scholarly journals Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut ( Arachis hypogaea L.)

2019 ◽  
Vol 17 (12) ◽  
pp. 2356-2369 ◽  
Author(s):  
Huaiyong Luo ◽  
Manish K. Pandey ◽  
Aamir W. Khan ◽  
Bei Wu ◽  
Jianbin Guo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Arachis Hypogaea ◽  
Bacterial Wilt ◽  
Genomic Region ◽  
Diagnostic Markers ◽  
Next Generation ◽  
Arachis Hypogaea L ◽  
Generation Sequencing

Genetic and epigenetic characterization of the cry1Ab coding region and its 3′ flanking genomic region in MON810 maize using next-generation sequencing

2018 ◽  
Vol 244 (8) ◽  
pp. 1473-1485 ◽  
Author(s):  
Sina-Elisabeth Ben Ali ◽  
Alexandra Schamann ◽  
Stefanie Dobrovolny ◽  
Alexander Indra ◽  
Sarah Zanon Agapito-Tenfen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Region ◽  
Next Generation ◽  
Coding Region ◽  
Generation Sequencing ◽  
Mon810 Maize

scholarly journals Next-Generation Sequencing and Genotype Association Studies Reveal the Association of HLA-DRB3*02:02 With Delayed Hypersensitivity to Penicillins

2021 ◽  
Author(s):  
Jean Louis Gueant ◽  
A Romano ◽  
Abderrahim OUSSALAH ◽  
Celine Chery ◽  
Rosa Maria Rodriguez-Gueant ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Association Studies ◽  
Genomic Region ◽  
Delayed Hypersensitivity ◽  
Next Generation ◽  
Immediate Hypersensitivity ◽  
Increased Risk ◽  
Delayed Reactions ◽  
Generation Sequencing ◽  
Immediate Reactions

Background: Nonimmediate (delayed) allergic reactions to penicillins are common and some of them can be life-threatening. The genetic factors influencing these reactions are unknown/poorly known/poorly understood. We assessed the genetic predictors of a delayed penicillin allergy that cover the HLA loci. Methods: Using next-generation sequencing (NGS), we genotyped the MHC region in 24 patients with delayed hypersensitivity compared with 20 patients with documented immediate hypersensitivity to penicillins recruited in Italy. Subsequently, we analyzed in silico Illumina Immunochip genotyping data that covered the HLA loci in 98 Spanish patients with delayed hypersensitivity and 315 with immediate hypersensitivity compared to 1,308 controls. Results: The two alleles DRB3*02:02:01:02 and DRB3*02:02:01:01 were reported in twenty cases with delayed reactions (83%) and ten cases with immediate reactions (50%), but not in the Allele Frequency Net Database. Bearing at least one of the two alleles increased the risk of delayed reactions compared to immediate reactions, with an OR of 8.88 (95% CI, 3.37–23.32; P <0.0001). The haplotype (ACAA) from rs9268835, rs6923504, rs6903608, and rs9268838 genetic variants of the HLA-DRB3 genomic region was significantly associated with an increased risk of delayed hypersensitivity to penicillins (OR, 1.7; 95% CI: 1.06–1.92; P=0.001), but not immediate hypersensitivity. Conclusion: We showed that the HLA-DRB3 locus is strongly associated with an increased risk of delayed penicillin hypersensitivity, at least in Southwestern Europe. The determination of HLA-DRB3*02:02 alleles in the risk management of severe delayed hypersensitivity to penicillins should be evaluated further in larger population samples of different origins.

scholarly journals A Spontaneous Deletion of the US1.67/US2 Genomic Region on the Bovine Herpesvirus 1 Strain Cooper

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
F. S. Campos ◽  
W. P. Paim ◽  
A. G. Silva ◽  
R. N. Santos ◽  
R. M. Firpo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Viral Genome ◽  
Gene Deletion ◽  
Bovine Herpesvirus ◽  
Genomic Region ◽  
Next Generation ◽  
Bovine Herpesvirus 1 ◽  
A Genome ◽  
Herpesvirus 1 ◽  
Generation Sequencing

Bovine herpesvirus 1 (BoHV-1) is an alphaherpesvirus with a genome of 135 kb. Some BoHV-1 genes are nonessential and may be deleted from the viral genome. Here, a spontaneous gene deletion was identified in the BoHV-1 strain Cooper. Genes of the US1.67/US2 region were absent, as determined by next-generation sequencing.

scholarly journals Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes

2021 ◽  
Author(s):  
Jianbo Zhang ◽  
Dilip R Panthee
Keyword(s):  
Next Generation Sequencing ◽  
Bulked Segregant Analysis ◽  
Genomic Region ◽  
Parental Genome ◽  
Next Generation ◽  
Genome Sequences ◽  
Original Algorithm ◽  
Structural Variant ◽  
Variant Method ◽  
Generation Sequencing

