1
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Voorter CEM, Groeneweg M, Olieslagers TI, Fae I, Fischer GF, Andreani M, Troiano M, Vidan-Jeras B, Montanic S, Hepkema BG, Bungener LB, Tilanus MGJ, Wieten L. Resolving unknown nucleotides in the IPD-IMGT/HLA database by extended and full-length sequencing of HLA class I and II alleles. Immunogenetics 2024; 76:109-121. [PMID: 38400869 PMCID: PMC10944811 DOI: 10.1007/s00251-024-01333-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024]
Abstract
In the past, identification of HLA alleles was limited to sequencing the region of the gene coding for the peptide binding groove, resulting in a lack of sequence information in the HLA database, challenging HLA allele assignment software programs. We investigated full-length sequences of 19 HLA class I and 7 HLA class II alleles, and we extended another 47 HLA class I alleles with sequences of 5' and 3' UTR regions that were all not yet available in the IPD-IMGT/HLA database. We resolved 8638 unknown nucleotides in the coding sequence of HLA class I and 2139 of HLA class II. Furthermore, with full-length sequencing of the 26 alleles, more than 90 kb of sequence information was added to the non-coding sequences, whereas extension of the 47 alleles resulted in the addition of 5.5 kb unknown nucleotides to the 5' UTR and > 31.7 kb to the 3' UTR region. With this information, some interesting features were observed, like possible recombination events and lineage evolutionary origins. The continuing increase in the availability of full-length sequences in the HLA database will enable the identification of the evolutionary origin and will help the community to improve the alignment and assignment accuracy of HLA alleles.
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Affiliation(s)
- Christina E M Voorter
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Timo I Olieslagers
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ingrid Fae
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Gottfried F Fischer
- Department for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria
| | - Marco Andreani
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maria Troiano
- Laboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Bouke G Hepkema
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura B Bungener
- Transplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel G J Tilanus
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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2
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Voorter CEM, Groeneveld L, Heidt S, Wieten L. Evaluation of 19 years of international external proficiency testing for high-resolution HLA typing. Front Genet 2024; 14:1290915. [PMID: 38348410 PMCID: PMC10859402 DOI: 10.3389/fgene.2023.1290915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/11/2023] [Indexed: 02/15/2024] Open
Abstract
The international high-resolution external proficiency testing (EPT) started in 2004 with high-resolution typing of human leucocyte antigen (HLA) class I (HLA-A,B,C) and HLA class II (HLA-DRB1, DRB345, DQB1, and DPB1) alleles, since possibilities for such an EPT within Europe were limited and all existing EPTs at that time made use of the comparison of HLA typing results without a reference. This EPT was set up as a collaboration between the HLA laboratory of Leiden, providing DNA samples to the participants, and the laboratory of Maastricht, performing the high-resolution typing as the reference result and evaluating the results of all participants according to the prevailing European Federation for Immunogenetics (EFI) standards. Once a year, 12 samples were sent to the participating laboratories, and evaluation and certificates were provided at the end of that same year. During the years, the EPT was extended to low-resolution HLA class I and II typing, high-resolution typing including DQA1 and DPA1, and allelic resolution typing for HLA class I, the latter one being unique in this field. Evaluation of the high-resolution typing results of the last 19 years showed a clear increase in the number of loci tested by the participating laboratories and a clear change of method from Sanger sequencing with additional other techniques (SSO/SSP) to the nowadays widely used next-generation sequencing method. By strictly using the EFI rules for high-resolution HLA typing, the participants were made aware of the ambiguities within exons 2 and 3 for class I and exon 2 for class II and the presence of null alleles even in a two-field HLA typing. There was an impressive learning curve, resulting in >98% correctly typed samples since 2017 and a 100% fulfillment of EFI rules for all laboratories for all loci submitted in the last 2 years. Overall, this EPT meets the need of an EPT for high-resolution typing for EFI accreditation.
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Affiliation(s)
- C. E. M. Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - L. Groeneveld
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
| | - S. Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Eurotransplant Reference Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | - L. Wieten
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, Netherlands
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3
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Hod‐Dvorai R, Schiller JJ, Riddick MC, Gallay B. Identification of a
DRB1*04:07
–
DRB4*01:03:01:02N
haplotype in a native
American
individual. HLA 2022; 100:500-504. [DOI: 10.1111/tan.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Reut Hod‐Dvorai
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | | | - Mary C. Riddick
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | - Brian Gallay
- Department of Medicine SUNY Upstate Medical University Syracuse New York USA
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4
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Lemin AJ, Foster L. HLA-DPB1 allele frequencies in the West Midlands region of the United Kingdom: A critical evaluation against the common, intermediate and well-documented allele catalogues CWD 2.0.0, EFI CWD and CIWD 3.0.0. HLA 2021; 98:5-13. [PMID: 33934529 DOI: 10.1111/tan.14291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/27/2021] [Indexed: 01/08/2023]
Abstract
The Birmingham H&I laboratory performed HLA typing on 456 potential deceased solid organ donors in the UK between 2014 and 2016. Accurate DPB1 typing is essential for determining HLA compatibility in transplantation, thus we report HLA-DPB1 for potential deceased solid organ donors. To correctly interpret HLA typing data, laboratories must understand both international and local HLA allele frequencies. In this analysis, we determined HLA-DPB1 allele and genotype frequencies for these 456 donors. HLA-DPB1 diversity was evaluated against the common and well-documented (CWD) alleles 2.0.0 catalogue, the European Federation for Immunogenetics (EFI) CWD catalogue and the common, intermediate and well-documented (CIWD) 3.0.0 catalogue. Additionally, we determined which alleles are common in our local deceased donor population. We observed 27 HLA-DPB1 alleles with DPB1*04:01 being the most frequently observed (allele frequency = 0.4342). All alleles detected locally were present in CIWD 3.0.0, however, DPB1*124:01 and *135:01 were not present in CWD 2.0.0 and DPB1*104:01 and *135:01 were not present in EFI CWD. Twenty of 27 DPB1 alleles identified were defined as locally common and also listed as common in CIWD 3.0.0 representing 62.5% of common alleles in the subset of CIWD 3.0.0 from individuals of a European geographic, ancestral or ethnic background. The alleles HLA-DPB1*16:01 and *20:01 are locally common but not listed as common in EFI CWD and DPB1*104:01 is not listed as common in CWD 2.0.0 catalogue. Our analysis showed that the detected alleles and locally common alleles within our population were aligned with the CIWD 3.0.0 catalogue.
