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Mirza A, Ali Qadri MM, Zeshan B, Hafiz K, Abbas S, Ahmad N, Iqbal M. HLA class-I polymorphisms among the Punjabi population of Pakistan: A comparative analysis with country's other ethnic groups. Hum Immunol 2024; 85:111083. [PMID: 39111186 DOI: 10.1016/j.humimm.2024.111083] [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: 09/23/2023] [Revised: 07/20/2024] [Accepted: 07/31/2024] [Indexed: 09/15/2024]
Abstract
The Punjabi population, constituting over 45 % of the country's total population, holds the highest prevalence in Pakistan. To understand their HLA genetics, we genotyped 389 Punjabi subjects for major Class-I loci using the PCR-SSO Luminex® method. Our study identified a total of 162 alleles, including 41 different HLA-A, 72 HLA-B, and 49 HLA-C alleles. The most common alleles included A*11:01 (14.6 %), A*01:01 (11.8 %), A*24:02 (11.3 %); B*40:06 (13.3 %), B*08:01 (10.9 %), B*51:01 (8.7 %); C*15:02 (15.5 %), C*07:02 (15.3 %), and C*04:01 (10.8 %). However, only locus B showed a significant deviation from HWE. The dominant Class I haplotype was A*24:02-B*40:06-C*15:02, followed by A*11:01-B*40:06-C*15:02, while significant LD was observed between all pairs of HLA loci. A distinct genetic makeup was observed in the Pakistani Punjabis as compared to Indian Punjabis, emphasizing the impact of the Indo-Pak partition and religious choices for marriage. In comparison to country's other ethnic groups, the Pakistani population exhibited 76 different alleles at a low field-resolution, with the Punjabi population having highest polymorphism. Phylogenetic analysis revealed that the Punjabi population is most closely related to the Sindhi population, while both populations sharing ancient connections with the Burusho population. These findings have significant implications for transplantation procedures, personalized medicine, disease susceptibility, and evolutionary studies.
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Affiliation(s)
- Aliza Mirza
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Mian Mubeen Ali Qadri
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan.
| | - Basit Zeshan
- Faculty of Sustainable Agriculture, University Malaysia Sabah (Sandakan Campus), 9000 Sabah, Malaysia.
| | - Kashif Hafiz
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Saba Abbas
- School of Medical Lab Technology, Minhaj University Lahore, Main Campus, 45770 Lahore, Pakistan
| | - Nabeel Ahmad
- Pakistan Kidney and Liver Institute (PKLI) and Research Center, One PKLI Avenue, Opposite DHA Phase 6, 54792 Lahore, Pakistan
| | - Maryam Iqbal
- School of Medical Lab Technology, Riphah International University, Gulberg III Campus, 25 Raza Saeed Rd, 54660 Lahore, Pakistan
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Cha J, Hur M, Kim H, Yun S, Nam M, Cho Y, Nam M. Comparative Assessment of Risk and Turn-Around Time between Sequence-Based Typing and Next-Generation Sequencing for HLA Typing. Diagnostics (Basel) 2024; 14:1793. [PMID: 39202281 PMCID: PMC11353627 DOI: 10.3390/diagnostics14161793] [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: 07/03/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
This study compared laboratory risk and turn-around time (TAT) between sequence-based typing (SBT) and next-generation sequencing (NGS) for human leukocyte antigen (HLA) typing. For risk assessment, we utilized the risk priority number (RPN) score based on failure mode and effect analysis (FMEA) and a risk acceptability matrix (RAM) according to the Clinical Laboratory Standards Institute (CLSI) guidelines (EP23-A). Total TAT was documented for the analytical phase, and hands-on time was defined as manual processes conducted by medical technicians. NGS showed a significantly higher total RPN score than SBT (1169 vs. 465). NGS indicated a higher mean RPN score, indicating elevated severity and detectability scores in comparison to SBT (RPN 23 vs. 12, p = 0.001; severity 5 vs. 3, p = 0.005; detectability 5 vs. 4, p < 0.001, respectively). NGS required a greater number of steps than SBT (44 vs. 25 steps), all of which were acceptable for the RAM. NGS showed a longer total TAT, total hands-on time, and hands-on time per step than SBT (26:47:20 vs. 12:32:06, 03:59:35 vs. 00:47:39, 00:05:13 vs. 00:01:54 hh:mm:ss, respectively). Transitioning from SBT to NGS for HLA typing involves increased risk and an extended TAT. This study underscored the importance of evaluating these factors to optimize laboratory efficiency in HLA typing.
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Affiliation(s)
- Jaehyun Cha
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 02841, Republic of Korea; (J.C.); (S.Y.); (M.N.); (Y.C.)
| | - Mina Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul 05030, Republic of Korea; (M.H.)
| | - Hanah Kim
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul 05030, Republic of Korea; (M.H.)
| | - Seunggyu Yun
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 02841, Republic of Korea; (J.C.); (S.Y.); (M.N.); (Y.C.)
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Myunghyun Nam
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 02841, Republic of Korea; (J.C.); (S.Y.); (M.N.); (Y.C.)
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 02841, Republic of Korea; (J.C.); (S.Y.); (M.N.); (Y.C.)
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Minjeong Nam
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 02841, Republic of Korea; (J.C.); (S.Y.); (M.N.); (Y.C.)
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
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3
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Mantzios P, Athanassiades T, Kouniaki D, Kitsiou V, Tsirogianni A. Identification of the new allele HLA-C*04:01:01:186 in a Greek individual using next generation sequencing. HLA 2024; 104:e15569. [PMID: 39016219 DOI: 10.1111/tan.15569] [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: 05/25/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/18/2024]
Abstract
The newly discovered HLA-C*04:01:01:186 allele differs from HLA-C*04:01:01:01 by a single nucleotide substitution in intron 3.
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Affiliation(s)
- Petros Mantzios
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | | | - Diamanto Kouniaki
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Vasiliki Kitsiou
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Alexandra Tsirogianni
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
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4
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Mantzios P, Athanassiades T, Mantziou P, Kitsiou V, Tsirogianni A. Identification of the new allele HLA-A*24:632 in a Greek individual using next generation sequencing. HLA 2024; 104:e15622. [PMID: 39041361 DOI: 10.1111/tan.15622] [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: 07/07/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
The HLA-Α*24:632 allele differs from HLA-A*24:02:01:01 by a single nucleotide substitution in exon 2.
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Affiliation(s)
- Petros Mantzios
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | | | - Panagiota Mantziou
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Vasiliki Kitsiou
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
| | - Alexandra Tsirogianni
- Immunology and Histocompatibility Department, Evangelismos General Hospital, Athens, Greece
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Mallis P, Siorenta A, Stamathioudaki E, Vrani V, Paterakis G. Frequency distribution of HLA class I and II alleles in Greek population and their significance in orchestrating the National Donor Registry Program. Int J Immunogenet 2024; 51:164-172. [PMID: 38459565 DOI: 10.1111/iji.12663] [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: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Human leukocyte antigens (HLA) represent one of the most polymorphic systems in humans, responsible for the identification of foreign antigens and the presentation of immune responses. Therefore, HLA is considered to play a major role in human disorders, donor-recipient matching and transplantation outcomes. This study aimed to determine the HLA class I and II alleles and haplotypes in the Greek population. Moreover, a comparative analysis of HLA alleles and haplotype frequencies found in Greek and pooled European populations was also performed to acquire a better knowledge about the HLA alleles distribution. A total number of 1896 healthy individuals were typed for their HLA alleles in the National Tissue Typing Center of Greece. High-resolution HLA typing for the HLA-A, -B, -C and -DR, -DQ, -DP with the use of the next-generation sequencing analysis was performed, followed by data analysis for establishing the HLA allele and haplotype differences. The results of this study showed that the most frequent alleles for the HLA-A were the A*02:01:01 (27.1%), *24:02:01 (14.4%), *01:01:01 (9.3%), for the HLA-B were the B*51:01:01 (15.3%), *18:01:01 (9.7%), *35:01:01 (6.8%) and for the HLA-C were the C*04:01:01 (15.4%), *07:01:01 (13.1%), *12:03:01 (9.6%). For the HLA class II, the most frequent alleles for the HLA-DRB1 were the DRB1*11:04:01 (16.4%), *16:01:01 (11.3%), *11:01:01 (9.5%), for the HLA-DQB1 were the DQB1*03:01:01 (30.5%), *05:02:01 (15.1%), *05:01:01 (10.6%) and for the HLA-DPB1 were the DPB1*04:01:01 (34.8%), *02:01:01 (11.6%), *04:02:01 (7.3%). Additionally, the most frequent haplotypes were the A*02:01:01∼C*07:01:01-B*18:01:01∼DRB1*11:04:01 (2.3%), followed by the A*01:01:01∼C*07:01:01∼B*08:01:01∼DRB1*03:01:01 (2.2%), A*24:02:01∼C*04:01:01∼B*35:02:01∼DRB1*11:04:01 (1.4%) and A*02:01:01∼C*04:01:01∼B*35:01:01-DRB1*14:01:01 (1.2%). The results herein were comparable to those obtained from the pooled European populations. Moreover, these results can be used for the improvement of the donor-recipient matching procedure and to understand better the disease association in Greece.
