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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/28422925/dynamics-of-b-cell-recovery-following-kidney-bone-marrow-transplant-recipients
#1
Baoshan Gao, Yiming Gu, Chunshu Rong, Carolina Moore, Fabrice Porcheray, Waichi Wong, Frederic Preffer, Susan L Saidman, Yaowen Fu, Benedict Cosimi, David H Sachs, Tatsuo Kawai, Megan Sykes, Emmanuel Zorn
BACKGROUND: Previous studies identified B cell gene signatures and predominance of specific B cell subsets as a marker of operational tolerance following kidney transplantation. These findings suggested a role for B cells in the establishment or maintenance of tolerance. Here we analyzed B cell recovery in 4 subjects, 3 of whom achieved tolerance after combined kidney/bone marrow transplantation. METHODS: Peripheral B cell subsets were examined longitudinally by flow cytometry...
April 19, 2017: Transplantation
https://www.readbyqxmd.com/read/28419628/hla-hd-an-accurate-hla-typing-algorithm-for-next-generation-sequencing-data
#2
Shuji Kawaguchi, Koichiro Higasa, Masakazu Shimizu, Ryo Yamada, Fumihiko Matsuda
The accurate typing of HLA alleles is critical 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. Here we developed a new algorithm for determining HLA alleles using next-generation sequencing (NGS) results. The method consists of constructing an extensive dictionary of HLA alleles, precise mapping of the NGS reads, and calculating a score based on weighted read counts to select the most suitable pair of alleles...
April 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28417556/an-hla-b7-specific-antibody-in-an-hla-b-07-positive-patient-explained-by-a-nonexpressed-allele-hla-b-07-181n
#3
S Wenda, I Faé, G F Fischer
Antibody identification by a bead array assay in a kidney patient revealed several HLA-specific antibodies including one directed against the HLA-B7 antigen. Low-resolution typing of the patient indicated the presence of an HLA-B*07 allele. To rule out an HLA-specific autoantibody the HLA-typing of the patient was further refined by nucleotide sequencing on a next-generation sequencing platform and eventually showed an HLA-B*39:01:01:03 and HLA-B*07:181N genotype. Thereby the allospecific nature of the antibody was proven...
April 17, 2017: HLA
https://www.readbyqxmd.com/read/28358734/intracellular-hiv-1-rna-and-cd4-t-cell-activation-in-patients-starting-antiretrovirals
#4
Ramy El-Diwany, Florian P Breitwieser, Mary Soliman, Alyza M Skaist, Geetha Srikrishna, Joel N Blankson, Stuart C Ray, Sarah J Wheelan, David L Thomas, Ashwin Balagopal
OBJECTIVE: To assess if the reduction in HIV-1 RNA in CD4+ T cells is correlated with the persistence of immune activation following early antiretroviral therapy (ART). DESIGN: Clinical trial (NCT01285050). METHODS: Next-generation sequencing was used to study total RNA from activated CD4+ T cells (CD38 and HLA-DR expressing) collected from 19 treatment-naïve HIV-1/HCV infected patients before and early after ART initiation (≥12 weeks after plasma HIV RNA < 50 c/ml)...
March 29, 2017: AIDS
https://www.readbyqxmd.com/read/28340809/corrected-panel-reactive-antibody-positivity-rates-for-hypersensitized-patients-in-turkish-population-with-calculated-panel-reactive-antibody-software
#5
S T Karadeniz, S U Akgul, Y Ogret, H S Ciftci, A Bayraktar, H Bakkaloglu, Y Caliskan, K Yelekci, A Turkmen, A E Aydin, F S Oguz, M Carin, F Aydin
INTRODUCTION: High rates of panel-reactive antibody (PRA) may decrease the chance of kidney transplantation and may result in long waiting periods before transplantation. The calculated PRA (cPRA) is performed based on unacceptable HLA antigens. These antigens are identified by a program that was created based on the antibodies that developed against the HLA antigens circulating in serum and on the risk of binding of these antibodies to antigens. The antigen profile of the population and antigen frequencies can be measured, and more realistic cPRA positivity rates may be obtained using this method...
