82 Loginova M, Repnicyna K, Paramonov I. Next-generation sequencing identifies two novel HLA-DRB1 alleles, HLA-DRB1*04:362 and HLA-DRB1*07:148. [Extracted from the article]

The Genotype List (GL) String grammar for reporting HLA and Killer‐cell Immunoglobulin‐like Receptor (KIR) genotypes in a text string was described in 2013. Since this initial description, GL Strings have been used to describe HLA and KIR genotypes for more than 40 million subjects, allowing these data to be recorded, stored and transmitted in an easily parsed, text‐based format. After a decade of working with HLA and KIR data in GL String format, with advances in HLA and KIR genotyping technologies that have fostered the generation of full‐gene sequence data, the need for an extension of the GL String system has become clear. Here, we introduce the new GL String delimiter "?," which addresses the need to describe ambiguity in assigning a gene sequence to gene paralogs. GL Strings that do not include a "?" delimiter continue to be interpreted as originally described. This extension represents version 1.1 of the GL String grammar. [ABSTRACT FROM AUTHOR]

Jose Samuel da Silva, Aparecida de Goiania Goias, BrazilA*02:1095HG00050863OQ357646Histogenetics, Ossining, USAA*02:1096HG00050862OQ357645Histogenetics, Ossining, USAA*02:1097HG00050868OQ436003Histogenetics, Ossining, USAA*02:10982018TB10688OQ556862Dr. Antonio Nieto, Cadiz, SpainA*33:03:64HG00050800OQ267715Histogenetics, Ossining, USAA*33:235HG00050772OQ102512Histogenetics, Ossining, USAA*33:236HG00050774OQ102514Histogenetics, Ossining, USAA*33:2370548-21OQ104609Dr. Jose Samuel da Silva, Aparecida de Goiania Goias, BrazilC*12:381HG00050922OQ472871Histogenetics, Ossining, USAC*12:382HG00050886OQ435996Histogenetics, Ossining, USAC*12:383HG00050882OQ357643Histogenetics, Ossining, USAC*12:3842310040049OQ606806Dr. Alexandre Walencik, Nantes, FranceA*03:459HG00050778OQ102518Histogenetics, Ossining, USAA*03:460HG00050869OQ436004Histogenetics, Ossining, USAA*11:439HG00050388OP205586Histogenetics, Ossining, USAA*11:440JMDP01K0458LC744060Dr. [Extracted from the article]

The article discusses the challenges posed by repeat regions in HLA genes during next-generation sequencing (NGS) for HLA typing. These repeat regions, found mainly in introns, can lead to ambiguities in allele identification due to variations in the lengths of homopolymers and microsatellites. The study highlights the need for accurate interpretation of repeat region ambiguities (RRAs) to avoid errors in HLA typing, especially as NGS-based assays become more common. The authors emphasize the importance of addressing RRAs in HLA typing to ensure accurate clinical and research outcomes. [Extracted from the article]

Eight novel HLA class I alleles have been identified using full gene sequencing. [ABSTRACT FROM AUTHOR]

The following sequences have been submitted to the Nomenclature Committee since the July, August and September 2022 nomenclature update[1] and, following agreed policy, have been assigned official allele designations.[2] Full details of all sequences will be published in a forthcoming report. [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

The following sequences have been submitted to the Nomenclature Committee since the April, May and June 2022 nomenclature update (Marsh, 2022) and, following agreed policy, have been assigned official allele designations (Marsh et al., 2010). [Extracted from the article]

The guidelines for the implementation and reporting of HLA nomenclature for the World Marrow Donor Association have served as a reliable standard for communication of HLA data in the hematopoietic cell transplantation process. Wider use of next‐generation sequencing made a special provision of the guidelines increasingly pertinent: how to communicate novel HLA alleles. Novel alleles need to be recognized by the WHO Nomenclature Committee for Factors of the HLA system to obtain official allele designations. Until then they have to be handled according to the specific rules. Leaving the actual rules basically unchanged we give some advice on how to communicate novel alleles to best facilitate the search process for cases where novel alleles are identified on donor or patient side. [ABSTRACT FROM AUTHOR]

