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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/29036181/juvenile-myasthenia-gravis-in-norway-hla-drb1-04-04-is-positively-associated-with-prepubertal-onset
#1
T H Popperud, M K Viken, E Kerty, B A Lie
BACKGROUND: Juvenile myasthenia gravis (MG) is a rare autoantibody mediated autoimmune disorder targeting the neuromuscular endplate. The clinical hallmark is muscle weakness and fatigability. Disease aetiology is complex, including both genetic and environmental factors. The involvement of genes in the human leukocyte antigen (HLA) is well established in adult MG. However, HLA associations in European juvenile MG have not been studied. This case-control study aimed to investigate and characterize genetic risk factors in prepubertal and postpubertal onset juvenile MG...
2017: PloS One
https://www.readbyqxmd.com/read/29032017/editorial-next-generation-sequencing-technology-a-new-tool-for-killer-cell-immunoglobulin-like-receptor-allele-typing-in-hematopoietic-stem-cell-transplantation
#2
B Maniangou, C Retière, K Gagne
Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017)...
October 11, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
https://www.readbyqxmd.com/read/29030947/identification-of-the-novel-hla-b-57-91-allele-by-next-generation-sequencing-in-a-spanish-individual
#3
E Enrich, E Campos, J L Caro-Oleas, M J Herrero-Mata, F Rudilla
HLA-B*57:91 differs from HLA-B*57:01:01 by a single nucleotide substitution resulting in an amino acid change.
October 14, 2017: HLA
https://www.readbyqxmd.com/read/28987960/frequencies-of-gene-variant-ccr5-%C3%AE-32-in-87-countries-based-on-next-generation-sequencing-of-1-3-million-individuals-sampled-from-3-national-dkms-donor-centers
#4
Ute V Solloch, Kathrin Lang, Vinzenz Lange, Irina Böhme, Alexander H Schmidt, Jürgen Sauter
Homozygous carriers of CCR5-Δ32, a gene variant of CC-type chemokine receptor 5 (CCR5), are highly resistant to infections with human immunodeficiency virus type 1 (HIV-1) and therefore preferred stem cell donors for HIV-infected patients. We analyzed CCR5 typing data of 1,333,035 potential hematopoietic stem cell donors enlisted with three national DKMS donor centers. Allele and genotype frequencies were determined for 87 countries of origin as self-assessed by the donors. CCR5-Δ32 allele frequencies ranged from 16...
October 5, 2017: Human Immunology
https://www.readbyqxmd.com/read/28951201/genetic-susceptibility-to-infectious-diseases-current-status-and-future-perspectives-from-genome-wide-approaches
#5
Alessandra Mozzi, Chiara Pontremoli, Manuela Sironi
Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes >2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility...
September 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28934310/sanger-and-next-generation-sequencing-data-for-characterization-of-ctl-epitopes-in-archived-hiv-1-proviral-dna
#6
Camille Tumiotto, Lionel Riviere, Pantxika Bellecave, Patricia Recordon-Pinson, Alice Vilain-Parce, Gwenda-Line Guidicelli, Hervé Fleury
One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes...
2017: PloS One
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#7
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28881764/detection-of-nasopharyngeal-carcinoma-susceptibility-with-single-nucleotide-polymorphism-analysis-using-next-generation-sequencing-technology
#8
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...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28842944/high-throughput-next-generation-sequencing-to-genotype-six-classical-hla-loci-from-96-donors-in-a-single-miseq-run
#9
P K Ehrenberg, A Geretz, R K Sindhu, T Vayntrub, M A Fernández Viña, R Apps, N L Michael, R Thomas
Next generation sequencing (NGS) methods have been established as an efficient approach for HLA typing because unlike traditional Sanger sequencing, they provide unambiguous results at a reasonable cost. We previously developed a multi-locus index method to genotype four HLA loci (A, B, C, and DRB1) on the Illumina MiSeq platform. We have now expanded this method to include two additional loci, HLA-DPB1 and DQB1. Contiguous full-length amplicons from 5'UTR through 3'UTR regions were generated using one long-range PCR reaction per locus for each of the six loci from 96 individuals of different ethnicities...
