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Next-generation sequencing HLA

Tslil Gabrieli, Hila Sharim, Gil Nifker, Jonathan Jeffet, Tamar Shahal, Rani Arielly, Michal Levy-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is a distinct product of active DNA demethylation that is linked to gene regulation, development, and disease. In particular, 5-hmC levels dramatically decline in many cancers, potentially serving as an epigenetic biomarker. The noise associated with next-generation 5-hmC sequencing hinders reliable analysis of low 5-hmC containing tissues such as blood and malignant tumors. Additionally, genome-wide 5-hmC profiles generated by short-read sequencing are limited in providing long-range epigenetic information relevant to highly variable genomic regions, such as the 3...
June 20, 2018: ACS Nano
Z-R Quan, X-X Zhong, S-Q Gao
HLA-B*15:296 differs from HLA-B*15:01:01:01 in exon 3 by a single nucleotide. This article is protected by copyright. All rights reserved.
June 12, 2018: HLA
Sandra P D'Angelo, Luca Melchiori, Melinda S Merchant, Donna B Bernstein, John Glod, Rosandra N Kaplan, Stephan A Grupp, William D Tap, Karen Chagin, Gwendolyn K Binder, Samik Basu, Daniel E Lowther, Ruoxi Wang, Natalie Bath, Alex Tipping, Gareth Betts, Indu Ramachandran, Jean-Marc Navenot, Hua Zhang, Daniel K Wells, Erin Van Winkle, Gabor Kari, Trupti Trivedi, Tom Holdich, Lini N Pandite, Rafael Amado, Crystal L Mackall
We evaluated safety and activity of autologous T cells expressing NY-ESO-1c259, an affinity-enhanced T cell receptor (TCR) recognizing an HLA-A2-restricted NY-ESO-1/LAGE-1a-derived peptide, in patients with metastatic synovial sarcoma (NY-ESO-1c259T cells). Confirmed antitumor responses occurred in 50% of patients (6/12) and were characterized by tumor shrinkage over several months. Circulating NY-ESO-1c259T cells were present post-infusion in all patients and persisted for at least 6 months in all responders...
June 11, 2018: Cancer Discovery
Vani Seshasubramanian, Nirmal Kumar Manisekar, Aruna Devi Sathishkannan, Chandramouleeswaran Naganathan, Saranya Narayan
B:C:DRB1:DQB1 allele and haplotype frequencies were determined among India, Andhra Pradesh, Telugu speaking population from South India by Next Generation Sequencing. 180 bone marrow registry donors and 6 cord blood units from Jeevan Stem Cell Foundation (part of Be The Cure Registry), Chennai, Tamilnadu state were included in the study.
June 8, 2018: Human Immunology
Shuji Kawaguchi, Koichiro Higasa, Ryo Yamada, Fumihiko Matsuda
HLA allele information is essential for a variety of medical applications, such as genomic studies of multifactorial diseases, including immune system and inflammation-related disorders, and donor selection in organ transplantation and regenerative medicine. To obtain this information, an accurate HLA typing method that is applicable for any allele registered in HLA allele databases is needed. Here, we describe a method for determining alleles from a current HLA database using next-generation sequencing (NGS) results...
2018: Methods in Molecular Biology
Sebastian Boegel, Thomas Bukur, John C Castle, Ugur Sahin
Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., "sequencing reads"). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., "RNA-Seq") has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample's (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt's lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3...
2018: Methods in Molecular Biology
Takashi Shiina, Shingo Suzuki, Jerzy K Kulski, Hidetoshi Inoko
Super high resolution-single molecule-sequence-based typing (SS-SBT) is an HLA DNA typing method to the field 4 level of allelic resolution (formerly known as 8-digit typing) to efficiently detect novel and null alleles without phase ambiguity by combination of long ranged PCR amplification and next-generation sequencing (NGS) technologies. In this chapter, we describe three basic steps, long ranged PCR, NGS, and allele assignment.
2018: Methods in Molecular Biology
Yuxin Yin, James Lan, Qiuheng Zhang
Next-generation sequencing (NGS) is increasingly recognized for its ability to deliver high-resolution and high-throughput HLA genotyping. As a result, there is active interest in applying NGS technologies to perform high volume bone marrow donor recruitment typing. Currently, buccal-based DNA specimens are considered a noninvasive and cost-effective method for registry typing. Here, we describe the feasibility of using long-range PCR and clonal sequencing by Illumina MiSeq to deliver unambiguous HLA typing on buccal-based donor recruitment samples...
2018: Methods in Molecular Biology
Philip K Ehrenberg, Aviva Geretz, Rasmi Thomas
The human leukocyte antigen (HLA) genes regulate and drive the immune system, and are among the most polymorphic loci in the human genome. HLA diversity is known to play an important role in transplantation and disease association studies. There are multiple approaches to DNA-based HLA genotyping and recent advances in next-generation sequencing (NGS) technologies have facilitated the development of whole gene sequencing methods. We describe an accurate, efficient, scalable, and cost-effective approach to contiguously amplify and sequence full-length genes of six HLA class I and II loci from 96 individuals on a single Illumina MiSeq run...
