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32 results for “Targeted next-generation sequencing”
Comparative assessment of line-probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis
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Development and application of Faba_bean_130K Targeted Next-Generation Sequencing SNP genotyping platform based on transcriptome sequencing
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Data from: Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: A multicentre clinical study of two end-to-end commercial workflows
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Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease
Objective: To investigate the effectiveness of targeted NGS panels in achieving a molecular diagnosis in CMT and related disorders in a clinical setting Methods: We prospectively enrolled 220 patients from two tertiary referral centres, one in London, UK (n=120) and one in Iowa, US (n=100) in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon completion of the diagnostic process. Results: After targeted NGS sequencing a definite molecular diagnosis, defined as a pathogenic or likely pathogenic variant, was reached in 30% of cases (n=67). The diagnostic rate was similar in London (32%) and Iowa (29%). Variants of unknown significance were found in an additional 33% of cases. Mutations in GJB1, MFN2, MPZ accounted for 39% of cases who received genetic confirmation, while the remainder of positive cases had mutations in diverse genes, including SH3TC2, GDAP1, IGHMBP2, LRSAM1, FDG4, GARS and another 12 less common genes. Copy number changes in PMP22, MPZ, MFN2, SH3TC2 and FDG4 were also accurately detected. A definite genetic diagnosis was more likely in cases with an early onset, a positive family history of neuropathy or consanguinity and a demyelinating neuropathy. Conclusions: NGS panels are effective tools in the diagnosis of CMT leading to the genetic confirmation in one third cases negative for PMP22 duplication/deletion, thus highlighting how rarer and previously undiagnosed subtypes represent today a relevant part of the genetic landscape of CMT.
Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease
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Data from: aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data
Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest. Results: Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with divergent sequences, we assembled >1,000 genes from six taxa ranging from 25 – 110 million years divergent from the reference taxon. The gene recovery was between 97 – 99% from each taxon. Conclusions: aTRAM can quickly assemble genes across distantly-related taxa, obviating the need for draft genome assembly of all taxa of interest. Because aTRAM uses a targeted approach, loci can be assembled in minutes depending on the size of the target. Our results suggest that this software will be useful in rapidly assembling genes for phylogenomic projects covering a wide taxonomic range, as well as other applications. The software is freely available: http://www.github.com/juliema/aTRAM
Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing in ICU Patients.
ClinicalTrials.gov study NCT06157372. IPD Sharing: NO. Countries: 0. Publications: 6.
Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics
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Data from: Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR
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Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics
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Data from: aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data
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Next Gen(etics): targeted genome enrichment and next-generation sequencing enhances phenotype-driven forward genetics and gene-driven reverse genetics
GEO Series GSE22024. Rattus norvegicus. 30 samples. Type: Genome variation profiling by high throughput sequencing.
Mapping protein selectivity landscapes using multi-target selective screening and next-generation sequencing of combinatorial libraries
GEO Series GSE289251. Saccharomyces cerevisiae. 9 samples. Type: Other.
The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [MeDIP-seq]
GEO Series GSE121687. Mus musculus. 6 samples. Type: Methylation profiling by high throughput sequencing.
The next-generation RNA and ATAC sequencing of MLL-ENL transformed cell lines reveals that C/EBP transcription factors coordinate the expression of the MLL-ENL/Hoxa target genes [ATAC-seq]
GEO Series GSE153623. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [miRNA-seq]
GEO Series GSE121701. Mus musculus. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis
GEO Series GSE121702. Mus musculus. 24 samples. Type: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [RNA-seq]
GEO Series GSE121700. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Targeted Next-Generation Sequencing for profiling frequently mutated genes in early-stage colon cancer
GEO Series GSE172190. Homo sapiens. 44 samples. Type: Other.
Next-generation Sequencing of Small Cell Lung Cancer to Identify Actionable Targets for Treatment
ClinicalTrials.gov study NCT02297087. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.