HLA serological specificities were defined by the reactivity of HLA molecules with sets of sera and monoclonal antibodies. Many recently identified alleles defined by molecular typing lack their serotype assignment. We surveyed the literature describing the correlation of the reactivity of serologic reagents with AA residues. 20 ‐ 25 AA residues determining epitopes (DEP) that correlated with 82 WHO serologic specificities were identified for HLA class I loci. Thirteen DEP each located in the beta‐1 domains that correlated with 24 WHO serologic specificities were identified for HLA‐DRB1 and ‐DQB1 loci. The designation of possible HLA‐DPB1, ‐DQA1, ‐DPA1, and additional serological specificities that result from epitopes defined by residues located at both ‐DQA1 and ‐DQB1 subunits were also examined. HATS software was developed for automated serotype assignments to HLA alleles in one of the three hierarchical matching criteria: (1) all DEP (FULL); (2) selected DEP specific to each serological specificity (SEROTYPE); (3) one AA mismatch with one or more SEROTYPES (INCOMPLETE). Results were validated by evaluating the alleles whose serotypes do not correspond to the first field of the allele name listed in the HLA dictionary. Additional 85 and 21 DEP patterns that do not correspond to any WHO serologic specificities for common HLA class I and DRB1 alleles were identified, respectively. A comprehensive antibody identification panel would allow for accurate unacceptable antigen listing and compatibility predictions in solid organ transplantation. We propose that antibody‐screening panels should include all serologic specificities identified in this study. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Two novel alleles, HLA‐G*01:04:09 and HLA‐DPB1*04:01:01:136, were identified in a single healthy individual. [ABSTRACT FROM AUTHOR]

Two novel non‐classical HLA class I alleles have been characterized, HLA‐F*01:16 and ‐F*01:17. [ABSTRACT FROM AUTHOR]

HLA‐E*01:03:02:25 sequenced from blood and buccal samples of an ALL patient. [ABSTRACT FROM AUTHOR]

Two novel HLA class II alleles were characterized, HLA‐DRB1*03:01:01:05 and HLA‐DPB1*04:02:01:21. [ABSTRACT FROM AUTHOR]

44 Loginova M, Paramonov I, Verevkina L, Zarubin M. A novel HLA-B*08 allele, HLA-B*08:253, was identified by next generation sequencing in two Russian individuals. Detection of the novel HLA-B allele, HLA-B*27:199, in a Korean individual. 64 Song J, Kim H, Im J, Yoon CE, Park Y. The novel HLA-B allele, HLA-B*44:345N, discovered in a Korean family. 65 Ananeva A, Sergeeva I, Gaifullina R, Shagimardanova E. A novel HLA-B allele, HLA-B*44:493, detected in a potential hematopoietic stem cell donor. 70 Liu L, Han B, Chi X, Jiao S. A novel HLA-B*52 allele, B*52:100, was identified by sequencing-based typing. [Extracted from the article]

The following sequences have been submitted to the Nomenclature Committee since the April, May and June 2020 nomenclature update (Marsh, 2020) and, following agreed policy, have been assigned official allele designations (Marsh et al., 2010). The novel HLA-C*03:04:01:47 allele sequence identified using Pacific biosciences SMRT sequencing. [Extracted from the article]

While the success of allogeneic stem cell transplantation depends on a high degree of HLA compatibility between donor and patient, finding a suitable donor remains challenging due to the hyperpolymorphic nature of HLA genes. We calculated high‐resolution allele, haplotype and phenotype frequencies for HLA‐A, ‐C, ‐B, ‐DRB1 and ‐DQB1 for 10 subpopulations of the Anthony Nolan (AN) register using an in‐house expectation‐maximisation (EM) algorithm run on mixed resolution HLA data, covering 676 155 individuals. Sample sizes range from 599 410 for British/Irish North West European (BINWE) individuals, the largest subpopulation in the United Kingdom to 1105 for the British Bangladeshi population. Calculation of genetic distance between the subpopulations based on haplotype frequencies shows three broad clusters, each following a major continental group: European, African and Asian. We further analysed the HLA haplotype and phenotype diversity of each subpopulation, and found that 35.52% of BINWE individuals ranging to 98.34% of Middle Eastern individuals on the register had a unique phenotype within their subpopulation. These analyses and the allele, haplotype and phenotype frequency data of the subpopulation on the AN register are a valuable resource in understanding the HLA diversity in the United Kingdom and can be used to improve the accuracy of match likelihoods and to inform future donor recruitment strategies. [ABSTRACT FROM AUTHOR]

The following sequences have been submitted to the Nomenclature Committee since the April, May, and June 2020 nomenclature update1 and, following agreed policy, have been assigned official allele designations.2 Full details of all sequences will be published in a forthcoming report. [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

The following sequences have been submitted to the Nomenclature Committee since the July, August and September 2019 nomenclature update (Marsh, [24]) and, following agreed policy, have been assigned official allele designations (Marsh et al., [25]). [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

Novel allele HLA‐B*56:67 potentially formed by recombination between B*56:01:01:03 and B*40:01:01. [ABSTRACT FROM AUTHOR]

Pacific Biosciences SMRT sequencing used to identify the novel allele, HLA‐A*02:01:02:206. [ABSTRACT FROM AUTHOR]

Two charts are presented that list the newly assigned sequences and confirmations of previously reported sequences for human leukocyte antigen (HLA) submitted to the Nomenclature Committee as of May 2016.