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Affiliation(s)
- Panagiotis Mallis
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Alexandra Siorenta
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Erasmia Stamathioudaki
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - Vasiliki Vrani
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
| | - George Paterakis
- Immunology Department & National Tissue Typing Center, General Hospital of Athens "G. Gennimatas", Athens, Greece
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Geo JA, Ameen R, Al Shemmari S, Thomas J. Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine. Med Princ Pract 2024; 33:215-231. [PMID: 38442703 PMCID: PMC11175610 DOI: 10.1159/000538176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.
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Affiliation(s)
- Jeethu Anu Geo
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Reem Ameen
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Salem Al Shemmari
- Department of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Jibu Thomas
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
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7
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Gil-Etayo FJ, Niño Ramírez JE, Vicente Parra A, Arroyo-Sánchez D, Tejeda Velarde A. Characterization of seven novel HLA-DPA1*01:03:01 non-coding variants by next-generation sequencing. HLA 2024; 103:e15385. [PMID: 38358076 DOI: 10.1111/tan.15385] [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: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
Seven different single nucleotide substitutions in non-coding regions gave rise to novel HLA-DPA1*01:03:01 variants.
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Affiliation(s)
- Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Jairo Eduardo Niño Ramírez
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
| | - Ariadna Vicente Parra
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Daniel Arroyo-Sánchez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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8
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Arroyo-Sánchez D, Gil-Etayo FJ, Niño Ramírez JE, Terradillos-Sánchez P, Tejeda Velarde A. Discovery of three HLA-DQB1*03:01:01 variants: HLA-DQB1*03:01:01:54, -DQB1*03:01:01:56 and -DQB1*03:01:01:58. HLA 2024; 103:e15403. [PMID: 38403836 DOI: 10.1111/tan.15403] [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: 02/02/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Three nucleotide substitutions in intronic regions give rise to the novel alleles: HLA-DQB1*03:01:01:54, -DQB1*03:01:01:56, -DQB1*03:01:01:58.
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Affiliation(s)
- Daniel Arroyo-Sánchez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Jairo Eduardo Niño Ramírez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
| | - Pilar Terradillos-Sánchez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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9
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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11
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Tran JN, Sherwood KR, Mostafa A, Benedicto RV, ElaAlim A, Greenshields A, Keown P, Liwski R, Lan JH. Novel alleles in the era of next-generation sequencing-based HLA typing calls for standardization and policy. Front Genet 2023; 14:1282834. [PMID: 37900182 PMCID: PMC10611506 DOI: 10.3389/fgene.2023.1282834] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Next-Generation Sequencing (NGS) has transformed clinical histocompatibility laboratories through its capacity to provide accurate, high-throughput, high-resolution typing of Human Leukocyte Antigen (HLA) genes, which is critical for transplant safety and success. As this technology becomes widely used for clinical genotyping, histocompatibility laboratories now have an increased capability to identify novel HLA alleles that previously would not be detected using traditional genotyping methods. Standard guidelines for the clinical verification and reporting of novelties in the era of NGS are greatly needed. Here, we describe the experience of a clinical histocompatibility laboratory's use of NGS for HLA genotyping and its management of novel alleles detected in an ethnically-diverse population of British Columbia, Canada. Over a period of 18 months, 3,450 clinical samples collected for the purpose of solid organ or hematopoietic stem cell transplantation were sequenced using NGS. Overall, 29 unique novel alleles were identified at a rate of ∼1.6 per month. The majority of novelties (52%) were detected in the alpha chains of class II (HLA-DQA1 and -DPA1). Novelties were found in all 11 HLA classical genes except for HLA-DRB3, -DRB4, and -DQB1. All novelties were single nucleotide polymorphisms, where more than half led to an amino acid change, and one resulted in a premature stop codon. Missense mutations were evaluated for changes in their amino acid properties to assess the potential effect on the novel HLA protein. All novelties identified were confirmed independently at another accredited HLA laboratory using a different NGS assay and platform to ensure validity in the reporting of novelties. The novel alleles were submitted to the Immuno Polymorphism Database-Immunogenetics/HLA (IPD-IMGT/HLA) for official allele name designation and inclusion in future database releases. A nationwide survey involving all Canadian HLA laboratories confirmed the common occurrence of novel allele detection but identified a wide variability in the assessment and reporting of novelties. In summary, a considerable proportion of novel alleles were identified in routine clinical testing. We propose a framework for the standardization of policies on the clinical management of novel alleles and inclusion in proficiency testing programs in the era of NGS-based HLA genotyping.
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Affiliation(s)
- Jenny N. Tran
- British Columbia Provincial Immunology Laboratory, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Karen R. Sherwood
- British Columbia Provincial Immunology Laboratory, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Ahmed Mostafa
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rey Vincent Benedicto
- British Columbia Provincial Immunology Laboratory, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Allaa ElaAlim
- British Columbia Provincial Immunology Laboratory, Vancouver Coastal Health, Vancouver, BC, Canada
| | | | - Paul Keown
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, University of British Columbia, Vancouver, BC, Canada
| | - Robert Liwski
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - James H. Lan
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, University of British Columbia, Vancouver, BC, Canada
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12
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Kalomoiri M, Prakash CR, Lagström S, Hauschulz K, Ewing E, Shchetynsky K, Kular L, Needhamsen M, Jagodic M. Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing. Front Immunol 2023; 14:1251772. [PMID: 37691926 PMCID: PMC10484099 DOI: 10.3389/fimmu.2023.1251772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
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Affiliation(s)
- Maria Kalomoiri
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chandana Rao Prakash
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sonja Lagström
- Diagnostics and Genomics Group, Agilent Technologies Sweden AB, Sundbyberg, Sweden
| | - Kai Hauschulz
- Diagnostics and Genomics Group, Agilent Technologies Deutschland GmbH, Waldbronn, Germany
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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13
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Niño Ramírez JE, Gil-Etayo FJ, Jiménez Hernaz I, García Sanz R, Tejeda Velarde A. The novel HLA-DQB1*03:02:01:14 allele was possibly generated by a recombination event. HLA 2023. [PMID: 37127400 DOI: 10.1111/tan.15051] [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: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
The novel HLA-DQB1*03:02:01:14 was likely generated by a recombination event between DQB1*03:02:01:01 and DQB1*03:03:02:01.
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Affiliation(s)
- Jairo Eduardo Niño Ramírez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
| | - Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Isabel Jiménez Hernaz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ramón García Sanz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
- Centro de Investigación del Cáncer (CIC), Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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14
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Detection and characterization of the novel HLA-DPA1*02:66:02N allele, with a premature stop codon in exon 2. Hum Immunol 2023; 84:296-300. [PMID: 36797092 DOI: 10.1016/j.humimm.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
The failure to identify HLA null alleles in bone marrow transplantation could be life-threatening because this could result in an HLA mismatch with the ability to trigger the graft-vs-host disease (GVHD) and to reduce patient's survival. In this report we describe the identification and characterization of the novel HLA-DPA1*02:66:02N allele with a non-sense codon in exon 2. This new allele was discovered in two unrelated bone marrow donors during routine HLA-typing using next-generation sequencing (NGS). DPA1*02:66:02N is homologous to DPA1*02:01:01:03 with a single nucleotide difference in exon 2, codon 50, where the replacement of C located at genomic position 3825 by T, causes the formation of a premature stop codon (TGA), resulting in a null allele. This description illustrates the benefits of HLA typing by NGS since it permits to reduce ambiguities, identify new alleles, analyze multiple HLA loci and improve transplantation outcome.
