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484 results for “Next-Generation Sequencing”
Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called genotyping-by-sequencing (GBS), to produce a data set for genetic mapping in an F1 population of apples (Malus x domestica) segregating for skin color. We show that GBS produces a relatively large, but extremely sparse, genotype matrix: over 270,000 SNPs were discovered, but most SNPs have too much missing data across samples to be useful for genetic mapping. After filtering for genotype quality and missing data, only 6% of the 85 million DNA sequence reads contributed to useful genotype calls. Despite this limitation, using existing software and a set of simple heuristics, we generated a final genotype matrix containing 3967 SNPs from 89 DNA samples from a single lane of Illumina HiSeq and used it to create a saturated genetic linkage map and to identify a known QTL underlying apple skin color. We therefore demonstrate that GBS is a cost effective method for generating genome-wide SNP data suitable for genetic mapping in a highly diverse and heterozygous agricultural species. We anticipate future improvements to the GBS analysis pipeline presented here that will enhance the utility of next-generation DNA sequence data for the purposes of genetic mapping across diverse species.
A Streamlined and High-Throughput Error-Corrected Next-Generation Sequencing Method for Low Variant Allele Frequency Quantitation
<p></p><p>Quantifying mutant or variable allele frequencies (VAFs) of ≤10−3 using next-generation sequencing (NGS) has utility in both clinical and nonclinical settings. Two common approaches for quantifying VAFs using NGS are tagged single-strand sequencing and duplex sequencing. While duplex sequencing is reported to have sensitivity up to 10−8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥10−4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10−5 to 10−1, then applied and tested on native genomic DNA. For both sources of DNA, there is a proportional increase in the observed VAF to input VAF from 10−4 to 100% mutant samples. Variability of quantitation was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥10−4, and it was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with the potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal-appearing tissue.</p><p></p>
Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.
Figure 7 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 7 - Carebara phragmotica sp. n. Minor worker (paratype: CASENT0709554). A head in full-face view B body in profile view C body in dorsal view.
Figure 4 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 4 - Carebara thoracica (Weber, 1950) – original drawings. A minor worker full-face view B minor worker profile of body C major worker full-face view D major worker profile.
Figure 3 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 3 - Carebara elmenteitae (Patrizi, 1948) – original drawings. Holotype phragmotic worker (I), dorsal view (II): A head in ventral view B head in oblique dorsolateral view C mesosoma and waist in profile.
Figure 6 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 6 - Carebara phragmotica sp. n. Phragmotic worker (paratype: CASENT0709550). A head in full-face view B body in profile view C body in dorsal view. Major worker (paratype: CASENT0906158) D head in full-face view E body in profile view F body in dorsal view.
Figure 5 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 5 - Carebara lilith sp. n. Phragmotic worker (holotype: CASENT0709545). A head in full-face view B body in profile view C body in dorsal view. Minor worker (paratype: CASENT0709546) D head in full-face view E body in profile view F body in dorsal view.
Figure 1 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 1 - A, B full-face view of phragmotic major workers of Carebara phragmotica sp. n. and C, D Carebara lilith sp. n. A, C on the left side the head is depicted in the state that it was found in the samples, with debris sticking to cephalic shield B, D right view: same specimens with debris removed in ultrasonic bath.
Figure 2 from: Fischer G, Azorsa F, Hita Garcia F, Mikheyev AS, Economo EP (2015) Two new phragmotic ant species from Africa: morphology and next-generation sequencing solve a caste association problem in the genus Carebara Westwood. ZooKeys 525: 77-105. https://doi.org/10.3897/zookeys.525.6057
Figure 2 - Maximum likelihood tree of sequenced Carebara specimens reconstructed with ExaML v3.0.14. Most nodes are supported with more than 0.95% of bootstraps (represented by open circles) except for five, which have between 0.5 and 0.95% support (black circles). The tree shows the division between Carebara phragmotica sp. n. specimens with ten antennal segments (previous IDs: [*] Carebara elmenteitae, [**] Carebara thoracica) and all other sampled specimens, including Carebara thoracica with nine antennal segments, which are closer related to 9-segmented Carebara alluaudi.
Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections
ClinicalTrials.gov study NCT03846804. IPD Sharing: NO. Countries: 1. Publications: 0.
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.
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
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Data from: Nonspecific PCR amplification by high-fidelity polymerases: implications for next-generation sequencing of AFLP markers.
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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: Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms
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Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)
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Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing
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Data from: De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques.
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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.
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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.