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Next-generation sequencing HLA

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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
#1
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
#2
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 anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 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
#3
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-beta-motifs-specific-to-hla-b27-ankylosing-spondylitis-by-deep-repertoire-sequence-analysis
#4
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 striking association with HLA-B27. One hypothesis suggests that a common antigen that binds to HLA-B27 is important for AS disease pathogenesis. We utilized T-cell repertoire next-generation sequencing to determine sequences and motifs that are shared among HLA-B27 positive (B27(+) ) AS patients. METHODS: To identify motifs enriched among B27(+) AS patients, we performed T-cell receptor beta (TCRβ) repertoire sequencing from 191 B27(+) AS patients, 43 B27(neg) AS patients and 227 controls, and we obtained >77 million TCRβ clonotype sequences...
December 21, 2016: 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
#5
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.
December 16, 2016: 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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/27679434/generation-of-full-length-class-i-human-leukocyte-antigen-gene-consensus-sequences-for-novel-allele-characterization
#10
Peter M Clark, Jamie L Duke, Deborah Ferriola, Valia Bravo-Egana, Tunde Vago, Aniqa Hassan, Anna Papazoglou, Dimitri Monos
BACKGROUND: Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs...
December 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27531697/from-hla-typing-to-anti-hla-antibody-detection-and-beyond-the-road-ahead
#11
REVIEW
Antonietta Picascia, Vincenzo Grimaldi, Claudio Napoli
The complex polymorphism of the HLA genes and the need of a proper identification of anti-HLA antibodies have led to continuously develop novel practical and feasible technologies in the field of organ and tissue transplantation. Technologies to identify HLA molecules have evolved from the serological to the molecular methods and a true innovation in the DNA sequencing has taken place with the development of next generation sequencing. An interesting field to explore is how the information resulting from the HLA-DNA sequencing can be applied in the clinical setting by including the alloimmunization assessment...
October 2016: Transplantation Reviews
https://www.readbyqxmd.com/read/27524804/hla-genotyping-in-the-clinical-laboratory-comparison-of-next-generation-sequencing-methods
#12
T Profaizer, E Lázár-Molnár, D W Close, J C Delgado, A Kumánovics
Implementation of human leukocyte antigen (HLA) genotyping by next-generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA-NGS typing kits, labs must make numerous decisions concerning capital equipment and address labor considerations. Therefore, careful and unbiased evaluation of available methods is imperative. In this report, we compared our in-house developed HLA NGS typing with two commercially available kits from Illumina and Omixon using 10 International Histocompatibility Working Group (IHWG) and 36 clinical samples...
July 2016: HLA
https://www.readbyqxmd.com/read/27492698/next-generation-sequencing-with-a-semi-conductor-technology-ion-torrent-pgm%C3%A2-for-hla-typing-overall-workflow-performance-and-debate
#13
Virginie Moalic-Allain, Bernard Mercier, Paul Gueguen, Claude Ferec
Current high resolution HLA typing technologies produce ambiguous results, and it is often necessary to perform additionnal tests to resolve these ambiguities. Next generation sequencing is a promising technology, which can overcome this problem. It is going to usher a new strategy to determine HLA compatibility between donor and recipient. It can lead to non ambiguous results by analysing the full amplified sequence of HLA genes and by eliminating heterozygote phase ambiguities. Instead, as many new techniques, we can face several problems, such as analysis difficulties because of incomplete HLA sequences in the database or errors related to the sequencing instrumentation...
August 1, 2016: Annales de Biologie Clinique
https://www.readbyqxmd.com/read/27397612/personalized-peptide-vaccine-induced-immune-response-associated-with-long-term-survival-of-a-metastatic-cholangiocarcinoma-patient
#14
Markus W Löffler, P Anoop Chandran, Karoline Laske, Christopher Schroeder, Irina Bonzheim, Mathias Walzer, Franz J Hilke, Nico Trautwein, Daniel J Kowalewski, Heiko Schuster, Marc Günder, Viviana A Carcamo Yañez, Christopher Mohr, Marc Sturm, Huu-Phuc Nguyen, Olaf Riess, Peter Bauer, Sven Nahnsen, Silvio Nadalin, Derek Zieker, Jörg Glatzle, Karolin Thiel, Nicole Schneiderhan-Marra, Stephan Clasen, Hans Bösmüller, Falko Fend, Oliver Kohlbacher, Cécile Gouttefangeas, Stefan Stevanović, Alfred Königsrainer, Hans-Georg Rammensee
BACKGROUND & AIMS: We report a novel experimental immunotherapeutic approach in a patient with metastatic intrahepatic cholangiocarcinoma. In the 5year course of the disease, the initial tumor mass, two local recurrences and a lung metastasis were surgically removed. Lacking alternative treatment options, aiming at the induction of anti-tumor T cells responses, we initiated a personalized multi-peptide vaccination, based on in-depth analysis of tumor antigens (immunopeptidome) and sequencing...
