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Raos M, Zunec R, Mocibob M, Gojceta K, Lukic M, Golubic Cepulic B. Susceptible and protective HLA‐DR and HLA‐DQ alleles for Fy
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alloimmunization in the Croatian population. Transfusion 2018; 59:1118-1124. [DOI: 10.1111/trf.15087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/11/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Mirela Raos
- Clinical Department of Transfusion Medicine and Transplantation BiologyUniversity Hospital Center Zagreb Zagreb Croatia
| | - Renata Zunec
- Clinical Department of Transfusion Medicine and Transplantation BiologyUniversity Hospital Center Zagreb Zagreb Croatia
| | - Marko Mocibob
- Department of Chemistry, Faculty of ScienceUniversity of Zagreb Zagreb Croatia
| | - Koraljka Gojceta
- Clinical Department of Transfusion Medicine and Transplantation BiologyUniversity Hospital Center Zagreb Zagreb Croatia
| | - Marija Lukic
- Clinical Department of Transfusion Medicine and Transplantation BiologyUniversity Hospital Center Zagreb Zagreb Croatia
| | - Branka Golubic Cepulic
- Clinical Department of Transfusion Medicine and Transplantation BiologyUniversity Hospital Center Zagreb Zagreb Croatia
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McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A. Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing. Hum Immunol 2015; 76:917-22. [PMID: 26027778 DOI: 10.1016/j.humimm.2015.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 02/05/2023]
Abstract
We report the development of a general methodology to genotype HLA class I and class II loci. A Whole Genome Amplification (WGA) step was used as a sample sparing methodology. HLA typing data could be obtained with as few as 300 cells, underlining the usefulness of the methodology for studies for which limited cells are available. The next generation sequencing platform was validated using a panel of cell lines from the International Histocompatibility Working Group (IHWG) for HLA-A, -B, and -C. Concordance with the known, previously determined HLA types was 99%. We next developed a panel of primers to allow HLA typing of alpha and beta chains of the HLA DQ and DP loci and the beta chain of the DRB1 locus. For the beta chain genes, we employed a novel strategy using primers in the intron regions surrounding exon 2, and the introns surrounding exons 3 through 4 (DRB1) or 5 (DQB1 and DPB1). Concordance with previously determined HLA Class II types was also 99%. To increase throughput and decrease cost, we developed strategies combining multiple loci from each donor. Multiplexing of 96 samples per run resulted in increases in throughput of approximately 8-fold. The pipeline developed for this analysis (HLATyphon) is available for download at https://github.com/LJI-Bioinformatics/HLATyphon.
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Affiliation(s)
- Denise M McKinney
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Zheng Fu
- Bioinformatics Core Facility, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Lucas Le
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Jason A Greenbaum
- Bioinformatics Core Facility, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA.
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Yang J, Lu H, Guo R, Yan D, Ye P, Jin L, Chen C, Cao H, Diao H, Li L. Molecular profile of the T cell receptor beta variable in peripheral blood lymphocytes from chronic asymptomatic HBV carriers. Pathog Dis 2014; 73:1-9. [PMID: 25722488 DOI: 10.1093/femspd/ftu018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Renyong Guo
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Ping Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Linfeng Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Chunlei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Hongcui Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
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Silvy M, Beley S, Granier T, Ba A, Chiaroni J, Bailly P. Heterogeneity of alleles encoding high- and low-prevalence red blood cell antigens across Africa: useful data to facilitate transfusion in African patients. Br J Haematol 2013; 163:528-36. [PMID: 24032660 DOI: 10.1111/bjh.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/20/2013] [Indexed: 11/27/2022]
Abstract
Ethnic variations in red blood cell (RBC) antigens can be a source of alloimmunization, especially in migrant populations. To improve transfusion safety in continental Africa and countries with African migrants, we performed RBC genotyping to determine allele frequencies coding for high- and low-prevalence antigens. A total of 481 blood samples were collected in ethnic groups from West, Central and East Africa. Molecular typing was performed using a polymerase chain reaction - reverse sequence specific oligonucleotide method. Results demonstrated no DI*1, DI*3, YT*2, SC*2, LW*7, KN*2 alleles in any sample and the CO*2 allele was rare. The frequency of LU*1 was comparable to that of European-Caucasians (2%) except in Biaka pygmies (8%). The frequency of CROM*-1 was high in Mbuti pygmies (13%). High frequency of KN*7 and KN*6 may reflect selection pressure in the countries investigated. Analysis of Dombrock allele patterns confirmed uneven distribution of the DO*1 and DO*2 alleles with high frequencies of DO*-4 and DO*-5 in all groups. Altogether, findings demonstrated extensive allele-frequency heterogeneity across Africa and suggested that knowledge of patient ethnicity gives information about the high-prevalence antigens that may be lacking. These data are medically useful to support transfusion care of African migrants living in countries where the majority of the population is from a different ethnical background.
