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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/29469182/identification-of-the-novel-allele-hla-a-01-234-in-the-mother-of-a-german-cord-blood-donor
#1
J Strobel, B Hauck-Dlimi, K Dullinger, V Weisbach, J Zingsem
HLA-A*01:234 was identified by next generation sequencing and confirmed by Sanger sequencing.
February 22, 2018: HLA
https://www.readbyqxmd.com/read/29424002/perpetual-complexity-predicting-human-cd8-t-cell-responses-to-pathogenic-peptides
#2
REVIEW
Anthony R Di Carluccio, Cristina F Triffon, Weisan Chen
The accurate prediction of human CD8+ T cell epitopes has great potential clinical and translational implications in the context of infection, cancer and autoimmunity. Prediction algorithms have traditionally focused on calculated peptide affinity for the binding groove of MHC-I. However, over the years it has become increasingly clear that the ultimate T cell recognition of MHC-I-bound peptides is governed by many contributing factors within the complex antigen presentation pathway. Recent advances in next-generation sequencing and immunnopeptidomics have increased the precision of HLA-I sub-allele classification, and have led to the discovery of peptide processing events and individual allele-specific binding preferences...
February 9, 2018: Immunology and Cell Biology
https://www.readbyqxmd.com/read/29419929/identification-of-the-novel-allele-hla-c-01-136-in-a-german-cord-blood-donor-originating-from-azerbaijan
#3
J Zingsem, B Hauck-Dlimi, K Dullinger, V Weisbach, J Strobel
HLA-C*01:136 identified by next generation sequencing and confirmed by Sanger sequencing.
February 8, 2018: HLA
https://www.readbyqxmd.com/read/29379821/multiplex-family-with-gad65-abs-neurologic-syndromes
#4
Aude Belbezier, Bastien Joubert, Gonzalo Montero-Martin, Marcelo Fernandez-Vina, Nicole Fabien, Véronique Rogemond, Emmanuel Mignot, Jérôme Honnorat
Objective: Neurologic autoimmune syndromes associated with anti-glutamate acid decarboxylase 65 antibodies (GAD65-Abs) are rare and mostly sporadic. Methods: We describe a niece and her aunt with GAD65-Abs neurologic syndromes. High-resolution HLA typing of Class I and Class II alleles was performed using next-generation sequencing. Results: The proband had cerebellar ataxia and probable limbic encephalitis features, whereas her niece had stiff-person syndrome...
January 2018: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/29364590/next-generation-sequencing-based-typing-of-a-new-allele-hla-dqb1-03-01-01-20-in-a-chinese-family
#5
R Wu, H Li, N Wang, D Peng, H Sun
DQB1*03:01:01:20 showed one nucleotide difference when compared to DQB1*03:01:01:01 at 224 (C>T).
January 24, 2018: HLA
https://www.readbyqxmd.com/read/29364589/the-novel-hla-dqb1-03-01-01-12-allele-identified-by-next-generation-sequencing-in-a-chinese-family
#6
R Wu, R Li, Y Zhang, H Li, H Sun
DQB1*03:01:01:12 differs from DQB1*03:01:01:01 at nucleotide 2016 (G>T), 3495 (G>A), 3897 (G>A), and 6909 (T>C).
January 24, 2018: HLA
https://www.readbyqxmd.com/read/29364580/hla-a-02-01-01-28-a-novel-hla-allele-identified-by-next-generation-sequencing-in-a-chinese-family
#7
R Wu, D Peng, R Li, H Li, H Sun
HLA-A*02:01:01:28 differs from A*02:01:01:01 by one nucleotide transition, T>A 2952 in intron 6.
January 24, 2018: HLA
https://www.readbyqxmd.com/read/29338738/rapid-hiv-disease-progression-following-superinfection-in-an-hla-b-27-05-b-57-01-positive-transmission-recipient
#8
Jacqui Brener, Astrid Gall, Jacob Hurst, Rebecca Batorsky, Nora Lavandier, Fabian Chen, Anne Edwards, Chrissy Bolton, Reena Dsouza, Todd Allen, Oliver G Pybus, Paul Kellam, Philippa C Matthews, Philip J R Goulder
BACKGROUND: The factors determining differential HIV disease outcome among individuals expressing protective HLA alleles such as HLA-B*27:05 and HLA-B*57:01 remain unknown. We here analyse two HIV-infected subjects expressing both HLA-B*27:05 and HLA-B*57:01. One subject maintained low-to-undetectable viral loads for more than a decade of follow up. The other progressed to AIDS in < 3 years. RESULTS: The rapid progressor was the recipient within a known transmission pair, enabling virus sequences to be tracked from transmission...
