scholarly journals High-throughput sequencing defines donor and recipient HLA B-cell epitope frequencies for prospective matching in transplantation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jenny N. Tran ◽  
◽  
Oliver P. Günther ◽  
Karen R. Sherwood ◽  
Franz Fenninger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Cell Epitope ◽  
Human Leukocyte ◽  
Gene Complex ◽  
Leukocyte Antigen ◽  
Hla Genes ◽  
In Silico Mapping ◽  
B Cell Epitope ◽  
High Degree ◽  
Generation Sequencing

AbstractCompatibility for human leukocyte antigen (HLA) genes between transplant donors and recipients improves graft survival but prospective matching is rarely performed due to the vast heterogeneity of this gene complex. To reduce complexity, we have combined next-generation sequencing and in silico mapping to determine transplant population frequencies and matching probabilities of 150 antibody-binding eplets across all 11 classical HLA genes in 2000 ethnically heterogeneous renal patients and donors. We show that eplets are more common and uniformly distributed between donors and recipients than the respective HLA isoforms. Simulations of targeted eplet matching shows that a high degree of overall compatibility, and perfect identity at the clinically important HLA class II loci, can be obtained within a patient waiting list of approximately 250 subjects. Internal epitope-based allocation is thus feasible for most major renal transplant programs, while regional or national sharing may be required for other solid organs.

scholarly journals Population Frequencies Determined by Next-generation Sequencing Provide Strategies for Prospective HLA Epitope Matching for Transplantation

2020 ◽  
Author(s):  
Jenny Tran ◽  
Oliver Gunther ◽  
Karen Sherwood ◽  
Franz Fenninger ◽  
Lenka Allan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Renal Transplant ◽  
Human Leukocyte ◽  
Gene Complex ◽  
Next Generation ◽  
Leukocyte Antigen ◽  
Hla Genes ◽  
In Silico Mapping ◽  
High Degree ◽  
Generation Sequencing

Abstract Compatibility for human leukocyte antigen (HLA) genes between transplant donors and recipients improves graft survival but prospective matching is rarely performed due to the vast heterogeneity of this gene complex. To reduce complexity, we have combined next-generation sequencing and in silico mapping to determine population frequencies and matching probabilities of 150 antibody-binding eplets across all 11 classical HLA genes in 2000 ethnically heterogeneous renal patients and donors. We show that eplets are more common and more uniformly distributed between donors and recipients than the respective HLA isoforms. Simulation of targeted eplet matching shows that a high degree of overall compatibility, and perfect identity at the clinically important HLA class II loci, can be obtained within a patient waiting list of approximately 250 subjects. Internal epitope-based allocation is thus feasible for most major renal transplant programs, while regional or national sharing may be required for other solid organs.

scholarly journals Familial Pemphigus Vulgaris Occured in a Father and Son as the First Confirmed Cases

2016 ◽  
Vol 2016 ◽  
pp. 1-4
Author(s):  
Ali Haydar Eskiocak ◽  
Birgul Ozkesici ◽  
Soner Uzun
Keyword(s):  
Genetic Predisposition ◽  
Human Leukocyte ◽  
Pemphigus Vulgaris ◽  
Hla Typing ◽  
Enzyme Linked Immunosorbent Assay ◽  
Leukocyte Antigen ◽  
Hla Genes ◽  
Mother And Daughter ◽  
First Occurrence ◽  
Father And Son

Pemphigus vulgaris (PV) is a chronic autoimmune bullous disease of the skin and mucous membranes. Although there is some evidence pointing towards a genetic predisposition by some human leukocyte antigen (HLA) genes, familial occurrence of PV is very rare. Most of the familial PV cases so far reported have been in mother and daughter and in siblings. PV in father and son, as presented here, has not been reported in the literature before, except an unconfirmed report. The diagnosis of PV was established by histologic, cytologic studies and enzyme linked immunosorbent assay (ELISA) in Case1and by ELISA and BIOCHIP indirect immunofluorescence test in Case2. The son was responsive to moderate doses of methylprednisolone, with the treatment continuing with tapered doses. The father was in a subclinic condition; consequently, only close follow-up was recommended. HLA typing studies revealed identical HLA alleles of HLA-DR4 (DRB1⁎04) and HLA-DQB1⁎03in both of our cases; this had been found to be associated with PV in prior studies. Familial occurrences of PV and related HLA genes indicate the importance of genetic predisposition. The first occurrence of confirmed familial PV in father and son is reported here.

