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Next-generation sequencing HLA

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https://www.readbyqxmd.com/read/29179676/hla-genotyping-by-next-generation-sequencing-of-complementary-dna
#1
Hidenobu Segawa, Yoji Kukita, Kikuya Kato
BACKGROUND: Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis...
November 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29171935/single-molecule-real-time-smrt%C3%A2-dna-sequencing-of-hla-genes-at-ultra-high-resolution-from-126-international-hla-and-immunogenetics-workshop-cell-lines
#2
T R Turner, J D Hayhurst, D R Hayward, W P Bultitude, D J Barker, J Robinson, J Alejandro Madrigal, N P Mayor, S G E Marsh
The hyperpolymorphic HLA genes play important roles in disease and transplantation and act as genetic markers of migration and evolution. A panel of 107 B-lymphoblastoid cell lines (B-LCLs) was established in 1987 at the 10(th) International Histocompatibility Workshop as a resource for the immunogenetics community. These B-LCLs are well characterised and represent diverse ethnicities and HLA haplotypes. Here we have applied Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing to HLA type 126 B-LCL, including the 107 IHIW cells, to ultra-high resolution...
November 24, 2017: HLA
https://www.readbyqxmd.com/read/29135082/hla-dqb1-02-102-a-novel-allele-identified-by-next-generation-sequencing-in-a-spanish-individual
#3
E Enrich, L Mongay, J L Caro-Oleas, M J Herrero-Mata, F Rudilla
HLA-DQB1*02:102 differs from DQB1*02:01:01 by a single nucleotide substitution resulting in an amino acid change.
November 14, 2017: HLA
https://www.readbyqxmd.com/read/29131543/hla-class-ii-polymorphism-in-saudi-patients-with-multiple-sclerosis
#4
M Al Jumah, S Kojan, A M Al Shehri, M Al Balwi, I Al Abdulkarim, E M Masuadi, Y Alhaidan, A Alabdulrahman, H M Fakhoury, A H Hajeer
Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS). However, only few studies have considered the association of high resolution HLA type and MS, with none yet from Saudi Arabia. The aim of this study was to investigate the association of HLA class II alleles with MS in the Saudi population. We used next generation sequencing to investigate HLA association with MS. This study was conducted at King Abdulaziz Medical City in Riyadh, Saudi Arabia. We found that several HLA-DRB1 and DQB1 alleles were associated with MS...
November 13, 2017: HLA
https://www.readbyqxmd.com/read/29123971/concepts-of-genomics-in-kidney-transplantation
#5
William S Oetting, Casey Dorr, Rory P Remmel, Arthur J Matas, Ajay K Israni, Pamala A Jacobson
Purpose of review: Identification of genetic variants to aid in individualized treatment of solid organ allograft recipients would improve graft survival. We will review the current state of knowledge for associations of variants with transplant outcomes. Recent findings: Many studies have yet to exhibit robust and reproducible results, however, pharmacogenomic studies focusing on cytochrome P450 (CYP) enzymes, transporters and HLA variants have shown strong associations with outcomes and have relevance towards drugs used in transplant...
June 2017: Current Transplantation Reports
https://www.readbyqxmd.com/read/29036181/juvenile-myasthenia-gravis-in-norway-hla-drb1-04-04-is-positively-associated-with-prepubertal-onset
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
October 2017: Human Immunology
https://www.readbyqxmd.com/read/28755385/building-and-validating-a-prediction-model-for-paediatric-type-1-diabetes-risk-using-next-generation-targeted-sequencing-of-class-ii-hla-genes
#17
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 1 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 technology to genotype class II genes and applied an object-oriented regression 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
#18
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
#19
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...
October 2017: Human Immunology
https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#20
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...
November 2017: Journal of Neuro-oncology
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