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Affiliation(s)
- Monique Silvy
- Etablissement Français du Sang Alpes Méditerranée, Marseille, France; Aix Marseille Université, EFS, ADES UMR, 7268, Marseille, France
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Yoshizawa A, Egawa H, Yurugi K, Hishida R, Tsuji H, Ashihara E, Miyagawa-Hayashino A, Teramukai S, Maekawa T, Haga H, Uemoto S. Significance of semiquantitative assessment of preformed donor-specific antibody using luminex single bead assay in living related liver transplantation. Clin Dev Immunol 2013; 2013:972705. [PMID: 23818917 DOI: 10.1155/2013/972705] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 03/19/2013] [Accepted: 04/24/2013] [Indexed: 01/18/2023]
Abstract
Aim. To analyze the risks of preoperatively produced donor-specific antibody (DSA) in liver transplantation. Methods. DSA was assessed using direct complement-dependent cytotoxicity (CDC) and anti-human globulin- (AHG-) CDC tests, as well as the Luminex Single Antigen assay. Among 616 patients undergoing blood type identical or compatible living donor liver transplantation (LDLT), 21 patients were positive for CDC or AHG-CDC tests, and the preserved serum from 18 patients was examined to determine targeted Class I and II antigens. The relationships between the mean fluorescence intensity (MFI) of DSA and the clinical outcomes were analyzed. Results. Patients were divided into 3 groups according to the MFI of anti-Class I DSA: high (11 patients with MFI > 10,000), low (2 patients with MFI < 10,000), and negative (5 patients) MFI groups. Six of 11 patients with high Class-I DSA showed positive Class-II DSA. Hospital death occurred in 7 patients of the high MFI group. High MFI was a significant risk factor for mortality (P = 0.0155). Univariate analysis showed a significant correlation between MFI strength and C4d deposition (P = 0.0498). Conclusions. HLA Class I DSA with MFI > 10,000 had a significant negative effect on the clinical outcome of patients with preformed DSA in LDLT.
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Kaewmanee M, Phoksawat W, Romphruk A, Romphruk AV, Jumnainsong A, Leelayuwat C. Development of a multiplex polymerase chain reaction-sequence-specific primer method for NKG2D and NKG2F single-nucleotide polymorphism typing using isothermal multiple displacement amplification products. ACTA ACUST UNITED AC 2013; 81:419-27. [PMID: 23530727 DOI: 10.1111/tan.12105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
Abstract
Natural killer group 2 member D (NKG2D) on immune effector cells recognizes multiple stress-inducible ligands. NKG2D single-nucleotide polymorphism (SNP) haplotypes were related to the levels of cytotoxic activity of peripheral blood mononuclear cells. Indeed, these polymorphisms were also located in NKG2F. Isothermal multiple displacement amplification (IMDA) is used for whole genome amplification (WGA) that can amplify very small genomic DNA templates into microgram with whole genome coverage. This is particularly useful in the cases of limited amount of valuable DNA samples requiring multi-locus genotyping. In this study, we evaluated the quality and applicability of IMDA to genetic studies in terms of sensitivity, efficiency of IMDA re-amplification and stability of IMDA products. The smallest amount of DNA to be effectively amplified by IMDA was 200 pg yielding final DNA of approximately 16 µg within 1.5 h. IMDA could be re-amplified only once (second round of amplification), and could be kept for 5 months at 4°C and more than a year at -20°C without loosing genome coverage. The amplified products were used successfully to setup a multiplex polymerase chain reaction-sequence-specific primer for SNP typing of the NKG2D/F genes. The NKG2D/F multiplex polymerase chain reaction (PCR) contained six PCR mixtures for detecting 10 selected SNPs, including 8 NKG2D/F SNP haplotypes and 2 additional NKG2D coding SNPs. This typing procedure will be applicable in both clinical and research laboratories. Thus, our data provide useful information and limitations for utilization of genome-wide amplification using IMDA and its application for multiplex NKG2D/F typing.
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Affiliation(s)
- M Kaewmanee
- Biomedical Sciences Program, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
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Sun C, Wei L, Luo F, Li Y, Li J, Zhu F, Kang P, Xu R, Xiao L, Liu Z, Xu P. HLA-DRB1 alleles are associated with the susceptibility to sporadic Parkinson's disease in Chinese Han population. PLoS One 2012; 7:e48594. [PMID: 23139797 PMCID: PMC3490875 DOI: 10.1371/journal.pone.0048594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/26/2012] [Indexed: 12/19/2022] Open
Abstract
Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The χ(2) test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate.
