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Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan. Eur J Hum Genet 2021; 29:1259-1271. [PMID: 33753913 PMCID: PMC8384866 DOI: 10.1038/s41431-021-00845-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.
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2
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Schmidt AH, Sauter J, Baier DM, Daiss J, Keller A, Klussmeier A, Mengling T, Rall G, Riethmüller T, Schöfl G, Solloch UV, Torosian T, Means D, Kelly H, Jagannathan L, Paul P, Giani AS, Hildebrand S, Schumacher S, Markert J, Füssel M, Hofmann JA, Schäfer T, Pingel J, Lange V, Schetelig J. Immunogenetics in stem cell donor registry work: The DKMS example (Part 2). Int J Immunogenet 2020; 47:139-148. [PMID: 32034894 PMCID: PMC7079094 DOI: 10.1111/iji.12479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
DKMS is a leading stem cell donor registry with more than 9 million donors. Donor registry activities share many touch points with topics from immunogenetics or population genetics. In this two-part review article, we deal with these aspects of donor registry work by using the example of DKMS. In the second part of the review, we focus on donor typing of non-HLA genes, the impact of donor age, gender and CMV serostatus on donation probabilities, the identification of novel HLA, KIR and MIC alleles by high-throughput donor typing, the activities of the Collaborative Biobank and pharmacogenetics in the donor registry context.
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Affiliation(s)
- Alexander H. Schmidt
- DKMSTübingenGermany
- DKMS Life Science LabDresdenGermany
- Clinical Trials UnitDKMSDresdenGermany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Latha Jagannathan
- DKMS‐BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | | | | | | | | | - Johannes Schetelig
- Clinical Trials UnitDKMSDresdenGermany
- Medizinische Klinik IUniversity Hospital Carl Gustav CarusDresdenGermany
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3
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Shimizu M, Kuroda Y, Uchida M, Takada S, Kamada H, Takahashi D, Nakajima F, Miyata S, Igarashi S, Satake M. A new HLA-C allele with an alternative splice site in exon 3: HLA-C*03:23N. HLA 2020; 95:555-560. [PMID: 32034867 DOI: 10.1111/tan.13832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/25/2019] [Accepted: 02/05/2020] [Indexed: 11/26/2022]
Abstract
We identified a probable new null HLA-C allele, C*03:23N, which originated from C*03:04:01:02, but does not react with Cw3 antibodies. This allele was identified by sequence analysis, which indicated that a single G-to-A substitution at position 406 in exon 3 created a null allele under a new mechanism: the mutation changes the position of the intron 2-exon 3 splice site to be further into exon 3, leading to a frameshift and a premature stop codon. Sequence analysis of cDNA confirmed the existence of the causative alternative acceptor splice site and the resultant deletion of 64 nucleotides in exon 3. Analysis of 220 blood or bone marrow donors in Japan with C*03:23N demonstrated that Japanese HLA-C*03:23N is on the haplotype A*26:01∼C*03:23N∼B*40:02∼DRB1*09:01.
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Affiliation(s)
- Marie Shimizu
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukari Kuroda
- Kyushu Block Blood Center, Japanese Red Cross Society, Fukuoka, Japan
| | - Miyuki Uchida
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Hiromi Kamada
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Fumiaki Nakajima
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Shigeki Miyata
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Shigeru Igarashi
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
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4
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Bishara A, Brautbar C, Cereb N, Israel S. Identification of 33 novel HLA alleles in Arab potential bone marrow donors. HLA 2019; 95:128-130. [PMID: 31738479 DOI: 10.1111/tan.13764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
Between 2008 and April 2018, we recruited more than 37 000 potential Arab donors to the Hadassah Bone Marrow Donor Registry, all of whom were typed for high resolution HLA-A, -B, and -DRB1. In addition, more than 22% of them were also typed for their HLA-C and -DQB1 alleles. A comparison of the sequences obtained from these donors with the IPD-IMGT/HLA Database showed 33 novel alleles from five loci (HLA-A, -B, -C, -DR, -DQ). All of these novel HLA alleles were detected in the local Arab communities; 79% of these alleles have not been described in other groups yet and remain unique to the local Arab communities.
