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Next-generation sequencing HLA

Y Liu, Y Cao, Y Lin, W-M Dong, R-R Lin, Q Gu, X-B Xie, W-Y Gu
The presence of recurrent gene mutations is increasingly important in acute myeloid leukemia (AML) and sheds new insights into the understanding of leukemogenesis, prognostic evaluation, and clinical therapeutic efficacy. Until now, ten-eleven translocation 2 (TET2) and isocitrate dehydrogenase 2 (IDH2) mutations were reported to be mutually exclusive in AML patients. Similarly, nucleophosmin (NPM1) and additional sex comb-like 1 (ASXL1) mutations were rarely coexisted in AML. A 47-year-old man diagnosed with high-risk AML presented simultaneous mutations of TET2-IDH2 and NPM1-ASXL1 revealed by next-generation sequencing...
April 2018: Transplantation Proceedings
Keiichi Sakurai, Kazuyoshi Ishigaki, Hirofumi Shoda, Yasuo Nagafuchi, Yumi Tsuchida, Shuji Sumitomo, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Kazuhiko Yamamoto, Keishi Fujio
OBJECTIVE: Shared epitope (SE) alleles are the most significant genetic susceptibility locus in rheumatoid arthritis (RA); however, their target populations in CD4+ T cells are not well elucidated. We analyzed the association between SE alleles and the T cell receptor (TCR) repertoire diversity of naive and memory CD4+ T cells using next-generation sequencing (NGS). METHODS: The TCR beta chains in naive and memory CD4+ T cells from the peripheral blood of 22 patients with RA and 18 age- and sex-matched healthy donors (HD) were analyzed by NGS...
April 15, 2018: Journal of Rheumatology
Maryam Rafati, Mohammad Mahdi Akhondi, Mohammad Reza Sadeghi, Seyedeh Zahra Tara, Saeed Reza Ghaffari
Hematopoietic Stem Cell Transplantation (HSCT) is the only therapeutic option in a number of heritable hematologic disorders as well as hematologic cancers. Many parents and families fail to find an HLA-identical donor for their affected family member. In such cases, conceiving for a savior baby remains the only option especially in countries without access to national registries. By means of Next Generation Sequencing (NGS) techniques, in a single experiment on single cell products of IVF, a healthy HLA-identical embryo can be implanted in the uterus of a concerned mother...
April 9, 2018: Biology of Blood and Marrow Transplantation
Mohan Liu, Jacob Degner, Justin Wade Davis, Kenneth B Idler, Ahmed Nader, Nael M Mostafa, Jeffrey F Waring
Anti-drug antibody formation occurs with most biological agents across disease states, but the mechanism by which they are formed is unknown. The formation of anti-drug antibodies to adalimumab (AAA) may decrease its therapeutic effects in some patients. HLA alleles have been reported to be associated with autoantibody formation against interferons and other TNF inhibitors, but not adalimumab. We analyzed samples from 634 subjects with either rheumatoid arthritis (RA) or hidradenitis suppurativa (HS): 37 subjects (17 RA and 20 HS) developed AAA (AAA+) during adalimumab treatment and 597 subjects (348 RA, 249 HS) did not develop AAA (AAA-) during the clinical trials...
2018: PloS One
Gerit Moser, Sascha Drewlo, Berthold Huppertz, D Randall Armant
BACKGROUND: Early during human development, the trophoblast lineage differentiates to commence placentation. Where the placenta contacts the uterine decidua, extravillous trophoblast (EVT) cells differentiate and invade maternal tissues. EVT cells, identified by expression of HLA-G, invade into uterine blood vessels (endovascular EVT), as well as glands (endoglandular EVT), and open such luminal structures towards the intervillous space of the placenta. Endoglandular invasion diverts the contents of uterine glands to the intervillous space, while glands near the margin of the placenta that also contain endoglandular EVT cells open into the reproductive tract...
March 28, 2018: Human Reproduction Update
Noriko K Steiner, Lihua Hou, Carolyn Katovich Hurley
Two novel HLA class II alleles, DRB4∗03:01N and DQB1∗03:276N, containing large deletions were identified during routine typing. Extraction of DNA encompassing the deletions was carried out with a panel of capture oligonucleotides followed by whole genome amplification. Next generation DNA sequencing was then used to characterize the sequences. DRB4∗03:01N has a 16 kilobase pair deletion stretching upstream from intron 2 toward centromeric DRB8. DQB1∗03:276N has two deletions separated by 844 nucleotides...
March 23, 2018: Human Immunology
Neda Nemat-Gorgani, Hugo G Hilton, Brenna M Henn, Meng Lin, Christopher R Gignoux, Justin W Myrick, Cedric J Werely, Julie M Granka, Marlo Möller, Eileen G Hoal, Makoto Yawata, Nobuyo Yawata, Lies Boelen, Becca Asquith, Peter Parham, Paul J Norman
The functions of human NK cells in defense against pathogens and placental development during reproduction are modulated by interactions of killer cell Ig-like receptors (KIRs) with HLA-A, -B and -C class I ligands. Both receptors and ligands are highly polymorphic and exhibit extensive differences between human populations. Indigenous to southern Africa are the KhoeSan, the most ancient group of modern human populations, who have highest genomic diversity worldwide. We studied two KhoeSan populations, the Nama pastoralists and the ≠Khomani San hunter-gatherers...
March 16, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Taigo Kato, Tatsuo Matsuda, Yuji Ikeda, Jae-Hyun Park, Matthias Leisegang, Sachiko Yoshimura, Tetsuro Hikichi, Makiko Harada, Makda Zewde, Sho Sato, Kosei Hasegawa, Kazuma Kiyotani, Yusuke Nakamura
Neoantigens are the main targets of tumor-specific T cells reactivated by immune checkpoint-blocking antibodies or when using tumor-infiltrating T cells for adoptive therapy. While cancers often accumulate hundreds of mutations and harbor several immunogenic neoantigens, the repertoire of mutation-specific T cells in patients might be restricted. To bypass suboptimal conditions, which impede the reactivation of existing T cells or the priming of neoantigen-specific T cells in a patient, we employ T cells of healthy donors with an overlapping HLA repertoire to target cancer neoantigens...
February 16, 2018: Oncotarget
J Pruszak, M Bernheiden, F Emmerich
HLA-B*50:01:09 differs by a synonymous nucleotide exchange in codon 17 from B*50:01:01.
March 9, 2018: HLA
Leilei Liang, Jingchao Xu, Meng Wang, Gaoran Xu, Ning Zhang, Guangzhi Wang, Yongfu Zhao
Long non-coding RNAs (lncRNAs), which are important functional regulators in cancer, have received increased attention in recent years. In this study, next-generation sequencing technology was used to identify aberrantly expressed lncRNAs in follicular thyroid carcinoma (FTC). The long non-coding RNA-HLA complex P5 (HCP5) was found to be overexpressed in FTC. The results of the qPCR analysis were consistent with the sequencing results. In addition, functional experiments showed that overexpression of HCP5 can promote the proliferation, migration, invasiveness and angiogenic ability of FTC cells...
March 7, 2018: Cell Death & Disease
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
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
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
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
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
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
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
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
C K Hurley, L Hou, A Lazaro, J Gerfen, E Enriquez, P Galarza, M B 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 to 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...
March 2018: HLA
V Balz, S Krause, J Fischer, J 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, four 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...
March 2018: HLA
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