October 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/27376474/performance-characteristics-and-validation-of-next-generation-sequencing-for-human-leucocyte-antigen-typing
#15
Eric T Weimer, Maureen Montgomery, Rosanne Petraroia, John Crawford, John L Schmitz
High-resolution human leukocyte antigen (HLA) matching reduces graft-versus-host disease and improves overall patient survival after hematopoietic stem cell transplant. Sanger sequencing has been the gold standard for HLA typing since 1996. However, given the increasing number of new HLA alleles identified and the complexity of the HLA genes, clinical HLA typing by Sanger sequencing requires several rounds of additional testing to provide allele-level resolution. Although next-generation sequencing (NGS) is routinely used in molecular genetics, few clinical HLA laboratories use the technology...
September 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27365532/analysis-of-the-hla-dr-peptidome-from-human-dendritic-cells-reveals-high-affinity-repertoires-and-nonconventional-pathways-of-peptide-generation
#16
M Teresa Ciudad, Nicoletta Sorvillo, Floris P van Alphen, Diego Catalán, Alexander B Meijer, Jan Voorberg, Dolores Jaraquemada
Dendritic cells (DCs) are the major professional APCs of the immune system; however, their MHC-II-associated peptide repertoires have been hard to analyze, mostly because of their scarce presence in blood and tissues. In vitro matured human monocyte-derived DCs (MoDCs) are widely used as professional APCs in experimental systems. In this work, we have applied mass spectrometry to identify the HLA-DR-associated self-peptide repertoires from small numbers of mature MoDCs (∼5 × 10(6) cells), derived from 7 different donors...
January 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/27352438/hla-genotyping-using-next-generation-sequencing
#17
C Lucan, Laura-Ancuta Pop, A Florian, Valentina Pileczki, B Petrushev, Delia Dima, Ioana Frinc, Ioana Berindan-Neagoe, A Irimie, C Berce, I-S Florian, Anca Bojan, C Tomuleasa
From an oncological perspective, the second most common malignancies in children are brain tumors. Despite the recent therapeutic breakthroughs in this field, concerning surgery, radiotherapy and chemotherapy alike, some cases still have poor outcomes in curability. This is especially the case in patients with high-risk histological types of tumors, and those suffering from residual, remitting and disseminated diseases. Due to the unique neuroanatomical emplacement of brain tumors and their aggressive infiltrative behavior, their total removal remains a demanding task...
April 2016: Romanian Journal of Internal Medicine, Revue Roumaine de Médecine Interne
https://www.readbyqxmd.com/read/27337483/paleogenetics-and-past-infections-the-two-faces-of-the-coin-of-human-immune-evolution
#18
Laurent Abi-Rached, Didier Raoult
With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes...
June 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27316915/french-intensive-care-society-international-congress-r%C3%A3-animation-2016
#19
(no author information available yet)
No abstract text is available yet for this article.
June 2016: Annals of Intensive Care
https://www.readbyqxmd.com/read/27301744/association-of-hla-class-i-and-ii-genes-with-cutaneous-leishmaniasis-a-case-control-study-from-sri-lanka-and-a-systematic-review
#20
Nilakshi Samaranayake, Sumadhya D Fernando, Nilaksha F Neththikumara, Chaturaka Rodrigo, Nadira D Karunaweera, Vajira H W Dissanayake
BACKGROUND: The outcome of leishmaniasis is an interplay between Leishamania and the host. Identifying contributory host genetic factors is complicated by the variability in phenotype, ethnicity and parasite species. Leishmaniasis is caused exclusively by L. donovani in Sri Lanka with localized cutaneous leishmaniasis (LCL) being the predominant form. We report here an association study of human leucocyte antigen (HLA) class I and II genes with LCL in Sri Lanka, the first on HLA associations in cutaneous leishmaniasis in a South Asian population...
2016: BMC Infectious Diseases
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