scholarly journals SOAPTyping: an open-source and cross-platform tool for Sanger sequence-based typing for HLA class I and II alleles

2019 ◽  
Author(s):  
Yong Zhang ◽  
Yongsheng Chen ◽  
Huixin Xu ◽  
Junbin Fang ◽  
Zijian Zhao ◽  
...  
Keyword(s):  
Open Source ◽  
Sanger Sequencing ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Hla Typing ◽  
Class I ◽  
Supplementary Information ◽  
Accurate Identification ◽  
Sanger Sequence ◽  
Cross Platform

ABSTRACTSummaryThe 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 gold standard technology for HLA typing – enables accurate identification of HLA alleles with high-resolution. However, there exists a current hurdle that only commercial software such as UType, SBT-Assign and SBTEngine, instead of any open source tools could be applied to perform HLA typing based on Sanger sequencing. To fill the gap, we developed a stand-alone, open-source and cross-platform software, known as SOAPTyping, for Sanger-based typing in HLA class I and II alleles.Availability and implementationSOAPTyping is implemented in C++ language and Qt framework, which is supported on Windows, Mac and Linux. Source code and detailed documentation are accessible via the project GitHub page: https://github.com/BGI-flexlab/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Mislabeled units of umbilical cord blood detected by a quality assurance program at the transplantation center

Blood ◽  
2009 ◽  
Vol 114 (8) ◽  
pp. 1684-1688 ◽  
Author(s):  
Jeffrey McCullough ◽  
David McKenna ◽  
Diane Kadidlo ◽  
David Maurer ◽  
Harriett J. Noreen ◽  
...  
Keyword(s):  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Hla Typing ◽  
Class I ◽  
Quality Assurance Program ◽  
Cord Blood Unit ◽  
Transplantation Center

Abstract We instituted procedures to check the identity of cord blood unit provided for transplantation by carrying out ABO and human leukocyte antigen (HLA) typing of the thawed units before transplantation. ABO typing is done using standard techniques. Rapid HLA class I serology is with monoclonal antibody trays (One Lambda Inc) using standard incubations. One mislabeled umbilical cord blood (UCB) unit was detected on the day of intended transplantation by repeat ABO typing of the thawed unit at our transplantation center. Because ABO typing will not detect all labeling errors, the rapid serologic class I HLA typing procedure was done on thawed units just before transplantation for all units without an attached segment. This procedure identified a second mislabeled unit. In a 6-year period, 2 of 871 (0.2%) cord blood units sent to us for transplantation were mislabeled and potentially would have been transplanted incorrectly. This error rate of 1 per 249 (0.4%) patients could have potentially devastating consequences.

scholarly journals SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yong Zhang ◽  
Yongsheng Chen ◽  
Huixin Xu ◽  
Junbin Fang ◽  
Zijian Zhao ◽  
...  
Keyword(s):  
Open Source ◽  
Hla Class I ◽  
Class I ◽  
Cross Platform

scholarly journals Evaluation of a Novel Mononuclear Cell Isolation Procedure for Serological HLA Typing

1998 ◽  
Vol 5 (6) ◽  
pp. 808-813 ◽  
Author(s):  
Peter Schlenke ◽  
Harald Klüter ◽  
Michael Müller-Steinhardt ◽  
Hans-Jörg Hammers ◽  
Kerstin Borchert ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Human Leukocyte ◽  
Standard Technique ◽  
Hla Class I ◽  
Isolation Procedure ◽  
Hla Typing ◽  
Class I ◽  
Isolated Cells ◽  
Peripheral Blood Mononuclear ◽  
High Background

ABSTRACT Despite recent advances in DNA-based genotyping, the microcytotoxicity test is still broadly used for the determination of human leukocyte class I antigens in patients as well as organ donors and also for the detection of HLA antibodies. Excellent purity and viability of peripheral blood mononuclear cells (PBMC) are essential for reliable HLA typing results. Background staining and cell loss can contribute to impaired typing results or even cause misinterpretations. A novel isolation procedure using cell preparation tubes (CPT) with prefilled Ficoll was compared with the standard Ficoll gradient. We determined the recovery, purity, and viability of the PBMC after several periods of storage. Finally, the isolated cells were used for HLA class I typing, and background reactivities were scored. By using the CPT method, the recovery of PBMC was significantly higher than recovery with the standard technique (P ≤ 0.001). Contamination by granulocytes increased considerably during the storage time for the standard protocol, whereas purity remained stable when CPT were used (P ≤ 0.001). With both methods, lymphocyte viability declined markedly over time. We found significantly more dead cells by using the CPT methods. Due to high background scores, HLA typing was impossible after 48 h. The isolation of PBMC by the CPT method resulted in a higher yield and improved purity compared to those obtained with the standard gradient technique. The decreasing viability after 48 h limits the use of both methods for HLA typing and HLA antibody screening.

scholarly journals Multiple sclerosis: disease modifying therapy and the human leukocyte antigen