August 25, 2017: HLA
https://www.readbyqxmd.com/read/28814775/mutational-profile-of-rare-variants-in-inflammasome-related-genes-in-beh%C3%A3-et-disease-a-next-generation-sequencing-approach
#10
Sergio Burillo-Sanz, Marco-Antonio Montes-Cano, José-Raúl García-Lozano, Lourdes Ortiz-Fernández, Norberto Ortego-Centeno, Francisco-José García-Hernández, Gerard Espinosa, Genaro Graña-Gil, Juan Sánchez-Bursón, María Rosa Juliá, Roser Solans, Ricardo Blanco, Ana-Celia Barnosi-Marín, Ricardo Gómez De la Torre, Patricia Fanlo, Mónica Rodríguez-Carballeira, Luis Rodríguez-Rodríguez, Teresa Camps, Santos Castañeda, Juan-Jose Alegre-Sancho, Javier Martín, María Francisca González-Escribano
Behçet's disease (BD) is an immune-mediated systemic disorder with a well-established association with HLA class I and other genes. BD has clinical overlap with many autoinflammatory diseases (AIDs). The aim of this study was to investigate the role of rare variants in seven genes involved in AIDs: CECR1, MEFV, MVK, NLRP3, NOD2, PSTPIP1 and TNFRSF1A using a next generation sequencing (NGS) approach in 355 BD patients. To check global association of each gene, 4 tests: SKAT, CollapseBt, C(α) and weighted KBAC were used...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28813642/buccal-swab-genomic-dna-fragmentation-predicts-likelihood-of-successful-hla-genotyping-by-next-generation-sequencing
#11
Maureen C Montgomery, Rosanne Petraroia, Eric T Weimer
Many clinical human leukocyte antigen (HLA) laboratories are adopting next-generation sequencing (NGS) technology for HLA genotyping. There have been several reports of the cost-benefit and reduction in turn-around-time provided by NGS. Ninety-six percent of buccal swabs and peripheral blood samples had reportable HLA genotyping by NGS. The HLA loci most likely to fail genotyping from buccal swabs were DQB1, DPB1, and DPA1. Successful buccal swab samples had significantly less genomic DNA fragmentation compared to buccal swab samples that were unsuccessful...
August 13, 2017: Human Immunology
https://www.readbyqxmd.com/read/28755385/building-and-validating-a-prediction-model-for-pediatric-type-1-diabetes-risk-using-next-generation-targeted-sequencing-of-class-ii-hla-genes
#12
Lue Ping Zhao, Annelie Carlsson, Helena Elding Larsson, Gun Forsander, Sten A Ivarsson, Ingrid Kockum, Johnny Ludvigsson, Claude Marcus, Martina Persson, Ulf Samuelsson, Eva Örtqvist, Chul-Woo Pyo, Hamid Bolouri, Michael Zhao, Wyatt C Nelson, Daniel E Geraghty, Åke Lernmark
AIM: It is of interest to predict possible lifetime risk of type diabetes (T1D) in young children for recruiting high-risk subjects into longitudinal studies of effective prevention strategies. METHODS: Utilizing a case-control study in Sweden, we applied a recently developed next generation targeted sequencing (NGTS) technology to genotype class II genes, and applied an object-oriented regression (OOR) to build and validate a prediction model for T1D. RESULTS: In the training set, estimated risk scores were significantly different between patients and controls (P=8...
July 29, 2017: Diabetes/metabolism Research and Reviews
https://www.readbyqxmd.com/read/28734101/hla-b-40-356-identified-by-next-generation-sequence-based-typing-in-a-chinese-tuberculosis-patient
#13
J Tang, X Chen, S Liu, X Tian
HLA-B*40:356 differs from B*40:02:01 by only one nucleotide transition, C>A 1040 in exon 6.
July 22, 2017: HLA
https://www.readbyqxmd.com/read/28732721/assessing-a-single-targeted-next-generation-sequencing-for-human-leukocyte-antigen-typing-protocol-for-interoperability-as-performed-by-users-with-variable-experience
#14
Manish J Gandhi, Deborah Ferriola, Curt Lind, Jamie L Duke, Anh Huynh, Anna Papazoglou, Kate Mackiewicz, Mette Christiansen, Wei Dong, Susan Hsu, Dawn Thomas, Brittany Schneider, Erin Pierce, Jane Kearns, Malek Kamoun, Dimitri Monos, Medhat Askar
BACKGROUND: A simplified protocol for HLA-typing -by NGS, developed for use with the Illumina MiSeq, was performed by technologists with varying NGS experience to assess accuracy and reproducibility. METHODS: Technologists from six laboratories typed the same 16 samples at HLA-A, B, C, DRB1, and DQB1. The protocol includes long range PCR, library preparation, and paired-end 250bp sequencing. Two indexing strategies were employed: locus-specific indexing whereby each locus was tagged uniquely and sample-specific indexing whereby all 5 loci for a sample were pooled prior to library preparation...
July 18, 2017: Human Immunology
https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#15
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
#16
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
#17
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
#18
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 25, 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
#19
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
#20
Xiuli Zhang, Samuel Kim, Jasreet Hundal, John M Herndon, Shunqiang Li, Allegra A Petti, Savas D Soysal, Lijin Li, Mike D McLellan, Jeremy Hoog, Tina Primeau, Nancy Myers, Tammi L Vickery, Mark Sturmoski, Ian S Hagemann, Chris A Miller, Matthew J Ellis, Elaine R Mardis, Ted Hansen, Timothy P Fleming, S 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 2,091 (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...
July 2017: Cancer Immunology Research
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