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Affiliation(s)
- Amal Bishara
- Tissue Typing and Immunogenetics Laboratory, Hadassah Medical Center, Jerusalem, Israel
| | - Chaim Brautbar
- Tissue Typing and Immunogenetics Laboratory, Hadassah Medical Center, Jerusalem, Israel
| | | | - Shoshana Israel
- Tissue Typing and Immunogenetics Laboratory, Hadassah Medical Center, Jerusalem, Israel
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5
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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6
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The Importance of New Generation Sequencing (NGS) HLA Typing in Renal Transplantation—Preliminary Report. Transplant Proc 2018; 50:1605-1615. [DOI: 10.1016/j.transproceed.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/14/2018] [Accepted: 05/07/2018] [Indexed: 01/03/2023]
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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: 66] [Impact Index Per Article: 11.0] [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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Gandhi MJ, Ferriola D, Lind C, Duke JL, Huynh A, Papazoglou A, Mackiewicz K, Christiansen M, Dong W, Hsu S, Thomas D, Schneider B, Pierce E, Kearns J, Kamoun M, Monos D, Askar M. Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience. Hum Immunol 2017; 78:642-648. [DOI: 10.1016/j.humimm.2017.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022]
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Robinson J, Guethlein LA, Cereb N, Yang SY, Norman PJ, Marsh SGE, Parham P. Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles. PLoS Genet 2017. [PMID: 28650991 PMCID: PMC5507469 DOI: 10.1371/journal.pgen.1006862] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HLA class I glycoproteins contain the functional sites that bind peptide antigens and engage lymphocyte receptors. Recently, clinical application of sequence-based HLA typing has uncovered an unprecedented number of novel HLA class I alleles. Here we define the nature and extent of the variation in 3,489 HLA-A, 4,356 HLA-B and 3,111 HLA-C alleles. This analysis required development of suites of methods, having general applicability, for comparing and analyzing large numbers of homologous sequences. At least three amino-acid substitutions are present at every position in the polymorphic α1 and α2 domains of HLA-A, -B and -C. A minority of positions have an incidence >1% for the 'second' most frequent nucleotide, comprising 70 positions in HLA-A, 85 in HLA-B and 54 in HLA-C. The majority of these positions have three or four alternative nucleotides. These positions were subject to positive selection and correspond to binding sites for peptides and receptors. Most alleles of HLA class I (>80%) are very rare, often identified in one person or family, and they differ by point mutation from older, more common alleles. These alleles with single nucleotide polymorphisms reflect the germ-line mutation rate. Their frequency predicts the human population harbors 8-9 million HLA class I variants. The common alleles of human populations comprise 42 core alleles, which represent all selected polymorphism, and recombinants that have assorted this polymorphism.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Lisbeth A. Guethlein
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Nezih Cereb
- Histogenetics, Ossining, New York, United States of America
| | - Soo Young Yang
- Histogenetics, Ossining, New York, United States of America
| | - Paul J. Norman
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Peter Parham
- Dept. of Structural Biology & Dept. of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, California, United States of America
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Bogunia-Kubik K, Łacina P. From genetic single candidate gene studies to complex genomics of GvHD. Br J Haematol 2017; 178:661-675. [DOI: 10.1111/bjh.14704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
- Laboratory of Tissue Immunology; Medical Centre; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; Wroclaw Poland
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11
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Gandhi MJ, Ferriola D, Huang Y, Duke JL, Monos D. Targeted Next-Generation Sequencing for Human Leukocyte Antigen Typing in a Clinical Laboratory: Metrics of Relevance and Considerations for Its Successful Implementation. Arch Pathol Lab Med 2017; 141:806-812. [PMID: 28234015 DOI: 10.5858/arpa.2016-0537-ra] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Numerous feasibility studies to type human leukocyte antigens (HLAs) by next-generation sequencing (NGS) have led to the development of vendor-supported kits for HLA typing by NGS. Some clinical laboratories have introduced HLA-NGS, and many are investigating the introduction. Standards from accrediting agencies form the regulatory framework for introducing this test into clinical laboratories. OBJECTIVES - To provide an assessment of metrics and considerations relevant to the successful implementation of clinical HLA-NGS typing, and to provide as a reference a validated HLA-NGS protocol used clinically since December 2013 at the Children's Hospital of Philadelphia (Philadelphia, Pennsylvania). DATA SOURCES - The HLA-NGS has been performed on 2532 samples. The initial 1046 and all homozygous samples were also typed by an alternate method. The HLA-NGS demonstrated 99.7% concordance with the alternate method. Ambiguous results were most common at the DPB1 locus because of a lack of phasing between exons 2 and 3 or the unsequenced exon 1 (533 of 2954 alleles; 18.04%) and the DRB1 locus because of not sequencing exon 1 (75 of 3972 alleles; 1.89%). No ambiguities were detected among the other loci. Except for 2 false homozygous samples, all homozygous samples (1891) demonstrated concordance with the alternate method. The article is organized to address the critical elements in the preanalytic, analytic, and postanalytic phases of introducing this assay into the clinical laboratory. CONCLUSIONS - The results demonstrate that HLA typing by NGS is a highly accurate, reproducible, efficient method that provides more-complete sequencing information for the length of the HLA gene and can be the single methodology for HLA typing in clinical immunogenetics laboratories.
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Affiliation(s)
| | | | | | | | - Dimitri Monos
- From the Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Dr Gandhi); the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Ms Ferriola and Drs Huang, Duke, and Monos); and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Dr Monos)
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12
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Marsh SGE. Nomenclature for factors of the HLA system, update December 2015. Int J Immunogenet 2016. [DOI: 10.1111/iji.12253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Affiliation(s)
- Steven G. E. Marsh
- Anthony Nolan Research Institute; Royal Free Hospital; NW3 2QG London UK
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14
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Nomenclature for factors of the HLA system, update December 2015. Hum Immunol 2016; 77:432-5. [PMID: 26829526 DOI: 10.1016/j.humimm.2016.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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