Abstract Genomic regions that control traits of interest can be rapidly identified using BSA-Seq, a technology in which next-generation sequencing (NGS) is applied to bulked segregant analysis (BSA). We recently developed the significant structural variant method for BSA-Seq data analysis that exhibits higher detection power than standard BSA-Seq analysis methods. Our original algorithm was developed to analyze BSA-Seq data in which genome sequences of one parent served as the reference sequences in genotype calling, and thus required the availability of high-quality assembled parental genome sequences. Here we modified the original script to effectively detect the genomic region-trait associations using only bulk genome sequences. We analyzed two public BSA-Seq datasets using our modified method and the standard allele frequency and G-statistic methods with and without the aid of the parental genome sequences. Our results demonstrate that the genomic region(s) associated with the trait of interest could be reliably identified via the significant structural variant method without using the parental genome sequences.

scholarly journals Next-Generation Sequencing and Genotype Association Studies Reveal the Association of HLA-DRB3*02:02 With Delayed Hypersensitivity to Penicillins

2021 ◽  
Author(s):  
Antonino Romano ◽  
Abderrahim OUSSALAH ◽  
Céline Chery ◽  
Rosa Maria Rodriguez-Gueant ◽  
Francesco Gaeta ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Association Studies ◽  
Genomic Region ◽  
Delayed Hypersensitivity ◽  
Next Generation ◽  
Immediate Hypersensitivity ◽  
Increased Risk ◽  
Delayed Reactions ◽  
Generation Sequencing ◽  
Immediate Reactions

Background: Nonimmediate (delayed) allergic reactions to penicillins are common and some of them can be life-threatening. The genetic factors influencing these reactions are unknown/poorly known/poorly understood. We assessed the genetic predictors of a delayed penicillin allergy that cover the HLA loci. Methods: Using next-generation sequencing (NGS), we genotyped the MHC region in 24 patients with delayed hypersensitivity compared with 20 patients with documented immediate hypersensitivity to penicillins recruited in Italy. Subsequently, we analyzed in silico Illumina Immunochip genotyping data that covered the HLA loci in 98 Spanish patients with delayed hypersensitivity and 315 with immediate hypersensitivity compared to 1,308 controls. Results: The two alleles DRB3*02:02:01:02 and DRB3*02:02:01:01 were reported in twenty cases with delayed reactions (83%) and ten cases with immediate reactions (50%), but not in the Allele Frequency Net Database. Bearing at least one of the two alleles increased the risk of delayed reactions compared to immediate reactions, with an OR of 8.88 (95% CI, 3.37–23.32; P <0.0001). The haplotype (ACAA) from rs9268835, rs6923504, rs6903608, and rs9268838 genetic variants of the HLA-DRB3 genomic region was significantly associated with an increased risk of delayed hypersensitivity to penicillins (OR, 1.7; 95% CI: 1.06–1.92; P=0.001), but not immediate hypersensitivity. Conclusion: We showed that the HLA-DRB3 locus is strongly associated with an increased risk of delayed penicillin hypersensitivity, at least in Southwestern Europe. The determination of HLA-DRB3*02:02 alleles in the risk management of severe delayed hypersensitivity to penicillins should be evaluated further in larger population samples of different origins.

scholarly journals Targeted next-generation sequencing of 565 neuro-oncology patients at UCLA: A single-institution experience

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Matthew S Ji ◽  
Blaine S C Eldred ◽  
Regina Liu ◽  
Sean T Pianka ◽  
Donna Molaie ◽  
...  
Keyword(s):  
Patient Outcome ◽  
Next Generation Sequencing ◽  
Diagnostic Markers ◽  
Cns Tumors ◽  
Next Generation ◽  
Oncology Patients ◽  
Targeted Next Generation Sequencing ◽  
Targeted Ngs ◽  
Unknown Significance ◽  
Generation Sequencing

Abstract Background Targeted next-generation sequencing (NGS) is frequently obtained at the University of California, Los Angeles (UCLA) for clinical characterization of CNS tumors. In this study, we describe the diagnostic reliability of the Foundation Medicine (FM) targeted NGS platform and its ability to explore and identify tumor characteristics of prognostic significance in gliomas. Methods Neuro-oncology patients seen at UCLA who have received FM testing between August 2012 and March 2019 were included in this study, and all mutations from FM test reports were recorded. Initial tumor diagnoses and diagnostic markers found via standard clinical methods were obtained from pathology reports. With overall and progression-free survival data, elastic net regularized Cox regression and Cox proportional hazards models were used to determine whether any mutations of unknown significance detected by FM could predict patient outcome in glioblastoma (GBM). Results Six hundred and three samples tested by FM from 565 distinct patients were identified. Concordance of diagnostic markers was high between standard clinical testing methods and FM. Oligodendroglial markers detected via FM were highly correlated with 1p19q codeletion in IDH mutated gliomas. FM testing of multiple tumor samples from the same patient demonstrated temporal and spatial mutational heterogeneity. Mutations in BCORL1, ERBB4, and PALB2, which are mutations of unknown significance in GBM, were shown to be statistically significant in predicting patient outcome. Conclusions In our large cohort, we found that targeted NGS can both reliably and efficiently detect important diagnostic markers in CNS tumors.

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