2018 ◽  
Vol 76 (10) ◽  
pp. 697-704 ◽  
Author(s):  
Lineu Cesar Werneck ◽  
Paulo José Lorenzoni ◽  
Cláudia Suemi Kamoi Kay ◽  
Rosana Herminia Scola
Keyword(s):  
Multiple Sclerosis ◽  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Class I ◽  
Interferon Β ◽  
Leukocyte Antigen ◽  
Specific Subset ◽  
Hla Type ◽  
Disease Modifying

ABSTRACT Objective: To investigate the potential relationship between the human leukocyte antigen (HLA) type (class I and II) and the response to several disease-modifying therapies (DMTs) in patients with multiple sclerosis (MS). Methods: We analyzed clinical data of 87 patients with MS at the beginning and end of each type of DMT including the disease duration, Expanded Disability Status Scale and Multiple Sclerosis Severity Score (MSSS). Genotyping of HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-A, HLA-B and HLA-C alleles were identified using high-resolution techniques. Statistical correlation between the HLA type and response to DMTs was done using the initial and final MSSS. Results: Statistical relationships (p < 0.05) were found for only 15 of 245 alleles tested. There was a reduction in the MSSS for patients treated with corticosteroids (DRB1*15:01, DPB1*04:01, DQB1*02:01 and DQB1*03:01), azathioprine (DRB1*03:01, DPB1*04:01, DQB1*03:02, DQB1*06:02, HLA-C*07:02), interferon β-1a 22 mcg (DRB1*11:04, DQB1*03:01 and DQB1*03:02), interferon β-1a 30 mcg (DPB1*02:01, HLA-C*05:01) and interferon β-1b (DQB1*02:01). Conclusion: These findings suggest a few relationships between the HLA and response to DMTs in the disability for some types of HLA class I and II alleles in a specific subset of MS patients.

Characteristics allelic of Human Leukocyte Antigen class I genotype and association with viral load and CD4 cell count in HIV-1 infected patients, Hanoi 2014 – 2016

2021 ◽  
Vol 31 (4) ◽  
pp. 43-50
Author(s):  
Tran Thi Minh Tam ◽  
Nguyen Thuy Linh ◽  
Phan Ha My ◽  
Nguyen Thi Lan Anh
Keyword(s):  
Viral Load ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Class I ◽  
Cd4 Cell Count ◽  
Leukocyte Antigen ◽  
Cell Counts ◽  
Cd4 Cell Counts ◽  
Cd4 Cell ◽  
Hiv 1

Human Leukocyte Antigen (HLA) class I plays a regulatory role in cellular immune response to HIV-1 infection. The role of HLA alleles in HIV progression via viral load and CD4 cell count is well known. HLA class I is polymorphic and distributed differently by nation. This descriptive cross-sectional study was performed on 303 HIV-1 infected patients in 2014 - 2016, with aims to (i) characterize HLA class I genotype with 4-digit nomenclature and (ii) identify specifc alleles in correlate with CD4 cell counts and HIV viral load. 117 allele genotypes have been identifed, including 28 HLA-A alleles, 54 HLA-B alleles and 35 HLA-C alleles. The results showed that the most prevalent alleles in the population include A*11:01 (30.7%), B*15:02 (15.2%) and C*08:01 (17.1%). The frequency of haplotype created from these alleles is 8.4%. A*02:03, B*46:01 related to gender and ethnicity respectively. In conclusion, the study provided detailed pattern of HLA class I expression in a study population of HIV-1 infected patients and reported for the frst time the associated B*51:01, C*14:02 alleles associated to an increase in CD4 cell counts.

scholarly journals Results of a randomized, double-blind phase II clinical trial of NY-ESO-1 vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in participants with high-risk resected melanoma

2020 ◽  
Vol 8 (1) ◽  
pp. e000410
Author(s):  
Jonathan S Cebon ◽  
Martin Gore ◽  
John F Thompson ◽  
Ian D Davis ◽  
Grant A McArthur ◽  
...  
Keyword(s):  
New York ◽  
High Risk ◽  
Phase Ii ◽  
Immune Escape ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Class I ◽  
Double Positive ◽  
Double Blind ◽  
Hla Class I Molecules