January 16, 2018: Retrovirology
https://www.readbyqxmd.com/read/29327506/next-generation-sequencing-characterizes-the-extent-of-hla-diversity-in-an-argentinian-registry-population
#9
C K Hurley, L Hou, A Lazaro, J Gerfen, E Enriquez, P Galarza, M Belen Rodriguez Cardozo, M Halagan, M Maiers, D Behm, J Ng
Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, and -DQB1 assignments of 1472 unrelated volunteers for the unrelated donor registry in Argentina. The analysis characterized all HLA exons and introns for class I alleles; at least exons 2, 3 for HLA-DRB1; and exons 2-6 for HLA-DQB1. Of the distinct alleles present, there are 330 class I and 98 class II. The majority (~98%) of the cumulative allele frequency at each locus is contributed by alleles that appear at a frequency of at least 1 in 1000...
January 12, 2018: HLA
https://www.readbyqxmd.com/read/29316364/more-than-150-novel-variants-of-hla-class-i-genes-detected-in-german-stem-cell-donor-registry-and-ucla-international-cell-exchange-samples
#10
Vera Balz, Stefan Krause, Johannes Fischer, Jürgen Enczmann
High throughput analysis using amplicon-based next-generation sequencing (NGS) of HLA class I genes in samples of registered stem cell donors of the German Stem Cell Donor Registry Düsseldorf revealed 151 novel variants. In addition, 4 new variants were identified in well-defined samples obtained from the UCLA International Cell Exchange program. New alleles included 37 HLA-A, 57 HLA-B, and 61 HLA-C variant alleles. All variants were confirmed by NGS of HLA-A, HLA-B, and HLA-C genes including the respective 5´ and 3´ untranslated regions as well as Sanger sequence analysis...
January 8, 2018: HLA
https://www.readbyqxmd.com/read/29289738/next-generation-sequencing-characterization-of-hla-in-multi-generation-families-of-kuwaiti-descent
#11
Reem Ameen, Salem Al Shemmari, Medhat Askar
The frequency of HLA genes in one population may not accurately represent frequencies in other populations. In this study, we characterized extended human leukocyte antigen (HLA) haplotypes in several families of Kuwaiti descent by high-resolution typing using next-generation technology. A total 81 members (including patients and related donors) from 21 families were enrolled. No haplotypes were shared among multiple families. Of 77 haplotypes identified, 23 were not listed in the HaploStats database. Two haplotypes were most common in African Americans, six in Asian Pacific Islanders, three in Caucasians, three in Hispanics, and three in Native Americans...
December 28, 2017: Human Immunology
https://www.readbyqxmd.com/read/29280562/ngs-typings-reveal-very-high-frequencies-of-particular-hla-class-ii-alleles-and-haplotypes
#12
T Goeury, L E Creary, M A Fernandez-Vina, J-M Tiercy, J M Nunes, A Sanchez-Mazas
A total of 72 unrelated Mandenka individuals from Eastern Senegal, Niokholo region, were typed using Next Generation Sequencing (library preparation with the Holotype HLA X2 and MIA FORA NGS HLA Typing kits, sequencing with Illumina MiSeq, and bio-informatic processing with HLA Twin v1.1.1 (Omixon) and MIA FORA NGS software) and yielded reliable genotypes for 8 HLA loci, namely A, B, C, DRB1, DQA1, DQB1, DPA1 and DPB1.
December 27, 2017: HLA
https://www.readbyqxmd.com/read/29247682/collection-and-storage-of-hla-ngs-genotyping-data-for-the-17th-international-hla-and-immunogenetics-workshop
#13
Chia-Jung Chang, Kazutoyo Osoegawa, Robert P Milius, Martin Maiers, Wenzhong Xiao, Marcelo Fernandez-Viňa, Steven J Mack
For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage...
December 13, 2017: Human Immunology
https://www.readbyqxmd.com/read/29246901/evolutionary-basis-of-hla-dpb1-alleles-affects-acute-gvhd-in-unrelated-donor-stem-cell-transplantation
#14
Satoko Morishima, Takashi Shiina, Shingo Suzuki, Seishi Ogawa, Aiko Sato-Otsubo, Koichi Kashiwase, Fumihiro Azuma, Toshio Yabe, Masahiro Satake, Shunichi Kato, Yoshihisa Kodera, Takehiko Sasazuki, Yasuo Morishima
HLA-DPB1 T-cell epitope (TCE) mismatching algorithm and rs9277534 SNP at the 3' untranslated region (3' UTR) in the HLA-DPB1 gene are key factors for transplant-related events in unrelated hematopoietic cell transplantation (UR-HCT). However, the association of these two mechanisms has not been elucidated. We analyzed 19 frequent HLA-DPB1 alleles derived from Japanese healthy subjects by next-generation sequencing (NGS) of the entire HLA-DPB1 gene region and multi-SNP data of the HLA region in 1589 UR-HCT pairs...