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15
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Cornaby C, Weimer ET. HLA Typing by Next-Generation Sequencing: Lessons Learned and Future Applications. Clin Lab Med 2022; 42:603-612. [PMID: 36368785 DOI: 10.1016/j.cll.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA.
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16
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Johansson T, Partanen J, Saavalainen P. HLA allele-specific expression: Methods, disease associations, and relevance in hematopoietic stem cell transplantation. Front Immunol 2022; 13:1007425. [PMID: 36248878 PMCID: PMC9554311 DOI: 10.3389/fimmu.2022.1007425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/09/2022] [Indexed: 11/27/2022] Open
Abstract
Varying HLA allele-specific expression levels are associated with human diseases, such as graft versus host disease (GvHD) in hematopoietic stem cell transplantation (HSCT), cytotoxic T cell response and viral load in HIV infection, and the risk of Crohn’s disease. Only recently, RNA-based next generation sequencing (NGS) methodologies with accompanying bioinformatics tools have emerged to quantify HLA allele-specific expression replacing the quantitative PCR (qPCR) -based methods. These novel NGS approaches enable the systematic analysis of the HLA allele-specific expression changes between individuals and between normal and disease phenotypes. Additionally, analyzing HLA allele-specific expression and allele-specific expression loss provide important information for predicting efficacies of novel immune cell therapies. Here, we review available RNA sequencing-based approaches and computational tools for NGS to quantify HLA allele-specific expression. Moreover, we explore recent studies reporting disease associations with differential HLA expression. Finally, we discuss the role of allele-specific expression in HSCT and how considering the expression quantification in recipient-donor matching could improve the outcome of HSCT.
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Affiliation(s)
- Tiira Johansson
- Translational Immunology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
- *Correspondence: Tiira Johansson,
| | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Genetics Research Program, Folkhälsan Research Center, Helsinki, Finland
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17
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Mulinacci G, Palermo A, Gerussi A, Asselta R, Gershwin ME, Invernizzi P. New insights on the role of human leukocyte antigen complex in primary biliary cholangitis. Front Immunol 2022; 13:975115. [PMID: 36119102 PMCID: PMC9471323 DOI: 10.3389/fimmu.2022.975115] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/11/2022] [Indexed: 01/04/2023] Open
Abstract
Primary Biliary Cholangitis (PBC) is a rare autoimmune cholangiopathy. Genetic studies have shown that the strongest statistical association with PBC has been mapped in the human leukocyte antigen (HLA) locus, a highly polymorphic area that mostly contribute to the genetic variance of the disease. Furthermore, PBC presents high variability throughout different population groups, which may explain the different geoepidemiology of the disease. A major role in defining HLA genetic contribution has been given by genome-wide association studies (GWAS) studies; more recently, new technologies have been developed to allow a deeper understanding. The study of the altered peptides transcribed by genetic alterations also allowed the development of novel therapeutic strategies in the context of immunotolerance. This review summarizes what is known about the immunogenetics of PBC with a focus on the HLA locus, the different distribution of HLA alleles worldwide, and how HLA modifications are associated with the pathogenesis of PBC. Novel therapeutic strategies are also outlined.
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Affiliation(s)
- Giacomo Mulinacci
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Andrea Palermo
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Merrill Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
- *Correspondence: Pietro Invernizzi,
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18
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He Y, Hong X, Zhang J, He J, Zhu F, Huang H. Analysis of the Genomic Sequence of ABO Allele Using Next-Generation Sequencing Method. Front Immunol 2022; 13:814263. [PMID: 35874750 PMCID: PMC9298404 DOI: 10.3389/fimmu.2022.814263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAlthough many molecular diagnostic methods have been used for ABO genotyping, there are few reports on the full-length genomic sequence analysis of the ABO gene. Recently, next-generation sequencing (NGS) has been shown to provide fast and high-throughput results and is widely used in the clinical laboratory. Here, we established an NGS method for analyzing the sequence of the start codon to the stop codon in the ABO gene.Study Design and MethodsTwo pairs of primers covering the partial 5’-untranslated region (UTR) to 3’-UTR of the ABO gene were designed. The sequences covering from the start codon to the stop codon of the ABO gene were amplified using these primers, and an NGS method based on the overlap amplicon was developed. A total of 110 individuals, including 88 blood donors with normal phenotypes and 22 ABO subtypes, were recruited and analyzed. All these specimens were first detected by serological tests and then determined by polymerase chain reaction sequence-based typing (PCR-SBT) and NGS. The sequences, including all the intron regions for the specimens, were analyzed by bioinformatics software.ResultsAmong the 88 blood donors with a normal phenotype, 48 homozygous individuals, 39 heterozygous individuals, and one individual with a novel O allele were found according to the results of the PCR-SBT method. Some single-nucleotide variants (SNV) in intronic regions were found to be specific for different ABO alleles from 48 homozygous individuals using the NGS method. Sequences in the coding region of all specimens using the NGS method were the same as those of the PCR-SBT method. Three intronic SNVs were found to be associated with the ABO subtypes, including one novel intronic SNV (c.28+5956T>A). Moreover, six specimens were found to exhibit DNA recombination.ConclusionAn NGS method was established to analyze the sequence from the start codon to the stop codon of the ABO gene. Two novel ABO alleles were identified, and DNA recombination was found to exist in the ABO alleles.
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Affiliation(s)
- Yanmin He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Xiaozhen Hong
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Jingjing Zhang
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ji He
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- Institute of Transfusion medicine, Blood Center of Zhejiang Province, Hangzhou, China
- Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
- *Correspondence: He Huang, ; Faming Zhu,
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, China
- *Correspondence: He Huang, ; Faming Zhu,
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19
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Shimizu M, Takahashi D, Suzuki S, Shigenari A, Ito S, Miyata S, Satake M, Matsuhashi M, Kulski JK, Murata M, Azuma F, Shiina T. A novel swab storage gel is superior to dry swab DNA collection, and enables long-range high resolution NGS HLA typing from buccal cell samples. HLA 2022; 99:590-606. [PMID: 35322605 DOI: 10.1111/tan.14611] [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: 11/04/2021] [Revised: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]
Abstract
HLA sequence-based DNA typing (SBT) by long-range PCR amplification (LR PCR) and next-generation sequencing (NGS) is a high-throughput DNA sequencing method (LR-NGS-SBT) for the efficient and sensitive detection of novel and null HLA alleles to the field-4 level of allelic resolution without phase ambiguity. However, the accuracy and reliability of the HLA typing results using buccal cells (BCs) and saliva as genetic source materials for the LR-NGS-SBT method are dependent largely on the quality of the extracted genomic DNA (gDNA) because a large degree of gDNA fragmentation can result in insufficient PCR amplification with the incorrect assignment of HLA alleles due to allele dropouts. In this study, we developed a new cost-efficient swab storage gel (SSG) for wet swab collection of BCs (BC-SSG) and evaluated its usefulness by performing different DNA analytical parameters including LR-NGS-SBT to compare the quality and quantity of gDNA extracted from BCs (in SSG or air dried), blood and saliva of 30 subjects. The BC-SSG samples after 5 days of storage revealed qualitative and quantitative DNA values equivalent to that of blood and/or saliva and better than swabs that were only air-dried (BC-nSSG). Moreover, all the gDNA extracted from blood, saliva and BC-SSG samples were HLA-typed successfully to an equivalent total of 408 alleles for each sample type. Therefore, the application of BC-SSG collection media for LR-NGS-SBT has benefits over BC dried samples (dry swabs) such as reducing retesting and the number of untestable BC samples due to insufficient DNA amplification. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marie Shimizu
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Shigeki Miyata
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Mika Matsuhashi
- Kanto-Koshinetsu Block Blood Center, Japanese Red Cross Society, Tokyo, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan.,Discipline of Psychiatry, Medical School, The University of Western Australia, Crawley, WA, Australia
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Fumihiro Azuma
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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20
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Immune Dysregulation in Autism Spectrum Disorder: What Do We Know about It? Int J Mol Sci 2022; 23:ijms23063033. [PMID: 35328471 PMCID: PMC8955336 DOI: 10.3390/ijms23063033] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental disorders characterized by a wide and variable set of neuropsychiatric symptoms, including deficits in social communication, narrow and restricted interests, and repetitive behavior. The immune hypothesis is considered to be a major factor contributing to autism pathogenesis, as well as a way to explain the differences of the clinical phenotypes and comorbidities influencing disease course and severity. Evidence highlights a link between immune dysfunction and behavioral traits in autism from several types of evidence found in both cerebrospinal fluid and peripheral blood and their utility to identify autistic subgroups with specific immunophenotypes; underlying behavioral symptoms are also shown. This review summarizes current insights into immune dysfunction in ASD, with particular reference to the impact of immunological factors related to the maternal influence of autism development; comorbidities influencing autism disease course and severity; and others factors with particular relevance, including obesity. Finally, we described main elements of similarities between immunopathology overlapping neurodevelopmental and neurodegenerative disorders, taking as examples autism and Parkinson Disease, respectively.
