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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#1
Chenan Zhang, Adam J de Smith, Ivan V Smirnov, John K Wiencke, Joseph L Wiemels, John S Witte, Kyle M Walsh
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described...
July 18, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28697761/hla-check-evaluating-hla-data-from-snp-information
#2
Marc Jeanmougin, Josselin Noirel, Cédric Coulonges, Jean-François Zagury
BACKGROUND: The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequencing methods (eg, Next-Generation Sequencing, NGS), the accurate genotyping of this region has become possible but remains relatively costly. In order to obtain the HLA information for the millions of samples already genotyped by chips in the past ten years, efficient bioinformatics tools, such as SNP2HLA or HIBAG, have been developed that infer HLA information from the linkage disequilibrium existing between HLA alleles and SNP markers in the MHC region...
July 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28687858/a-genomic-perspective-on-hla-evolution
#3
REVIEW
Diogo Meyer, Vitor R C Aguiar, Bárbara D Bitarello, Débora Y C Brandt, Kelly Nunes
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution...
July 7, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28674023/fast-and-accurate-hla-typing-from-short-read-next-generation-sequence-data-with-xhla
#4
Chao Xie, Zhen Xuan Yeo, Marie Wong, Jason Piper, Tao Long, Ewen F Kirkness, William H Biggs, Ken Bloom, Stephen Spellman, Cynthia Vierra-Green, Colleen Brady, Richard H Scheuermann, Amalio Telenti, Sally Howard, Suzanne Brewerton, Yaron Turpaz, J Craig Venter
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28623251/highly-functional-t-cell-receptor-repertoires-are-abundant-in-stem-memory-t-cells-and-highly-shared-among-individuals
#5
Takahiko Miyama, Takakazu Kawase, Kazutaka Kitaura, Ren Chishaki, Masashi Shibata, Kumi Oshima, Hiroshi Hamana, Hiroyuki Kishi, Atsushi Muraguchi, Kiyotaka Kuzushima, Hiroh Saji, Tadasu Shin-I, Ryuji Suzuki, Tatsuo Ichinohe
To expand our knowledge of the ontogeny of the T-cell receptor (TCR) repertoire of antigen-specific T-cell subsets, we combined next-generation deep sequencing and single-cell multiplex clonotype analysis to evaluate the diversity and frequency of paired TCRs, their functions and whether clonotypic TCRs are shared among different individuals. Using an HLA-A*02-restricted cytomegalovirus (CMV) pp65-derived immunogenic peptide, we found that the more dominant pp65-specific TCR clonotypes in the blood of healthy donors have higher binding affinities for the CMV peptide and arise from clonotypes that are highly shared among individuals...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619968/breast-cancer-neoantigens-can-induce-cd8-t-cell-responses-and-antitumor-immunity
#6
Xiuli Zhang, Samuel Kim, Jasreet Hundal, John M Herndon, Shunqiang Li, Allegra A Petti, Savas D Soysal, Lijin Li, Michael D McLellan, Jeremy Hoog, Tina Primeau, Nancy Myers, Tammi L Vickery, Mark Sturmoski, Ian S Hagemann, Christopher A Miller, Matthew J Ellis, Elaine R Mardis, Ted Hansen, Timothy P Fleming, Peter Goedegebuure, William E Gillanders
Next-generation sequencing technologies have provided insights into the biology and mutational landscape of cancer. Here we evaluate the relevance of cancer neoantigens in human breast cancers. Using patient-derived xenografts from three patients with advanced breast cancer (xenografts were designated as WHIM30, WHIM35, and WHIM37), we sequenced exomes of tumor and patient-matched normal cells. We identified 2091 (WHIM30), 354 (WHIM35), and 235 (WHIM37) nonsynonymous somatic mutations. A computational analysis identified and prioritized HLA class I-restricted candidate neoantigens expressed in the dominant tumor clone...
June 15, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/28597946/comprehensive-screening-for-monogenic-diabetes-in-89-japanese-children-with-insulin-requiring-antibody-negative-type-1-diabetes
#7
Kikumi Ushijima, Maki Fukami, Tadayuki Ayabe, Satoshi Narumi, Misako Okuno, Akie Nakamura, Toshikazu Takahashi, Kenji Ihara, Kazuhiro Ohkubo, Emiko Tachikawa, Shoji Nakayama, Junichi Arai, Nobuyuki Kikuchi, Toru Kikuchi, Tomoyuki Kawamura, Tatsuhiko Urakami, Kenichiro Hata, Kazuhiko Nakabayashi, Yoichi Matsubara, Shin Amemiya, Tsutomu Ogata, Ichiro Yokota, Shigetaka Sugihara
BACKGROUND: Mutations in causative genes for neonatal diabetes or maturity-onset diabetes of the young have been identified in multiple patients with autoantibody-negative type 1 diabetes (T1D). OBJECTIVES: We aimed to clarify the prevalence and phenotypic characteristics of monogenic abnormalities among 89 children with autoantibody-negative insulin-requiring T1D. METHODS: Mutations in 30 genes were screened using next-generation sequencing, and copy-number alterations of 4 major causative genes were examined using multiplex-ligation-dependent probe amplification...