April 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/28300170/cd8-t-cells-specific-for-the-islet-autoantigen-igrp-are-restricted-in-their-t-cell-receptor-chain-usage
#6
Yannick F Fuchs, Anne Eugster, Sevina Dietz, Christian Sebelefsky, Denise Kühn, Carmen Wilhelm, Annett Lindner, Anita Gavrisan, Jan Knoop, Andreas Dahl, Anette-G Ziegler, Ezio Bonifacio
CD8(+) T cells directed against beta cell autoantigens are considered relevant for the pathogenesis of type 1 diabetes. Using single cell T cell receptor sequencing of CD8(+) T cells specific for the IGRP265-273 epitope, we examined whether there was expansion of clonotypes and sharing of T cell receptor chains in autoreactive CD8(+) T cell repertoires. HLA-A*0201 positive type 1 diabetes patients (n = 19) and controls (n = 18) were analysed. TCR α- and β-chain sequences of 418 patient-derived IGRP265-273-multimer(+) CD8(+) T cells representing 48 clonotypes were obtained...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253087/genome-wide-association-studies-for-idiosyncratic-drug-induced-hepatotoxicity-looking-back-looking-forward-to-next-generation-innovation
#7
Zelalem Petros, Eyasu Makonnen, Eleni Aklillu
Idiosyncratic drug-induced hepatotoxicity is a formidable challenge for rational drug discovery and development, as well as the science of personalized medicine. There is evidence that hereditary factors, in part, contribute to drug toxicity. This expert analysis and review offer the insights gained, and the challenges ahead, for genome-wide association studies (GWASs) of idiosyncratic drug-induced hepatotoxicity. Published articles on genome-wide and subsequent replication studies were systematically searched in the PubMed electronic database...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28196473/2-7-million-samples-genotyped-for-hla-by-next-generation-sequencing-lessons-learned
#8
Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A Hofmann, Julia Pingel, Alexander H Schmidt, Vinzenz Lange
BACKGROUND: At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. RESULTS: Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28166716/pyhla-tests-for-the-association-between-hla-alleles-and-diseases
#9
Yanhui Fan, You-Qiang Song
BACKGROUND: Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughput and cost-effective approaches for identifying HLA types. Therefore, tools for downstream association analysis are highly desirable. Although several tools have been designed for multi-allelic marker association analysis, they were designed only for microsatellite markers and do not scale well with increasing data volumes, or they were designed for large-scale data but provided a limited number of tests...
February 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28145101/typing-and-copy-number-determination-for-hla-drb3-drb4-and-drb5-from-next-generation-sequencing-data
#10
Y Zhang, Y Song, H Cao, X Mo, H Yang, J Wang, Z Lu, T Zhang
BACKGROUND: HLA-DRB3, DRB4 and DRB5 (DRB3/4/5) are paralogues of HLA-DRB1. They have important roles in transplantation and have been reported to be related to many diseases. HLA typing methods for DRB3/4/5 based on NGS data have many limitations now, such as need of polymerase chain reaction (PCR) or low accuracy. MATERIALS AND METHODS: We present a HLA typing method for DRB3/4/5 based on read mapping and haplotype assembly from NGS data. Also, copy number of DRB3/4/5 is determined by a k-means clustering method according to ratio of sequencing depth between DRB3/4/5 and DRB1...
February 1, 2017: HLA
https://www.readbyqxmd.com/read/28138842/high-throughput-sequencing-of-the-major-histocompatibility-complex-following-targeted-sequence-capture
#11
Johannes Pröll, Carina Fischer, Gabriele Michelitsch, Martin Danzer, Norbert Niklas
The Human Major Histocompatibility Complex (MHC) is a highly polymorphic region full of immunoregulatory genes. The MHC codes for the human leukocyte antigens (HLA), proteins that present on the cellular surface and that are involved in self-non-self recognition. For matching donors and recipients for organ and stem-cell transplants it is important to know an individual's HLA haplotype determinable in this region. Now, as next-generation sequencing (NGS) platforms mature and become more and more accepted as a standard method, NGS applications have spread from research laboratories to the clinic, where they provide valid genetic insights...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28102036/combining-one-step-sanger-sequencing-with-phasing-probe-hybridization-for-hla-class-i-typing-yields-rapid-g-group-resolution-predicting-99-of-unique-full-length-protein-sequences
#12
Bin Tu, Carly Masaberg, Lihua Hou, Daniel Behm, Peter Brescia, Nuri Cha, Kanthi Kariyawasam, Jar How Lee, Thoa Nong, John Sells, Paul Tausch, Ruyan Yang, Jennifer Ng, Carolyn Katovich Hurley
BACKGROUND: Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS: Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry...
February 2017: HLA
https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#13
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of antitumor immunity as a dynamic spatiotemporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle by using next-generation sequencing. METHODS: Whole exome sequencing and RNA sequencing were performed in 20 patients with NSCLC (12 with adenocarcinoma, seven with squamous cell carcinoma, and one with large cell neuroendocrine carcinoma)...
May 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28032474/identification-of-3-novel-hla-b-alleles-b-08-173-b-18-72-03-and-b-53-05-02
#14
L Brunet, F Bettens, J Villard, S Ferrari-Lacraz, S Buhler
A total of 3 novel human leukocyte antigen-B (HLA-B) alleles were detected by next generation sequencing and confirmed by monoallelic sequencing.