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21
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Yang J, Liu H, Pan W, Song M, Lu Y, Wang-Ngai Chow F, Hang-Mei Leung P, Deng Y, Hori M, He N, Li S. Recent Advances of Human Leukocyte Antigen (HLA) Typing Technology Based on High-Throughput Sequencing. J Biomed Nanotechnol 2022; 18:617-639. [PMID: 35715925 DOI: 10.1166/jbn.2022.3280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The major histocompatibility complex (MHC) in humans is a genetic region consisting of cell surface proteins located on the short arm of chromosome 6. This is also known as the human leukocyte antigen (HLA) region. The HLA region consists of genes that exhibit complex genetic polymorphisms, and are extensively involved in immune responses. Each individual has a unique set of HLAs. Donor-recipient HLA allele matching is an important factor for organ transplantation. Therefore, an established rapid and accurate HLA typing technology is instrumental to preventing graft-verses-host disease (GVHD) in organ recipients. As of recent, high-throughput sequencing has allowed for an increase read length and higher accuracy and throughput, thus achieving complete and high-resolution full-length typing. With more advanced nanotechnology used in high-throughput sequencing, HLA typing is more widely used in third-generation single-molecule sequencing. This review article summarizes some of the most widely used sequencing typing platforms and evaluates the latest developments in HLA typing kits and their clinical applications.
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Affiliation(s)
- Jin Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Mengru Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yutong Lu
- School of Electrical and Information Engineering, Hunan University, Changsha 410012, Hunan, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Masahi Hori
- 2-16-5 Edagawa, Koto-Ku, Tokyo, 135-0051, Japan
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
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22
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Concurrent use of two independent methods prevents erroneous HLA typing of deceased organ donors – An important strategy for patient safety and accurate virtual crossmatching for broader sharing. Hum Immunol 2022; 83:458-466. [DOI: 10.1016/j.humimm.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 11/21/2022]
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23
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
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24
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Anzar I, Sverchkova A, Samarakoon P, Ellingsen EB, Gaudernack G, Stratford R, Clancy T. Personalized
HLA
typing leads to the discovery of novel
HLA
alleles and tumor‐specific
HLA
variants. HLA 2022; 99:313-327. [PMID: 35073457 PMCID: PMC9546058 DOI: 10.1111/tan.14562] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/29/2022]
Abstract
Accurate and full‐length typing of the HLA region is important in many clinical and research settings. With the advent of next generation sequencing (NGS), several HLA typing algorithms have been developed, including many that are applicable to whole exome sequencing (WES). However, most of these solutions operate by providing the closest‐matched HLA allele among the known alleles in IPD‐IMGT/HLA Database. These database‐matching approaches have demonstrated very high performance when typing well characterized HLA alleles. However, as they rely on the completeness of the HLA database, they are not optimal for detecting novel or less well characterized alleles. Furthermore, the database‐matching approaches are also not adequate in the context of cancer, where a comprehensive characterization of somatic HLA variation and expression patterns of a tumor's HLA locus may guide therapy and clinical outcome, because of the pivotal role HLA alleles play in tumor antigen recognition and immune escape. Here, we describe a personalized HLA typing approach applied to WES data that leverages the strengths of database‐matching approaches while simultaneously allowing for the discovery of novel HLA alleles and tumor‐specific HLA variants, through the systematic integration of germline and somatic variant calling. We applied this approach on WES from 10 metastatic melanoma patients and validated the HLA typing results using HLA targeted NGS sequencing from patients where at least one HLA germline candidate was detected on Class I HLA. Targeted NGS sequencing confirmed 100% performance for the 1st and 2nd fields. In total, five out of the six detected HLA germline variants were because of Class I ambiguities at the third or fourth fields, and their detection recovered the correct HLA allele genotype. The sixth germline variant let to the formal discovery of a novel Class I allele. Finally, we demonstrated a substantially improved somatic variant detection accuracy in HLA alleles with a 91% of success rate in simulated experiments. The approach described here may allow the field to genotype more accurately using WES data, leading to the discovery of novel HLA alleles and help characterize the relationship between somatic variation in the HLA region and immunosurveillance.
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Affiliation(s)
- Irantzu Anzar
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Angelina Sverchkova
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Pubudu Samarakoon
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | | | - Gustav Gaudernack
- Ultimovacs ASA, Oslo Cancer Cluster, Ullernchausseen 64/66 Oslo Norway
| | - Richard Stratford
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Trevor Clancy
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
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25
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Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-Khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Cruzado JCM, Mezey JG, Shakaki AA, Malek JA, Greenblatt MB, Fakhro KA, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail SI, Althani A, Crystal RG. The QChip1 knowledgebase and microarray for precision medicine in Qatar. NPJ Genom Med 2022; 7:3. [PMID: 35046417 PMCID: PMC8770564 DOI: 10.1038/s41525-021-00270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Ramzi Temanni
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Monika Markovic
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Eiman Al-Khayat
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Fatima Qafoud
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Weill Cornell Medicine, Doha, Qatar
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
| | | | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Khalid A Fakhro
- Weill Cornell Medicine, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Ajayeb Al-Nabet
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Nahla Afifi
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Andrew Brooks
- RUCDR Infinite Biologics, Piscataway, NJ, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | | | - Asmaa Althani
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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Reis ALM, Deveson IW, Madala BS, Wong T, Barker C, Xu J, Lennon N, Tong W, Mercer TR. Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome. Genome Biol 2022; 23:19. [PMID: 35022065 PMCID: PMC8753822 DOI: 10.1186/s13059-021-02579-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-complexity, and repetitive regions that are difficult to sequence and analyze. Despite their difficulty, these regions include many clinically important sequences that can inform the treatment of human diseases and improve the diagnostic yield of NGS. RESULTS To evaluate the accuracy by which these difficult regions are analyzed with NGS, we built an in silico decoy chromosome, along with corresponding synthetic DNA reference controls, that encode difficult and clinically important human genome regions, including repeats, microsatellites, HLA genes, and immune receptors. These controls provide a known ground-truth reference against which to measure the performance of diverse sequencing technologies, reagents, and bioinformatic tools. Using this approach, we provide a comprehensive evaluation of short- and long-read sequencing instruments, library preparation methods, and software tools and identify the errors and systematic bias that confound our resolution of these remaining difficult regions. CONCLUSIONS This study provides an analytical validation of diagnosis using NGS in difficult regions of the human genome and highlights the challenges that remain to resolve these difficult regions.
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Affiliation(s)
- Andre L M Reis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ted Wong
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chris Barker
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tim R Mercer
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Australian Institute for Biotechnology and Nanoengineering, University of Queensland, Brisbane, QLD, Australia
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27
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Naito T, Okada Y. HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases. Semin Immunopathol 2022; 44:15-28. [PMID: 34786601 PMCID: PMC8837514 DOI: 10.1007/s00281-021-00901-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.