June 9, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28596278/hla-drb1-07-01-hla-dqa1-02-01-hla-dqb1-02-02-haplotype-is-associated-with-a-high-risk-of-asparaginase-hypersensitivity-in-acute-lymphoblastic-leukemia
#8
Nóra Kutszegi, Xiaoqin Yang, András Gézsi, Géza Schermann, Dániel J Erdélyi, Ágnes F Semsei, Krisztina M Gábor, Judit C Sági, Gábor T Kovács, András Falus, Hongyun Zhang, Csaba Szalai
Hypersensitivity reactions are the most frequent dose-limiting adverse reactions to Escherichia coli-derived asparaginase in pediatric acute lymphoblastic leukemia patients. The aim of the present study was to identify associations between sequence-based Human Leukocyte Antigen Class II region alleles and asparaginase hypersensitivity in a Hungarian acute lymphoblastic leukemia population. Four-digit typing of HLA-DRB1 and HLA-DQB1 loci was performed in 359 pediatric acute lymphoblastic leukemia patients by using next-generation sequencing method...
June 8, 2017: Haematologica
https://www.readbyqxmd.com/read/28585303/different-drb1-03-01-dqb1-02-01-haplotypes-confer-different-risk-for-celiac-disease
#9
S Alshiekh, L P Zhao, Å Lernmark, D E Geraghty, Å T Naluai, D Agardh
Celiac disease is associated with the HLA-DR3-DQA1*05:01-DQB1*02:01 and DR4-DQA1*03:01-DQB1*03:02 haplotypes. In addition, there are currently over 40 non-HLA loci associated with celiac disease. This study extends previous analyses on different HLA haplotypes in celiac disease using next generation targeted sequencing. Included were 143 patients with celiac disease and 135 non-celiac disease controls investigated at median 9.8 years (1.4-18.3 years). PCR-based amplification of HLA and sequencing with Illumina MiSeq technology were used for extended sequencing of the HLA class II haplotypes HLA-DRB1, DRB3, DRB4, DRB5, DQA1 and DQB1, respectively...
June 5, 2017: HLA
https://www.readbyqxmd.com/read/28579987/killer-immunoglobulin-like-receptor-allele-determination-using-next-generation-sequencing-technology
#10
Bercelin Maniangou, Nolwenn Legrand, Mehdi Alizadeh, Ulysse Guyet, Catherine Willem, Gaëlle David, Eric Charpentier, Alexandre Walencik, Christelle Retière, Katia Gagne
The impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR(+) NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR(+) NK cells...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28556460/hla-genotyping-using-the-illumina-hla-trusight-next-generation-sequencing-kits-a-comparison
#11
T Profaizer, E Lázár-Molnár, A Pole, J C Delgado, A Kumánovics
Illumina first introduced their TruSight human leucocyte antigen (HLA) next-generation sequencing (NGS) typing kit in 2015 and subsequently followed up with a new version in 2016. Here we report on our experience comparing the two versions of the Illumina HLA NGS kits.
May 28, 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#12
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28539552/development-of-an-assay-system-for-large-scale-analysis-of-hla-class-ii-binding-peptides
#13
Hiroko Miyadera, Emiko Noguchi, Masashi Mizokami, Katsushi Tokunaga
  Genes encoding the human leukocyte antigens (HLA) are associated with diverse immunological disorders, including autoimmune diseases and infections. Recently, significant progresses have been made in the HLA typing technologies through the use of next generation sequencers. The reliable platforms for the SNP-based imputation of HLA genotypes have also been established. These technical advancements should enable further identification of HLA associations with diseases. One of the remaining questions is the mechanism through which HLA confer disease susceptibility...
2017: Nihon Rinshō Men'eki Gakkai Kaishi, Japanese Journal of Clinical Immunology
https://www.readbyqxmd.com/read/28509679/the-impact-of-next-generation-sequencing-in-immunogenetics-current-status-and-future-directions
#14
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...
August 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#15
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
#16
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
#17
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
#18
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
#19
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...
July 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
#20
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...
July 2017: HLA
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