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Affiliation(s)
- Congcong Sun
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lei Wei
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Feifei Luo
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
- Department of Neurology, The Third People’s Hospital of Chengdu, Chengdu, People’s Republic of China
| | - Yi Li
- Department of Neurology, Department of Neurology, Red-Cross Hospital in Guangzhou, Guangzhou, People’s Republic of China
| | - Jiaobiao Li
- Department of Neurology, HeYuan City Hospital, Guangdong, People’s Republic of China
| | - Feiqi Zhu
- Department of Neurology, Yuebei People's Hospital of Shantou University Medical College, Guangdong, People’s Republic of China
| | - Ping Kang
- Department of Neurology, The First People’s Hospital of Shaoguan, Guangdong, People’s Republic of China
| | - Rensi Xu
- Department of Neurology, The First Affiliated Hospital of NanChang University, NanChang, People’s Republic of China
| | - LuLu Xiao
- Department of Tissue Typing Center, Nanfang Hospital of Southern Medical University, Guangzhou, People’s Republic of China
| | - Zhuolin Liu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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Chainonthee W, Böttcher G, Gagne K, Füssel M, Bignon JD, Wassmuth R. Improved KIR gene and HLA-C KIR ligand sequence-specific primer polymerase chain reaction genotyping using whole genome amplification. ACTA ACUST UNITED AC 2010; 76:135-43. [PMID: 20403144 DOI: 10.1111/j.1399-0039.2010.01479.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular analysis of genetic polymorphism for clinical or research purposes may be compromised by genomic DNA of limited quality and quantity. In this study, we have successfully tested the feasibility of using whole genome amplification (WGA) to allow genotyping for killer cell immunoglobulin-like receptor (KIR) genes and human leucocyte antigen (HLA)-C KIR ligand dimorphism on HLA-C. WGA was achieved by multiple displacement amplification (MDA) using bacteriophage phi29 polymerase. For KIR genotyping, a revised sequence-specific primer polymerase chain reaction protocol consisting of 23 primer pairs was used avoiding hitherto undetected cross-priming involving KIR2DL1, KIR2DS1, KIR3DL1 and KIR3DS1 alleles. Similarly, MDA-amplified genomic DNA was analyzed for the detection of the HLA-C KIR ligand groups C1 and C2, based on the amino acid K/N dimorphism in position 80.
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Affiliation(s)
- W Chainonthee
- Medizinische Klinik u. Poliklinik I, Universitätsklinikum Carl Gustav Carus der Technischen Universität Dresden, Dresden, Germany
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Lemnrau AG, Cardoso S, Creary LE, Brown C, Miretti M, Girdlestone J, Navarrete CV. Human platelet antigen typing of neonatal alloimmune thrombocytopenia patients using whole genome amplified DNA and a 5'-nuclease assay. Transfusion 2009; 49:953-8. [PMID: 19175554 DOI: 10.1111/j.1537-2995.2008.02064.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND A serious constraint in the investigation of the human platelet antigen (HPA) status of potential neonatal alloimmune thrombocytopenia (NAIT) cases is the limited amount of DNA available from the neonates. Whole genome amplification (WGA) of these DNA samples could overcome this problem, but requires validation to ensure that it is sufficiently sensitive and accurate before its application in a clinical diagnostic setting. STUDY DESIGN AND METHODS This study has validated the use of WGA DNA for HPA-1, -2, -3, -4, -5, and -15 genotyping with a panel of six controls and 13 previously HPA-typed samples from neonates together with parental DNA, using a 5'-nuclease (TaqMan) assay. WGA was performed using titrated amounts of genomic and WGA DNA template. HPA typing was performed on genomic and amplified DNA using a 5'-nuclease assay or polymerase chain reaction with sequence-specific primers (PCR-SSP). RESULTS WGA DNA yields were in the suggested range of 400x to 800x, as assessed by spectrophotometry and gel analysis, and did not require further purification. HPA genotyping showed 100 percent concordance when using down to 5 ng of genomic or WGA template. CONCLUSION This study demonstrates that WGA can be used for HPA typing using PCR-SSP or plate-based 5'-nuclease assays. The use of WGA for HPA typing in clinical samples from NAIT patients was validated with 100 percent concordance, and it is suggested that this technology can be used for other analyses where DNA amounts are limited.
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Affiliation(s)
- Alina G Lemnrau
- Histocompatibility & Immunogenetics Department, NHSBT, London, UK
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