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Affiliation(s)
- Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan.
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
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28
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The Immunogenetics of Vasculitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:299-334. [DOI: 10.1007/978-3-030-92616-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Tait BD. The importance of establishing genetic phase in clinical medicine. Int J Immunogenet 2021; 49:1-7. [PMID: 34958529 DOI: 10.1111/iji.12567] [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: 08/28/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/27/2022]
Abstract
Haplotyping or determination of genetic phase has always played a pivotal role in MHC (HLA studies) both in helping to understand inheritance patterns in diseases such as type 1 diabetes (T1D) and in ensuring better matching in transplantation scenarios such as haematopoietic stem cell transplantation (HSCT), using donors genetically related to the patient. In recent years the need to establish genetic phase in a number of clinical scenarios has become apparent. These include: Genetic phasing for hematopoietic stem cell transplants using unrelated donors, where the HLA haplotypes are not known but where haplotype-matched recipients fare better clinically than allele matched, but haplotype mismatched patients. The use of checkpoint inhibitors is one of the most innovative and exciting developments in cancer treatment in years. An example is the use of the monoclonal ipilimumab to block the CTLA-4 receptor which is known to contain polymorphic sites. Until the phase of these polymorphisms is known it will not be possible to determine how effectively this monoclonal will perform in individual patients. The role of miRNA single strand molecules and their effect on gene expression. Thousands of non-coding genes have been identified and have been shown to be polymorphic, as have their target genes. Genetic phasing of polymorphism both in the miRNA source genes and their targets is clearly a fertile area of research In areas such a drug metabolism where the polymorphic family of CYP genes is responsible for the metabolism of the majority of prescription drugs, determining phase of SNPs is critical to understanding drug metabolism and efficacy. In multigenic disease studies combinations of single nucleotide polymorphisms (SNPs) in participating genes require accurate phasing in order to fully appreciate their role in the disease process. In addition, the level of expression of genes (point 3) is also important in understanding disease processes at the functional level. This review outlines the techniques that are currently available for approximating phase and discusses the clinical relevance of establishing genetic phase in areas of clinical medicine outlined in points 1-3.
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Affiliation(s)
- Brian D Tait
- Haplomic Technologies, Melbourne, Australia.,Department of Medicine, University of Melbourne, Royal Melbourne Hospital, Australia
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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31
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Piriyapongsa J, Sukritha C, Kaewprommal P, Intarat C, Triparn K, Phornsiricharoenphant K, Chaosrikul C, Shaw PJ, Chantratita W, Mahasirimongkol S, Tongsima S. PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. J Pers Med 2021; 11:1230. [PMID: 34834582 PMCID: PMC8618518 DOI: 10.3390/jpm11111230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addition, no tools exist to analyze human leukocyte antigen (HLA) genes for determining potential risks of immune-mediated adverse drug reaction (IM-ADR). We describe PharmVIP, a web-based PGx tool, for one-stop comprehensive analysis and interpretation of genome-wide variants obtained from NGS platforms. PharmVIP comprises three main interpretation modules covering analyses of pharmacogenes involved in pharmacokinetics, pharmacodynamics and IM-ADR. The Guideline module provides Clinical Pharmacogenetics Implementation Consortium (CPIC) drug guideline recommendations based on the translation of genotypic data in genes having guidelines. The HLA module reports HLA genotypes, potential adverse drug reactions, and the relevant drug guidelines. The Pharmacogenes module is employed for prioritizing variants according to variant effect on gene function. Detailed, customizable reports are provided as exportable files and as an interactive web version. PharmVIP is a new integrated NGS workflow for the PGx community to facilitate discovery and clinical application.
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Affiliation(s)
- Jittima Piriyapongsa
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chanathip Sukritha
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Pavita Kaewprommal
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chalermpong Intarat
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Kwankom Triparn
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Krittin Phornsiricharoenphant
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chadapohn Chaosrikul
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Phayathai, Bangkok 10400, Thailand;
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
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32
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Lee M, Seo JH, Song S, Song IH, Kim SY, Kim YA, Gong G, Kim JE, Lee HJ. A New Human Leukocyte Antigen Typing Algorithm Combined With Currently Available Genotyping Tools Based on Next-Generation Sequencing Data and Guidelines to Select the Most Likely Human Leukocyte Antigen Genotype. Front Immunol 2021; 12:688183. [PMID: 34659196 PMCID: PMC8517438 DOI: 10.3389/fimmu.2021.688183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022] Open
Abstract
Background High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate. Materials and Methods We compared availability, accuracy, correction score, and complementary ratio of eight HLA genotyping tools (OptiType, HLA-HD, PHLAT, seq2HLA, arcasHLA, HLAscan, HLA*LA, and Kourami) using 1,005 cases from the 1000 Genomes Project data. We created a new HLA-genotyping algorithm combining tools based on the precision and the accuracy of tools’ combinations. Then, we assessed the new algorithm’s performance in 39 in-house samples with normal whole-exome sequencing (WES) data and polymerase chain reaction–sequencing-based typing (PCR-SBT) results. Results Regardless of the type of tool, the calls presented by more than six tools concordantly showed high accuracy and precision. The accuracy of the group with at least six concordant calls was 100% (97/97) in HLA-A, 98.2% (112/114) in HLA-B, 97.3% (142/146) in HLA-C. The precision of the group with at least six concordant calls was over 98% in HLA-ABC. We additionally calculated the accuracy of the combination tools considering the complementary ratio of each tool and the accuracy of each tool, and the accuracy was over 98% in all groups with six or more concordant calls. We created a new algorithm that matches the above results. It was to select the HLA type if more than six out of eight tools presented a matched type. Otherwise, determine the HLA type experimentally through PCR-SBT. When we applied the new algorithm to 39 in-house cases, there were more than six matching calls in all HLA-A, B, and C, and the accuracy of these concordant calls was 100%. Conclusions HLA genotyping accuracy using NGS data could be increased by combining the current HLA genotyping tools. This new algorithm could also be useful for preliminary screening to decide whether to perform an additional PCR-based experimental method instead of using tools with NGS data.
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Affiliation(s)
- Miseon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jeong-Han Seo
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.,NeogenTC Corp, Seoul, South Korea
| | | | - In Hye Song
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Su Yeon Kim
- University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Gyungyub Gong
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Jeong Eun Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Hee Jin Lee
- Department of Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.,NeogenTC Corp, Seoul, South Korea.,Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
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33
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Cornaby C, Schmitz JL, Weimer ET. Next-generation sequencing and clinical histocompatibility testing. Hum Immunol 2021; 82:829-837. [PMID: 34521569 DOI: 10.1016/j.humimm.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
Histocompatibility testing is essential for donor identification and risk assessment in solid organ and hematopoietic stem cell transplant. Additionally, it is useful for identifying donor specific alleles for monitoring donor specific antibodies in post-transplant patients. Next-generation sequence (NGS) based human leukocyte antigen (HLA) typing has improved many aspects of histocompatibility testing in hematopoietic stem cell and solid organ transplant. HLA disease association testing and research has also benefited from the advent of NGS technologies. In this review we discuss the current impact and future applications of NGS typing on clinical histocompatibility testing for transplant and non-transplant purposes.