BackgroundTo compare the clinical efficacy of New York Esophageal squamous cell carcinoma-1 (NY-ESO-1) vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in a randomized, double-blind phase II study in participants with fully resected melanoma at high risk of recurrence.MethodsParticipants with resected stage IIc, IIIb, IIIc and IV melanoma expressing NY-ESO-1 were randomized to treatment with three doses of NY-ESO-1/ISCOMATRIX or ISCOMATRIX adjuvant administered intramuscularly at 4-week intervals, followed by a further dose at 6 months. Primary endpoint was the proportion free of relapse at 18 months in the intention-to-treat (ITT) population and two per-protocol populations. Secondary endpoints included relapse-free survival (RFS) and overall survival (OS), safety and NY-ESO-1 immunity.ResultsThe ITT population comprised 110 participants, with 56 randomized to NY-ESO-1/ISCOMATRIX and 54 to ISCOMATRIX alone. No significant toxicities were observed. There were no differences between the study arms in relapses at 18 months or for median time to relapse; 139 vs 176 days (p=0.296), or relapse rate, 27 (48.2%) vs 26 (48.1%) (HR 0.913; 95% CI 0.402 to 2.231), respectively. RFS and OS were similar between the study arms. Vaccine recipients developed strong positive antibody responses to NY-ESO-1 (p≤0.0001) and NY-ESO-1-specific CD4+and CD8+responses. Biopsies following relapse did not demonstrate differences in NY-ESO-1 expression between the study populations although an exploratory study demonstrated reduced (NY-ESO-1)+/Human Leukocyte Antigen (HLA) class I+double-positive cells in biopsies from vaccine recipients performed on relapse in 19 participants.ConclusionsThe vaccine was well tolerated, however, despite inducing antigen-specific immunity, it did not affect survival endpoints. Immune escape through the downregulation of NY-ESO-1 and/or HLA class I molecules on tumor may have contributed to relapse.

Evidence for HLA-related susceptibility for stroke in children with sickle cell disease

Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3562-3567 ◽  
Author(s):  
Lori A. Styles ◽  
Carolyn Hoppe ◽  
William Klitz ◽  
Elliott Vichinsky ◽  
Bertram Lubin ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Cerebral Infarction ◽  
Sickle Cell ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Increased Risk ◽  
Mri Scans ◽  
Comparison Of The Results

Abstract Cerebral infarction occurs in one quarter of all children with sickle cell anemia (SCA). There is an increased risk of stroke in siblings with SCA, suggesting genetic factors may influence risk of stroke. The authors investigated whether HLA type was associated with risk of stroke in children with SCA. Fifty-three patients with SCA underwent complete HLA typing at both HLA class I (HLA-A, B) and HLA class II (HLA-DR, DQ, DP) loci. Of the 53 patients, 22 had magnetic resonance imagining (MRI)–documented evidence of cerebral infarction, and the remaining 31 patients had negative MRI scans. Comparison of the results of HLA typing between the SCA patients with a positive and those with a negative MRI documented that the 2 groups differed with respect to the class I HLA-B (P = .012), and the class II HLA-DRB1 (P = .0008) and DQB1 (P = .029). Susceptibility associations at the HLA-DRB1 locus included both DR3 alleles, where DRB1*0301 and *0302 were both associated with an increased risk of stroke. Protective associations were found in the DR2 group, where DRB1*1501 was protective for stroke. DQB1*0201, which is in linkage disequilibrium with DRB1*0301, was also associated with stroke. Similarly, DQB1*0602, in linkage disequilibrium with DRB1*1501, was protective. Specific HLA alleles may influence the risk of stroke in children with SCA. HLA typing may prove useful in identifying SCA patients at higher risk for stroke.

scholarly journals Human Leukocyte Antigen (HLA) class I and II datasets for sudanese

Data in Brief ◽  
2019 ◽  
Vol 24 ◽  
pp. 104027
Author(s):  
Ameer Mohamed Dafalla ◽  
Hisham Atan Edinur ◽  
Mohammed Abdelwahed ◽  
Almutaz Abbas Elemam ◽  
Amel Abdeen Ibrahim ◽  
...  
Keyword(s):  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Class I ◽  
Leukocyte Antigen

scholarly journals Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura C. Demmers ◽  
Kai Kretzschmar ◽  
Arne Van Hoeck ◽  
Yotam E. Bar-Epraïm ◽  
Henk W. P. van den Toorn ◽  
...  
Keyword(s):  
Damage Control ◽  
Colorectal Cancer Patient ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Peptide Ligands ◽  
Class I ◽  
Viable Option ◽  
Leukocyte Antigen ◽  
Peptide Presentation ◽  
Tumor Mutational Burden

Abstract Tumor heterogeneity is a major cause of therapeutic resistance. Immunotherapy may exploit alternative vulnerabilities of drug-resistant cells, where tumor-specific human leukocyte antigen (HLA) peptide ligands are promising leads to invoke targeted anti-tumor responses. Here, we investigate the variability in HLA class I peptide presentation between different clonal cells of the same colorectal cancer patient, using an organoid system. While clone-specific differences in HLA peptide presentation were observed, broad inter-clone variability was even more prevalent (15–25%). By coupling organoid proteomics and HLA peptide ligandomics, we also found that tumor-specific ligands from DNA damage control and tumor suppressor source proteins were prominently presented by tumor cells, coinciding likely with the silencing of such cytoprotective functions. Collectively, these data illustrate the heterogeneous HLA peptide presentation landscape even within one individual, and hint that a multi-peptide vaccination approach against highly conserved tumor suppressors may be a viable option in patients with low tumor-mutational burden.

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