December 15, 2017: Blood
https://www.readbyqxmd.com/read/29233746/amino-acid-variants-of-hla-drb1-confer-susceptibility-to-dapsone-hypersensitivity-syndrome-in-addition-to-hla-b-13-01
#15
Zhenhua Yue, Yonghu Sun, Chuan Wang, Wenjun Yu, Jing Cao, Fangfang Bao, Zhenzhen Wang, Hong Liu, Furen Zhang
Dapsone hypersensitivity syndrome is a rare yet severe adverse drug reaction caused by dapsone, a principal drug in the multidrug therapy for leprosy. HLA-B*13:01 has been identified to be a strong risk factor of dapsone hypersensitivity syndrome, however its low positive predictive value indicated that additional genetic variants may involve in the disease development. To discover contributing genetic variants within HLA loci in addition to HLA-B*13:01, we performed a high coverage next-generation sequencing based HLA typing analysis in 103 dapsone-hypersensitive and 857 dapsone-tolerant HLA-B*13:01 positive leprosy patients in Chinese population...
December 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29179676/hla-genotyping-by-next-generation-sequencing-of-complementary-dna
#16
Hidenobu Segawa, Yoji Kukita, Kikuya Kato
BACKGROUND: Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis...
November 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29171935/single-molecule-real-time-smrt%C3%A2-dna-sequencing-of-hla-genes-at-ultra-high-resolution-from-126-international-hla-and-immunogenetics-workshop-cell-lines
#17
T R Turner, J D Hayhurst, D R Hayward, W P Bultitude, D J Barker, J Robinson, J Alejandro Madrigal, N P Mayor, S G E Marsh
The hyperpolymorphic HLA genes play important roles in disease and transplantation and act as genetic markers of migration and evolution. A panel of 107 B-lymphoblastoid cell lines (B-LCLs) was established in 1987 at the 10(th) International Histocompatibility Workshop as a resource for the immunogenetics community. These B-LCLs are well characterised and represent diverse ethnicities and HLA haplotypes. Here we have applied Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing to HLA type 126 B-LCL, including the 107 IHIW cells, to ultra-high resolution...
November 24, 2017: HLA
https://www.readbyqxmd.com/read/29135082/hla-dqb1-02-102-a-novel-allele-identified-by-next-generation-sequencing-in-a-spanish-individual
#18
E Enrich, L Mongay, J L Caro-Oleas, M J Herrero-Mata, F Rudilla
HLA-DQB1*02:102 differs from DQB1*02:01:01 by a single nucleotide substitution resulting in an amino acid change.
November 14, 2017: HLA
https://www.readbyqxmd.com/read/29131543/hla-class-ii-polymorphism-in-saudi-patients-with-multiple-sclerosis
#19
M Al Jumah, S Kojan, A M Al Shehri, M Al Balwi, I Al Abdulkarim, E M Masuadi, Y Alhaidan, A Alabdulrahman, H M Fakhoury, A H Hajeer
Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS). However, only few studies have considered the association of high resolution HLA type and MS, with none yet from Saudi Arabia. The aim of this study was to investigate the association of HLA class II alleles with MS in the Saudi population. We used next generation sequencing to investigate HLA association with MS. This study was conducted at King Abdulaziz Medical City in Riyadh, Saudi Arabia. We found that several HLA-DRB1 and DQB1 alleles were associated with MS...
November 13, 2017: HLA
https://www.readbyqxmd.com/read/29123971/concepts-of-genomics-in-kidney-transplantation
#20
William S Oetting, Casey Dorr, Rory P Remmel, Arthur J Matas, Ajay K Israni, Pamala A Jacobson
Purpose of review: Identification of genetic variants to aid in individualized treatment of solid organ allograft recipients would improve graft survival. We will review the current state of knowledge for associations of variants with transplant outcomes. Recent findings: Many studies have yet to exhibit robust and reproducible results, however, pharmacogenomic studies focusing on cytochrome P450 (CYP) enzymes, transporters and HLA variants have shown strong associations with outcomes and have relevance towards drugs used in transplant...
June 2017: Current Transplantation Reports
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