β-Thalassemia Major Association with Human Leukocyte Antigen (HLA) Genes in the Malaysian Population

Hemoglobin ◽  
2019 ◽  
Vol 43 (6) ◽  
pp. 345-345
Author(s):  
Wan Nurul Ain Mat Asuar ◽  
Haily Liduin Koyou ◽  
Too Chun Lai ◽  
Ezalia Esa ◽  
Norhazlin Mustafa ◽  
...  
Keyword(s):  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Thalassemia Major ◽  
Leukocyte Antigen ◽  
Malaysian Population ◽  
Hla Genes

scholarly journals Predicted epitope binding core motifs and common amino acid polymorphisms distinguish protective- from susceptibility-associated HLA alleles in leishmaniasis

2021 ◽  
Author(s):  
Nicky de Vrij ◽  
Pieter Meysman ◽  
Sofie Gielis ◽  
Wim Adriaensen ◽  
Kris Laukens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Epitope ◽  
Human Leukocyte ◽  
Common Amino Acid ◽  
Leukocyte Antigen ◽  
Susceptibility Factors ◽  
Binding Core ◽  
Epitope Discovery ◽  
Epitope Binding ◽  
Open Access Resource

AbstractSusceptibility for leishmaniasis is largely dependent on genetic- and immune factors of the host. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors, little is known on the mechanisms that mediate these associations. To characterize the functionality underpinning these associations between HLA and disease, we predicted the epitope binding repertoires for all known leishmaniasis-associated HLA variants collected in a thorough literature review. We identified several amino acid polymorphisms in the HLA sequences that distinguished protective-from risk-associated HLA-DRB1 alleles. Proteome-wide and multi-species T cell epitope binding predictions were carried out across these alleles, enabling us to map the effects on the epitope binding repertoires. The protective-associated HLA-DRB1 alleles were characterized by common binding core motifs, which map to the identified amino acid polymorphisms. These results strongly suggest that polymorphism in the HLA region, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes, of which a set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, were prioritized for further epitope discovery in the search for novel subunit-based vaccines.

scholarly journals Accuracy of programs for the determination of HLA alleles from NGS data

2017 ◽  
Author(s):  
Antti Larjo ◽  
Robert Eveleigh ◽  
Elina Kilpeläinen ◽  
Tony Kwan ◽  
Tomi Pastinen ◽  
...  
Keyword(s):  
Human Leukocyte ◽  
Hla Typing ◽  
Ensemble Prediction ◽  
Hla Alleles ◽  
Leukocyte Antigen ◽  
Peptide Antigens ◽  
Hla Genes ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

AbstractThe human leukocyte antigen (HLA) genes code for proteins that play a central role in the function of the immune system by presenting peptide antigens to T cells. As HLA genes show extremely high genetic polymorphism, HLA typing on the allele level is demanding and is based on DNA sequencing. Determination of HLA alleles is warranted as many HLA alleles are major genetic factors that confer susceptibility to autoimmune diseases and is important for the matching of HLA alleles in transplantation. Here, we compared the accuracy of several published HLA-typing algorithms that are based on next generation sequencing (NGS) data. As genome screens are becoming increasingly routine in research, we wanted to test how well HLA alleles can be deduced from genome screens not designed for HLA typing. The accuracies were assessed using datasets consisting of NGS data produced using the ImmunoSEQ platform, including the full 4 Mbp HLA segment, from 94 stem cell transplantation patients and exome sequences from the 1000 Genomes collection. When used with the default settings none of the methods gave perfect results for all the genes and samples. However, we found that ensemble prediction of the results or modifications of the settings could be used to improve accuracy. Most of the algorithms did not perform very well for the exome-only data. The results indicate that the use of these algorithms for accurate HLA allele determination based on NGS data is not straightforward.

scholarly journals arcasHLA: high resolution HLA typing from RNA seq

2018 ◽  
Author(s):  
Rose Orenbuch ◽  
Ioan Filip ◽  
Devon Comito ◽  
Jeffrey Shaman ◽  
Itsik Pe'er ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Mhc Class Ii ◽  
Critical Role ◽  
Human Leukocyte ◽  
Hla Typing ◽  
Sequencing Data ◽  
Leukocyte Antigen ◽  
Hla Genes ◽  
Biological Dataset ◽  
High Level

Human leukocyte antigen (HLA) locus makes up the major compatibility complex (MHC) and plays a critical role in host response to disease, including cancers and autoimmune disorders. In the clinical setting, HLA typing is necessary for determining tissue compatibility. Recent improvements in the quality and accessibility of next-generation sequencing have made HLA typing from standard short-read data practical. However, this task remains challenging given the high level of polymorphism and homology between the HLA genes. HLA typing from RNA sequencing is further complicated by post-transcriptional splicing and bias due to amplification. Here, we present arcasHLA: a fast and accurate in silico tool that infers HLA genotypes from RNA sequencing data. Our tool outperforms established tools on the gold-standard benchmark dataset for HLA typing in terms of both accuracy and speed, with an accuracy rate of 100% at two field precision for MHC class I genes, and over 99.7% for MHC class II. Importantly, arcasHLA takes as its input pre-aligned BAM files, and outputs three-field resolution for all HLA genes in less than 2 minutes. Finally, we discuss evaluate the performance of our tool on a new biological dataset of 447 single-end total RNA samples from nasopharyngeal swabs, and establish the applicability of arcasHLA in metatranscriptome studies. arcasHLA is available at https://github.com/RabadanLab/arcasHLA.

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