February 2017: HLA
https://www.readbyqxmd.com/read/28002888/discovery-of-t-cell-receptor-%C3%AE-motifs-specific-to-hla-b27-positive-ankylosing-spondylitis-by-deep-repertoire-sequence-analysis
#15
Malek Faham, Victoria Carlton, Martin Moorhead, Jianbiao Zheng, Mark Klinger, Francois Pepin, Thomas Asbury, Marissa Vignali, Ryan O Emerson, Harlan S Robins, James Ireland, Emily Baechler-Gillespie, Robert D Inman
OBJECTIVE: Ankylosing spondylitis (AS), a chronic inflammatory disorder, has a notable association with HLA-B27. One hypothesis suggests that a common antigen that binds to HLA-B27 is important for AS disease pathogenesis. This study was undertaken to determine sequences and motifs that are shared among HLA-B27-positive AS patients, using T cell repertoire next-generation sequencing. METHODS: To identify motifs enriched among B27-positive AS patients, we performed T cell receptor β (TCRβ) repertoire sequencing on samples from 191 B27-positive AS patients, 43 B27-negative AS patients, and 227 controls, and we obtained >77 million TCRβ clonotype sequences...
April 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27987261/confirmation-and-next-generation-sequencing-of-allele-hla-b-35-279-found-in-a-family-of-a-leukaemia-patient-with-western-asia-origin
#16
F Grünebach, A-L Huster, W Vogel, R Klein
The confirmation of novel allele HLA-B*35:279 in a family of a leukaemia patient with Western Asia origin is reported. Moreover, next-generation sequencing (NGS) resulted in whole-gene sequence data and revealed the inheritance of HLA-B*35:279 on the paternal haplotype.
February 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/27976839/limited-hla-sequence-variation-outside-of-antigen-recognition-domain-exons-of-360-10-of-10-matched-unrelated-hematopoietic-stem-cell-transplant-donor-recipient-pairs
#17
L Hou, C Vierra-Green, A Lazaro, C Brady, M Haagenson, S Spellman, C K Hurley
Traditional DNA-based typing focuses primarily on interrogating the exons of human leukocyte antigen (HLA) genes that form the antigen recognition domain (ARD). The relevance of mismatching donor and recipient for HLA variation outside the ARD on hematopoietic stem cell transplantation (HSCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in 10 of 10 (HLA-A, -B, -C, -DRB1, -DQB1) matched unrelated donor transplant pairs (n = 360). Next-generation DNA sequencing was used to characterize both HLA exons and introns for HLA-A, -B, -C alleles; exons 2, 3 and the intervening intron for HLA-DRB1 and exons only for HLA-DQA1 and -DQB1...
January 2017: HLA
https://www.readbyqxmd.com/read/27802932/evaluation-of-computational-programs-to-predict-hla-genotypes-from-genomic-sequencing-data
#18
Denis C Bauer, Armella Zadoorian, Laurence O W Wilson, Natalie P Thorne
MOTIVATION: Despite being essential for numerous clinical and research applications, high-resolution human leukocyte antigen (HLA) typing remains challenging and laboratory tests are also time-consuming and labour intensive. With next-generation sequencing data becoming widely accessible, on-demand in silico HLA typing offers an economical and efficient alternative. RESULTS: In this study we evaluate the HLA typing accuracy and efficiency of five computational HLA typing methods by comparing their predictions against a curated set of > 1000 published polymerase chain reaction-derived HLA genotypes on three different data sets (whole genome sequencing, whole exome sequencing and transcriptomic sequencing data)...
November 1, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27798706/application-of-high-throughput-next-generation-sequencing-for-hla-typing-on-buccal-extracted-dna-results-from-over-10-000-donor-recruitment-samples
#19
Yuxin Yin, James H Lan, David Nguyen, Nicole Valenzuela, Ping Takemura, Yung-Tsi Bolon, Brianna Springer, Katsuyuki Saito, Ying Zheng, Tim Hague, Agnes Pasztor, Gyorgy Horvath, Krisztina Rigo, Elaine F Reed, Qiuheng Zhang
BACKGROUND: Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA...
2016: PloS One
https://www.readbyqxmd.com/read/27683631/genetic-barriers-in-transplantation-medicine
#20
REVIEW
Hisham A Edinur, Siti M Manaf, Nor F Che Mat
The successful of transplantation is determined by the shared human leukocyte antigens (HLAs) and ABO blood group antigens between donor and recipient. In recent years, killer cell receptor [i.e., killer cell immunoglobulin-like receptor (KIR)] and major histocompatibility complex (MHC) class I chain-related gene molecule (i.e., MICA) were also reported as important determinants of transplant compatibility. At present, several different genotyping techniques (e.g., sequence specific primer and sequence based typing) can be used to characterize blood group, HLA, MICA and KIR and loci...
September 24, 2016: World Journal of Transplantation
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