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Affiliation(s)
- Andrew James Lemin
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, Birmingham, UK
| | - Luke Foster
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, Birmingham, UK
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5
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He Y, Li J, Mao W, Zhang D, Liu M, Shan X, Zhang B, Zhu C, Shen J, Deng Z, Wang Z, Yu W, Chen Q, Guo W, Su P, Lv R, Li G, Li G, Pei B, Jiao L, Shen G, Liu Y, Feng Z, Su Y, Xie Y, Di W, Liu X, Yang X, Wang J, Qi J, Liu Q, Han Y, He J, Cai J, Zhang Z, Zhu F, Du D. HLA common and well-documented alleles in China. HLA 2018; 92:199-205. [DOI: 10.1111/tan.13358] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/22/2018] [Accepted: 07/29/2018] [Indexed: 11/29/2022]
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6
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Voorter CEM, Matern B, Tran TH, Fink A, Vidan-Jeras B, Montanic S, Fischer G, Fae I, de Santis D, Whidborne R, Andreani M, Testi M, Groeneweg M, Tilanus MGJ. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Hum Immunol 2018; 79:763-772. [PMID: 30107213 DOI: 10.1016/j.humimm.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/27/2022]
Abstract
The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Ben Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Thuong Hien Tran
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annette Fink
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Gottfried Fischer
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Ingrid Fae
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Dianne de Santis
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Rebecca Whidborne
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
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7
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Sanchez-Mazas A, Nunes JM, Middleton D, Sauter J, Buhler S, McCabe A, Hofmann J, Baier DM, Schmidt AH, Nicoloso G, Andreani M, Grubic Z, Tiercy JM, Fleischhauer K. Common and well-documented HLA alleles over all of Europe and within European sub-regions: A catalogue from the European Federation for Immunogenetics. HLA 2018; 89:104-113. [PMID: 28102034 DOI: 10.1111/tan.12956] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND A catalogue of common and well-documented (CWD) human leukocyte antigen (HLA), previously established by the American Society for Histocompatibility and Immunogenetics (ASHI), is widely used as indicator for typing ambiguities to be resolved in tissue transplantation or for checking the universality of any HLA allele in the world. However, European population samples, which are characterized by a substantial level of genetic variation, are underrepresented in the ASHI catalogue. Therefore, the Population Genetics Working Group of the European Federation for Immunogenetics (EFI) has facilitated data collection for an European CWD catalogue. MATERIALS AND METHODS To this end, 2nd-field HLA-A, -B, -C,- DRB1,- DQA1,- DQB1 and -DPB1 data of 77 to 121 European population samples (21 571-3 966 984 individuals) from 3 large databases, HLA-net/Gene[VA], allelefrequencies.net and DKMS, were analysed. RESULTS The total number of CWD alleles is similar in the EFI (N = 1048) and ASHI (N = 1031) catalogues, but the former counts less common (N = 236 vs 377) and more well-documented (N = 812 vs 654) alleles than the latter, possibly reflecting differences in sample numbers and sizes. Interestingly, approximately half of the CWD alleles reported by EFI were not reported by ASHI and vice-versa, underlining the distinct features of the two catalogues. Also, although 78 common alleles are widely distributed across Europe, some alleles are only common within specific sub-regions, showing regional variability. CONCLUSION Although the definition of CWD alleles itself is affected by different parameters, calling for current updates of the list, the EFI CWD catalogue provides new insights into European population genetics and will be a very useful tool for tissue-typing laboratories in and beyond Europe.
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Affiliation(s)
- A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - D Middleton
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplant Immunology Laboratory, Royal Liverpool and Broadgreen University Hospital, Liverpool, UK
| | - J Sauter
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - S Buhler
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - A McCabe
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - J Hofmann
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - D M Baier
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - A H Schmidt
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - G Nicoloso
- Swiss Transfusion Swiss Red Cross (SRC)/Swiss Blood Stem Cells, Bern, Switzerland
| | - M Andreani
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Z Grubic
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Tissue Typing Center, University Hospital Center Zagreb, Zagreb, Croatia
| | - J-M Tiercy
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - K Fleischhauer
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
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8
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Turner TR, Hayhurst JD, Hayward DR, Bultitude WP, Barker DJ, Robinson J, Madrigal JA, Mayor NP, Marsh SGE. Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines. HLA 2017; 91:88-101. [PMID: 29171935 DOI: 10.1111/tan.13184] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/01/2017] [Accepted: 11/20/2017] [Indexed: 01/10/2023]
Abstract
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.
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Affiliation(s)
- T R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - J D Hayhurst
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - D R Hayward
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - W P Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - D J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - J Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - J A Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - N P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - S G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
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