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Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA
| | - John L Schmitz
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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34
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Vasoya D, Oliveira PS, Muriel LA, Tzelos T, Vrettou C, Morrison WI, de Miranda Santos IKF, Connelley T. High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations. HLA 2021; 98:93-113. [PMID: 34102036 DOI: 10.1111/tan.14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 06/02/2021] [Indexed: 01/16/2023]
Abstract
The major histocompatibility complex (MHC) contains many genes that play key roles in initiating and regulating immune responses. This includes the polymorphic MHCI and MHCII genes that present epitopes to CD8+ and CD4+ T-cells, respectively. Consequently, the characterisation of the repertoire of MHC genes is an important component of improving our understanding of the genetic variation that determines the outcomes of immune responses. In cattle, MHC (BoLA) research has predominantly focused on Holstein-Friesian animals (as the most economically important breed globally), although the development of high-throughput approaches has allowed the BoLA-DRB3 repertoire to be studied in a greater variety of breeds. In a previous study we reported on the development of a MiSeq-based method to enable high-throughput and high-resolution analysis of bovine MHCI repertoires. Herein, we report on the expansion of this methodology to incorporate analysis of the BoLA-DRB3 and its application to analyse MHC diversity in a large cohort of cattle from Brazil (>500 animals), including representatives from the three major Bos indicus breeds present in Brazil - Guzerat, Gir and Nelore. This large-scale description of paired MHCI-DRB3 repertoires in Bos indicus cattle has identified a small number of novel DRB3 alleles, a large number of novel MHCI alleles and haplotypes, and provided novel insights into MHCI-MHCII association - further expanding our knowledge of bovine MHC diversity.
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Affiliation(s)
- Deepali Vasoya
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Priscila Silva Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
| | - Laura Agundez Muriel
- Translational Synthetic Biology Department, Mammalian genome editing and gene therapy, Parque de Investigación Biomédica, Carrer del Dr, Barcelona, Spain
| | - Thomas Tzelos
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Christina Vrettou
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - W Ivan Morrison
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Timothy Connelley
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
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35
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Yabe T, Satake M, Odajima T, Watanabe-Okochi N, Azuma F, Kashiwase K, Matsumoto K, Orihara T, Yabe H, Kato S, Kato K, Kai S, Mori T, Morishima S, Takanashi M, Nakajima K, Murata M, Morishima Y. Combined impact of HLA-allele matching and the CD34-positive cell dose on optimal unit selection for single-unit cord blood transplantation in adults. Leuk Lymphoma 2021; 62:2737-2746. [PMID: 34128753 DOI: 10.1080/10428194.2021.1929958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The combined effects of HLA-allele matching at six-loci (HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1) and CD34+ cell dose on clinical outcomes were analyzed in 1,226 adult cases with single-unit unrelated cord blood transplantation. In the six-loci analysis, low HLA-allele matches did not significantly increase the overall mortality compared to higher matches, whereas in the five-loci analysis excluding HLA-DPB1, they caused a higher overall mortality (HR 1.42, p = .002), possibly due to the graft-versus-leukemia effect of HLA-DPB1 mismatches. A lower CD34+ cell dose (<.50 × 105/kg) resulted in higher mortality and lower engraftment; these inferior outcomes were offset by high HLA-allele matches (7-10/10 match), while the inferior outcomes of low HLA-allele matches were improved by increasing the CD34+ cell dose. Consideration of the combined effects of the CD34+ cell dose and HLA matching may expand the options for transplantable units when HLA matching or the CD34+ cell dose is inadequate.
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Affiliation(s)
- Toshio Yabe
- Kanto-Koshin-etsu Block Blood Center, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Blood Service Headquarters, Tokyo, Japan
| | - Takeshi Odajima
- Kanto-Koshin-etsu Block Blood Center, Tokyo, Japan.,Central Blood Institute, Japanese Red Cross Blood Service Headquarters, Tokyo, Japan
| | | | - Fumihiro Azuma
- Kanto-Koshin-etsu Block Blood Center, Tokyo, Japan.,Japanese Red Cross Blood Service Headquarters, Tokyo, Japan
| | | | | | | | | | | | - Koji Kato
- Central Japan Cord Blood Bank, Seto, Japan
| | | | - Tetsuo Mori
- Japanese Red Cross Kyushu Cord Blood Bank, Chikushino, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | - Kazunori Nakajima
- Kanto-Koshin-etsu Block Blood Center, Tokyo, Japan.,Japanese Red Cross Kanto-Koshin-etsu Cord Blood Bank, Tokyo, Japan
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuo Morishima
- Central Japan Cord Blood Bank, Seto, Japan.,Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan
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36
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Kong D, Lee N, Dela Cruz ID, Dames C, Maruthamuthu S, Golden T, Rajalingam R. Concurrent typing of over 4000 samples by long-range PCR amplicon-based NGS and rSSO revealed the need to verify NGS typing for HLA allelic dropouts. Hum Immunol 2021; 82:581-587. [PMID: 33980471 DOI: 10.1016/j.humimm.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Hematopoietic stem cell transplantation (HSCT) from HLA-matched donors significantly decreases the risks of graft-rejection and graft-versus-host disease. Long-range PCR- amplicon-based next-generation sequencing (NGS) is increasingly used as a standalone method in clinical laboratories to determine HLA compatibility for HSCT and solid-organ transplantation. We hypothesized that an allelic dropout is a frequent event in the long-range PCR amplicon-based NGS HLA typing method. To test the hypothesis, we typed 4,006 samples concurrently using a commercially available long-range PCR amplicon-based NGS-typing and short exon-specific amplicon-based reverse sequence-specific oligonucleotide (rSSO) methods. The concordance between the NGS and rSSO typing results was 100% at HLA-A, -B, -C, -DRB1, -DRB3, -DRB5, -DQA1, DPA1 loci. However, 4.5% of the samples (179/4006) showed allelic-dropouts at one of the other three loci: HLA-DRB4 (3.9%), HLA-DPB1 (0.4%), and HLA-DQB1*(0.15%). The allelic-dropouts are not associated with specific haplotypes, and some dropouts can be reagent lot-specific. Although DRB1-DRB3/4/5-DQB1 linkages help to diagnose these allelic-dropouts in some cases, the rSSO typing was crucial to identify the dropouts in DQB1 and DPB1 loci. These results uncover the critical limitations of using long-range PCR amplicon-based NGS as a standalone method in clinical histocompatibility laboratories and advocate the need for strategies to diagnose and resolve allelic-dropouts.
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Affiliation(s)
- Denice Kong
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nancy Lee
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Imma Donna Dela Cruz
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Charlyn Dames
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Stalinraja Maruthamuthu
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Todd Golden
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
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37
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Ji X, Ning B, Liu J, Roberts R, Lesko L, Tong W, Liu Z, Shi T. Towards population-specific pharmacogenomics in the era of next-generation sequencing. Drug Discov Today 2021; 26:1776-1783. [PMID: 33892143 DOI: 10.1016/j.drudis.2021.04.015] [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: 04/07/2020] [Revised: 01/22/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
Pharmacogenomics (PGx) has essential roles in identifying optimal drug responders, optimizing dosage regimens and avoiding adverse events. Population-specific therapeutic interventions that tackle the genetic root causes of clinical outcomes are an important precision medicine strategy. In this perspective, we discuss next-generation sequencing genotyping and its significance for population-specific PGx applications. We emphasize the potential of NGS for preemptive pharmacogenotyping, which is crucial to population-specific clinical studies and patient care. We also provide examples that use publicly available population-based genomics data for population-specific PGx studies. Last, we discuss the remaining challenges and regulatory efforts towards improvements in this field.
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Affiliation(s)
- Xiangjun Ji
- The Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences and School of Life Sciences, School of Statistics, East China Normal University, Shanghai 200241, China; Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Jinghua Liu
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Larry Lesko
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA; Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, University of Florida at Lake Nona, Orlando, FL, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences and School of Life Sciences, School of Statistics, East China Normal University, Shanghai 200241, China; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA; National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
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38
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Yin Y, Butler C, Zhang Q. Challenges in the application of NGS in the clinical laboratory. Hum Immunol 2021; 82:812-819. [PMID: 33892986 DOI: 10.1016/j.humimm.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS), also known as massively parallel sequencing, has revolutionized genomic research. The current advances in NGS technology make it possible to provide high resolution, high throughput HLA typing in clinical laboratories. The focus of this review is on the recent development and implementation of NGS in clinical laboratories. Here, we examine the critical role of NGS technologies in clinical immunology for HLA genotyping. Two major NGS platforms (Illumina and Ion Torrent) are characterized including NGS library preparation, data analysis, and validation. Challenges of NGS implementation in the clinical laboratory are also discussed, including sequencing error rate, bioinformatics, result interpretation, analytic sensitivity, as well as large data storage. This review aims to promote the broader applications of NGS technology in clinical laboratories and advocate for the novel applications of NGS to drive future research.