2018: Methods in Molecular Biology
Michael Wittig, Simonas Juzenas, Melanie Vollstedt, Andre Franke
PCR- or probe-based targeted capturing enables the enrichment of specific genomic loci prior to Next-Generation Sequencing (NGS). Here, we describe a probe-based protocol, which allows for high-resolution HLA typing of DNA samples by NGS. We also describe existing software tools that can be used for the subsequent HLA data analysis. Key prerequisites that warrant an accurate HLA calling are specific mappings of the sequencing reads, phasing of the mapped reads, and the possibility to perform a manual inspection/curation of the read mapping...
2018: Methods in Molecular Biology
Jashan P Abraham, Dominic J Barker, James Robinson, Giuseppe Maccari, Steven G E Marsh
The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication...
2018: Methods in Molecular Biology
Jun Qi, Tian-Ju Wang, Li-Ping Chen, Xiao-Fang Wang, Man-Ni Wang, Jun-Hua Wu
The human leucocyte antigen (HLA) is the most polymorphic region of the human genome. Compared with Sanger-sequencing-based typing (SBT) methods, next-generation sequencing (NGS) has significantly higher throughput and depth sequencing characteristics, having dramatic impacts on HLA typing in clinical settings. Here, we performed NGS technology with Ion Torrent S5 platform to evaluate the potential four novel HLA alleles detected in five donors from Chinese Marrow Donor Program (CMDP, Shaanxi Province) during routine Sanger SBT testing...
May 25, 2018: International Journal of Immunogenetics
J Pruszak, M Bernheiden, F Emmerich
HLA-C*04:01:85 differs in exon 1 from C*04:01:01 by a single nucleotide substitution in codon 3. This article is protected by copyright. All rights reserved.
May 23, 2018: HLA
J Pruszak, M Bernheiden, F Emmerich
HLA-C*03:376 differs from HLA-C*03:04:01 in exon 6 by a single nucleotide substitution. This article is protected by copyright. All rights reserved.
May 23, 2018: HLA
M Mazzocco, M Castagnetta, F Bottero, L Garbarino, N Sacchi
HLA-C*02:10:03 identified in a Venezuelan patient and characterized using next generation sequencing This article is protected by copyright. All rights reserved.
May 17, 2018: HLA
Kim N T Ton, Simone L Cree, Sabine J Gronert-Sum, Tony R Merriman, Lisa K Stamp, Martin A Kennedy
The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles...
2018: Frontiers in Genetics
J Pruszak, M Bernheiden, F Emmerich
HLA-C*14:93N differs from 14:02:01 by a single nucleotide substitution at position 502 in Exon 3. This article is protected by copyright. All rights reserved.
May 11, 2018: HLA
Hiroshi Ureshino, Takero Shindo, Hiroto Kojima, Yasushi Kusunoki, Yuki Miyazaki, Hidenori Tanaka, Hiroh Saji, Atsushi Kawaguchi, Shinya Kimura
Response to tyrosine kinase inhibitors (TKIs) is variable in chronic myeloid leukemia (CML), and elevated natural killer (NK) cells during TKI therapy are positively correlated with superior outcomes. NK cell function involves interactions of their killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I on target cells, and the avidity of KIR-HLA interactions depends on the combination of KIR and HLA alleles. We hypothesized that KIR and HLA polymorphisms may influence response to TKIs...
June 2018: Cancer Immunology Research
Carolyn Katovich Hurley, Jennifer Ng
Next generation DNA sequencing has facilitated the routine characterization of complete HLA gene sequences. These data complement structural and functional studies of HLA elements encoded outside of the exons specifying the antigen recognition domain. This commentary is focused on evaluating whether the interpretation of HLA clinical typing results should expand the region of the HLA gene considered in the assignment from the exon(s) encoding the antigen recognition domain to the full gene sequence. Our recommendation is that, at present, there is insufficient data to support considering variation in the regions outside of the antigen recognition domain in clinical decision-making...
April 21, 2018: Human Immunology
Asgeir Lande, Irene Andersen, Torstein Egeland, Benedicte A Lie, Marte K Viken
We report HLA-A, -C, -B, -DRB1, -DQB1 and -DPB1 allele frequencies and estimated haplotype frequencies from 4514 healthy Norwegians who volunteered to participate in the Norwegian Bone Marrow Donor Registry. HLA genotyping was conducted on a Next Generation Sequencing platform. Data were analyzed using Arlequin and Pypop software. No significant deviations from Hardy-Weinberg Equilibrium were noted at any of the loci studied. We discuss the representability for the Norwegian population and argue that the presented HLA data could serve as a Norwegian reference panel...
April 21, 2018: Human Immunology
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