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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/28509679/the-impact-of-next-generation-sequencing-in-immunogenetics-current-status-and-future-directions
#1
Valia Bravo-Egana, Dimitri Monos
PURPOSE OF REVIEW: Next-generation sequencing (NGS) has now been established, and widely recognized, to be the preferred choice for human leukocyte antigen (HLA) typing. This transformation is based upon the many scientific, operational and economic benefits this technology affords. In this report, we review the major advantages, existing limitations and significant promise derived from adopting this technology in immunogenetics. RECENT FINDINGS: Significant benefits have emerged from the usage of NGS in a relatively short period, whereby we realize that this technology not only helps addressing the technical and operational problems we have had with the legacy methods for HLA typing, but equally important, it also allows for creative applications in stem cell and organ transplantation, new ways to investigate associations of the major histocompatibility complex (MHC) with many diseases and enhance our understanding regarding the MHC and non-MHC genomic interactions...
May 13, 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#2
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28467961/detection-of-nasopharyngeal-carcinoma-susceptibility-with-single-nucleotide-polymorphism-analysis-using-next-generation-sequencing-technology
#3
Mu-Yun Wu, Shu-Jing Huang, Fan Yang, Xin-Tian Qin, Dong Liu, Ying Ding, Shu Yang, Xi-Cheng Wang
Nasopharyngeal carcinoma (NPC) is a head and neck cancer with high incidence in South China and East Asia. To provide a theoretical basis for NPC risk screening and early prevention, we conducted a meta-analysis of relevant literature on the association of single nucleotide polymorphisms (SNP)s with NPC susceptibility. Further, expression of 15 candidate SNPs identified in the meta-analysis was evaluated in a cohort of NPC patients and healthy volunteers using next-generation sequencing technology. Among the 15 SNPs detected in the meta-analysis, miR-146a (rs2910164, C>G), HCG9 (rs3869062, A>G), HCG9 (rs16896923, T>C), MMP2 (rs243865, C>T), GABBR1 (rs2076483, T>C), and TP53 (rs1042522, C>G) were associated with decreased susceptibility to NPC, while GSTM1 (+/DEL), IL-10 (rs1800896, A>G), MDM2 (rs2279744, T>G), MDS1-EVI1 (rs6774494, G>A), XPC (rs2228000, C>T), HLA-F (rs3129055, T>C), SPLUNC1 (rs2752903, T>C; and rs750064, A>G), and GABBR1 (rs29232, G>A) were associated with increased susceptibility to NPC...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28442289/hla-a-b-and-c-allele-and-haplotype-frequencies-defined-by-next-generation-sequencing-in-a-population-of-519-english-blood-donors
#4
Sue Davey, John Ord, Cristina Navarrete, Colin Brown
Whole gene next generation sequencing was used to determine the HLA class I haplotype and allele frequencies in a cohort of 519 English blood donors. This is the first report of HLA frequencies at third field resolution in a UK population with a total of 33, 52 and 30 alleles identified for HLA-A, -B and -C, respectively. Of the 1411 haplotypes determined, 281 had a frequency of greater than 0.05%. Data are available from the Allele Frequencies Net Database under the population name 'England Blood Donors of Mixed Ethnicity', identifier 3392...
April 22, 2017: Human Immunology
https://www.readbyqxmd.com/read/28422925/dynamics-of-b-cell-recovery-following-kidney-bone-marrow-transplant-recipients
#5
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
#6
Shuji Kawaguchi, Koichiro Higasa, Masakazu Shimizu, Ryo Yamada, Fumihiko Matsuda
The accurate typing of human leukocyte antigen (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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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