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Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Carrie Butler
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA.
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39
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Johansson T, Yohannes DA, Koskela S, Partanen J, Saavalainen P. HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression. Front Immunol 2021; 12:629059. [PMID: 33717155 PMCID: PMC7949471 DOI: 10.3389/fimmu.2021.629059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
The HLA gene complex is the most important single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. Most studies have focused on the vast allelic variation in these genes; only a few studies have explored differences in the expression levels of HLA alleles. In this study, we quantified mRNA expression levels of HLA class I and II genes from peripheral blood samples of 50 healthy individuals. The gene- and allele-specific mRNA expression was assessed using unique molecular identifiers, which enabled PCR bias removal and calculation of the number of original mRNA transcripts. We identified differences in mRNA expression between different HLA genes and alleles. Our results suggest that HLA alleles are differentially expressed and these differences in expression levels are quantifiable using RNA sequencing technology. Our method provides novel insights into HLA research, and it can be applied to quantify expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.
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Affiliation(s)
- Tiira Johansson
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Dawit A. Yohannes
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
| | - Satu Koskela
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Päivi Saavalainen
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
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40
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Cook S, Choi W, Lim H, Luo Y, Kim K, Jia X, Raychaudhuri S, Han B. Accurate imputation of human leukocyte antigens with CookHLA. Nat Commun 2021; 12:1264. [PMID: 33627654 PMCID: PMC7904773 DOI: 10.1038/s41467-021-21541-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
The recent development of imputation methods enabled the prediction of human leukocyte antigen (HLA) alleles from intergenic SNP data, allowing studies to fine-map HLA for immune phenotypes. Here we report an accurate HLA imputation method, CookHLA, which has superior imputation accuracy compared to previous methods. CookHLA differs from other approaches in that it locally embeds prediction markers into highly polymorphic exons to account for exonic variability, and in that it adaptively learns the genetic map within MHC from the data to facilitate imputation. Our benchmarking with real datasets shows that our method achieves high imputation accuracy in a wide range of scenarios, including situations where the reference panel is small or ethnically unmatched.
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Affiliation(s)
- Seungho Cook
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Wanson Choi
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyunjoon Lim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kunhee Kim
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Xiaoming Jia
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Buhm Han
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea.
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41
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Jekarl DW, Lee GD, Yoo JB, Kim JR, Yu H, Yoo J, Lim J, Kim M, Kim Y. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing. HLA 2021; 97:188-197. [PMID: 33314756 DOI: 10.1111/tan.14167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing. METHODS From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform. RESULTS A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing. CONCLUSIONS NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.
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Affiliation(s)
- Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jae Bin Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jung Rok Kim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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Kang K, Sun Y, Li YL, Chang B. Pathogenesis of liver injury in Takayasu arteritis: advanced understanding leads to new horizons. J Int Med Res 2020; 48:300060520972222. [PMID: 33275473 PMCID: PMC7720339 DOI: 10.1177/0300060520972222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver injury in Takayasu arteritis (TA) is a rare phenomenon. Most symptoms are nonspecific, and the exact pathogenesis remains to be elucidated. Early diagnosis and new treatment methods are important for an improved prognosis. A summary of the clinical information and mechanistic analyses may contribute to making an early diagnosis and development of new treatment methods. A PubMed search was conducted using the specific key words “Takayasu arteritis” and “liver” or “hepatitis” or “hepatic”. Symptoms and treatment of TA with an accompanying liver injury were reviewed retrospectively. Many factors are presumed to be involved in the mechanism of TA with liver injury, including the immune response, genes, infections, and gut microbiota. There are several lines of evidence indicating that immune dysfunction is the main pathogenic factor that triggers granuloma formation in TA patients. However, the role of genetics and infections has not been fully confirmed. Recently, the gut microbiota has emerged as an essential component in the process. We reviewed in detail the current concepts that support the complex pathogenesis of TA accompanied by liver injury, and we presented recent theories from the literature. Finally, we discussed future research directions of liver injury in TA.
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Affiliation(s)
- Kai Kang
- Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yue Sun
- Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yi Ling Li
- Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Bing Chang
- Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang, China
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43
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Analysis of HLA-G long-read genomic sequences in mother-offspring pairs with preeclampsia. Sci Rep 2020; 10:20027. [PMID: 33208885 PMCID: PMC7675977 DOI: 10.1038/s41598-020-77081-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/06/2020] [Indexed: 11/11/2022] Open
Abstract
Preeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.
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44
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Ingrassia F, Pecoraro A, Blando M, Bruno F, Lo Brutto A, Mistretta S, Bavetta R, Cappuzzo V. Identification of a single nucleotide deletion in the novel HLA-DQB1*06:379N allele, detected by Polymerase Chain Reaction-Sequence Based Typing but not by Next Generation Sequencing. HLA 2020; 96:709-713. [PMID: 33006267 DOI: 10.1111/tan.14083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
In this report we describe the characterization of a novel null HLA-DQB1 allele, detected by polymerase chain reaction-sequence-based typing but not by next-generation sequencing (NGS). The new allele, HLA-DQB1*06:379N, was discovered in an Italian patient with acute myeloid leukemia and also in one of her healthy siblings. The new allele is largely homologous to DQB1*06:02:01:01 with a T deletion in exon 2, in codon 11, which causes a frameshift and the formation of an unusual and premature TGA STOP in codon 27. This case report underlines the importance of not removing Sanger method sequencing from routine use for high-resolution HLA typing, but to maintain it together with NGS technology.
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Affiliation(s)
- Francesco Ingrassia
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Alice Pecoraro
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Maria Blando
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Floriana Bruno
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Angela Lo Brutto
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Serena Mistretta
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Rosalba Bavetta
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
| | - Valentina Cappuzzo
- Laboratorio Regionale di Tipizzazione Tessutale ed Immunologia dei Trapianti, U.O.C. Medicina Trasfusionale e dei Trapianti-A.O.R. Villa Sofia-Cervello, Palermo, Italy
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Novel HLA Class I Alleles Outside the Extended DR3 Haplotype Are Protective against Autoimmune Hepatitis. Clin Transl Gastroenterol 2020; 10:e00032. [PMID: 31211758 PMCID: PMC6613860 DOI: 10.14309/ctg.0000000000000032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
HLA class II allele, DRB1*03:01, is the most common genetic risk factor for autoimmune hepatitis (AIH), but other unrecognized HLA related risks exist.
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46
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HLA-B*39:01:01 is a novel risk factor for antithyroid drug-induced agranulocytosis in Japanese population. THE PHARMACOGENOMICS JOURNAL 2020; 21:94-101. [PMID: 32963330 DOI: 10.1038/s41397-020-00187-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 09/08/2020] [Indexed: 12/30/2022]
Abstract
Antithyroid drug (ATD) is a mainstay of Graves' disease (GD). About 0.1-0.5% of patients with GD treated with ATD exhibit ATD-induced agranulocytosis, which is characterized by severe reduction of circulating neutrophils. Immune-mediated responses have been proposed as a possible mechanism for the pathogenesis of ATD-induced agranulocytosis. Although it has been reported that the HLA class II allele (HLA-DRB1*08:03) was associated with ATD-induced agranulocytosis in multiple populations, the entire HLA region have not been explored in Japanese. Therefore, we performed HLA sequencing for 10 class I and 11 class II genes in 87 patients with ATD-induced agranulocytosis and 384 patients with GD who did not show ATD-induced agranulocytosis. By conducting case-control association studies at the HLA allele and haplotype levels, we replicated the association between HLA-DRB1*08:03:02 and ATD-induced agranulocytosis (P = 5.2 × 10-7, odds ratio = 2.80), and identified HLA-B*39:01:01 as an independent risk factor (P = 1.4 × 10-3, odds ratio = 3.35). To verify reproducibility of the novel association of HLA-B*39:01:01, we reanalyzed allele frequency data for HLA-B*39:01:01 from previous case-control association studies. The association of HLA-B*39:01:01 was significantly replicated in Chinese (P = 9.0 × 10-3), Taiwanese (P = 1.1 × 10-3), and European populations (P = 5.2 × 10-4). A meta-analysis combining results from the previous and current studies reinforced evidence of the association between HLA-B*39:01:01 and ATD-induced agranulocytosis (Pmeta = 1.2 × 10-9, pooled OR = 3.66, 95% CI; 2.41-5.57). The results of this study will provide a better understanding of the pathogenesis of ATD-induced agranulocytosis in the context of HLA-mediated hypersensitivity reactions.
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Zhang Y, Chen Y, Xu H, Fang J, Zhao Z, Hu W, Yang X, Ye J, Cheng Y, Wang J, Sun W, Wang J, Yang H, Yan J, Fang L. SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. BMC Bioinformatics 2020; 21:295. [PMID: 32640979 PMCID: PMC7646500 DOI: 10.1186/s12859-020-03624-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/22/2020] [Indexed: 12/30/2022] Open
Abstract
Background The human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing, the golden standard technology for HLA typing enables accurate identification of HLA alleles in high-resolution. However, only the commercial software, such as uTYPE, SBT-Assign, and SBTEngine, and very few open-source tools could be applied to perform HLA typing based on Sanger sequencing. Results We developed a user-friendly, cross-platform and open-source desktop application, known as SOAPTyping, for Sanger-based typing in HLA class I and II alleles. SOAPTyping can produce accurate results with a comprehensible protocol and featured functions. Moreover, SOAPTyping supports a more advanced group-specific sequencing primers (GSSP) module to solve the ambiguous typing results. We used SOAPTyping to analyze 36 samples with known HLA typing from the University of California Los Angeles (UCLA) International HLA DNA Exchange platform and 100 anonymous clinical samples, and the HLA typing results from SOAPTyping are identical to the golden results and 5.5 times faster than commercial software uTYPE, which shows the usability of SOAPTyping. Conclusions We introduce the SOAPTyping as the first open-source and cross-platform HLA typing software with the capability of producing high-resolution HLA typing predictions from Sanger sequence data.
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Affiliation(s)
- Yong Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Huixin Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Weipeng Hu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | | | - Jia Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Cheng
- Zhejiang Hospital, No 12 Lingyin Road, Hangzhou, 310013, Xihu District, China
| | - Jiayin Wang
- Department of Computer Science and Technology, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an, 710048, Shaanxi, China
| | - Weiqiang Sun
- Shanghai Institute for Advanced Communication and Data Science, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Science, Hangzhou, 310008, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Science, Hangzhou, 310008, China
| | - Jing Yan
- Zhejiang Hospital, No 12 Lingyin Road, Hangzhou, 310013, Xihu District, China.
| | - Lin Fang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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48
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Yamamoto F, Suzuki S, Mizutani A, Shigenari A, Ito S, Kametani Y, Kato S, Fernandez-Viña M, Murata M, Morishima S, Morishima Y, Tanaka M, Kulski JK, Bahram S, Shiina T. Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. Front Immunol 2020; 11:941. [PMID: 32547543 PMCID: PMC7272581 DOI: 10.3389/fimmu.2020.00941] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/22/2020] [Indexed: 12/19/2022] Open
Abstract
The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10-15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases.
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Affiliation(s)
- Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Akiko Mizutani
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Faculty of Health and Medical Science, Teikyo Heisei University, Toshima-ku, Tokyo, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Sayaka Ito
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shunichi Kato
- Division of Hematopoietic Cell Transplantation, Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Stanford Health Care, Palo Alto, CA, United States
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yasuo Morishima
- Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire OMICARE, Laboratoire International Associé INSERM FJ-HLA-Japan, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Faculté de Médecine, Université de Strasbourg, Service d'Immunologie Biologique, Nouvel Hôpital Civil, Strasbourg, France
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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49
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Do MD, Le LGH, Nguyen VT, Dang TN, Nguyen NH, Vu HA, Mai TP. High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing. Front Genet 2020; 11:383. [PMID: 32425978 PMCID: PMC7204072 DOI: 10.3389/fgene.2020.00383] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) genotyping displays the particular characteristics of HLA alleles and haplotype frequencies in each population. Although it is considered the current gold standard for HLA typing, high-resolution sequence-based HLA typing is currently unavailable in Kinh Vietnamese populations. In this study, high-resolution sequence-based HLA typing (3-field) was performed using an amplicon-based next-generation sequencing platform to identify the HLA-A, -B, -C, -DRB1, and -DQB1 alleles of 101 unrelated healthy Kinh Vietnamese individuals from southern Vietnam. A total of 28 HLA-A, 41 HLA-B, 21 HLA-C, 26 HLA-DRB1, and 25 HLA-DQB1 alleles were identified. The most frequently occurring HLA alleles were A∗11:01:01, B∗15:02:01, C∗07:02:01, DRB1∗12:02:01, and DQB1∗03:01:01. Haplotype calculation showed that A∗29:01:01∼B∗07:05:01, DRB1∗12:02:01∼DQB1∗3:01:01, A∗29:01:01∼C∗15:05:02∼B∗07:05:01, A∗33:03:01∼B∗58:01:01∼DRB1∗03:01:01, and A∗29:01:01∼C∗15:05:02∼B∗07:05:01∼DRB1∗10:01:01∼DQB1∗05:01:01 were the most common haplotypes in the southern Kinh Vietnamese population. Allele distribution and haplotype analyses demonstrated that the Vietnamese population shares HLA features with South-East Asians but retains unique characteristics. Data from this study will be potentially applicable in medicine and anthropology.
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Affiliation(s)
- Minh Duc Do
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Gia Hoang Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh The Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Ngoc Dang
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia Hoai Nguyen
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao Phuong Mai
- Department of Physiology, Pathophysiology and Immunology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
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50
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Del Río-Ospina L, Camargo M, Soto-De León SC, Sánchez R, Moreno-Pérez DA, Patarroyo ME, Patarroyo MA. Identifying the HLA DRB1-DQB1 molecules and predicting epitopes associated with high-risk HPV infection clearance and redetection. Sci Rep 2020; 10:7306. [PMID: 32350356 PMCID: PMC7190668 DOI: 10.1038/s41598-020-64268-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
Several determining factors are involved in HPV infection outcomes; human leukocyte antigen (HLA) polymorphisms have been described as related factors. This study has ascertained the effect of genetic variation on HLA-DRB1 and DQB1 genes on HPV-16/-18/-31/-33/-45 and -58 clearance and redetection in Colombian women. PCR and qPCR were used for viral identification and the Illumina MiSeq system was used for HLA-typing of cervical samples (n = 276). Survival models were adjusted for identifying alleles/haplotypes related to HPV clearance/redetection; L1/L2 protein-epitope binding to MHC-II molecules was also predicted. Significant associations suggested effects favouring or hampering clearance/redetection events depending on the viral type involved in infection, e.g. just DRB1*12:01:01G favoured HPV-16 (coeff: 4.8) and HPV-45 clearance (coeff: 12.65) whilst HPV-18 (coeff: 2E-15), HPV-31 (coeff: 8E-17) and HPV-58 hindered elimination (coeff: 1E-14). An effect was only observed for some alelles when configured as haplotypes, e.g. DRB1*04:07:01G (having the greatest frequency in the target population) was associated with DQB1*02:01:1G or *03:02:03. Epitope prediction identified 23 clearance-related peptides and 29 were redetection-related; eight might have been related to HPV-16/-18 and -58 persistence and one to HPV-18 elimination. HLA allele/haplotype relationship with the course of HPV infection (clearance/redetection) depended on the infecting HPV type, in line with the specific viral epitopes displayed.
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Affiliation(s)
- Luisa Del Río-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia
- Clinical Research Group, Instituto Nacional de Cancerología, Calle 1 # 9-85, Bogotá, Colombia
| | - Milena Camargo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia
- PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222 # 55-37, Bogotá, Colombia
| | - Sara C Soto-De León
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia
| | - Ricardo Sánchez
- Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45 # 26-85, Bogotá, Colombia
| | - Darwin A Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Manuel E Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia
- Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45 # 26-85, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Carrera 50 # 26-20, Bogotá, Colombia.
- School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia.
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