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Dataset results
27 results for “Genome Diagnostics”
NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
<p>We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing on a MiSeq platform. We sequenced the edited site of cell bulks to investigate the editing efficiencies of individual donors from the donor mixtures. For proof of concept, we isolated over 850 cellular clones from the edited cell bulks and sequenced the edited site and heterozygous positions flanking the edited site to determine the number of alleles at the edited site and detect copy-neutral loss of heterozygosity. Additionally, we sequenced the DNA donors to assess, the distribution of individual donors in the mixtures.</p>
Data for paper: Genomic data reveals new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)
<p>Files in this repository:</p><p>"COI_alignment.fas.zip" Zipped file of the FASTA alignment of the COI sequences.</p><p>"COI_IQtree.treefile" Newick treefile resulting from the IQ-tree analysis of the COI alignment.</p><p>"RAD-loci_alignment.nex.zip" Zipped file of the NEXUS alignment of RAD loci of 2295 samples.</p><p>"RAD-loci_IQtree.tre" Newick treefile resulting from the IQ-tree analysis of the RAD-loci alignment.</p><p>"RAD-SNP_alignment.usnps.nex" NEXUS alignment of the RAD-SNP data of 50 samples.</p><p>"RAD-SNP_SNAPP.trees" Set of Newick trees resulting from the BEAST SNAPP analysis.</p>
LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies
ClinicalTrials.gov study NCT02699190. IPD Sharing: NO. Countries: 1. Publications: 10.
NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
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Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
The article documents the public availability of RAD sequencing data and generated SNPs for the American mink (Neovison vison). 224,095 polymorphic loci were identified from 14 mink from which primers were designed for a subset of 380 SNPs. The panel was tested on 211 mink. Fisher's F-statistics (Fis, FIT and FST) as well as observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity was calculated for the SNPs and 194 SNPs was validated as being useful for population genetic studies.
Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.
Diagnostic Odyssey: Whole Genome Sequencing (WGS)
ClinicalTrials.gov study NCT03458962. IPD Sharing: NO. Countries: 1. Publications: 2.
Diagnostic Significance of Single Center, Open and Prospective Evaluation of <Sup>18<Sup>F-FDG PET/CT Dynamic Imaging and Genomic Sequencing in Detecting Metastatic Lesions and Differentiating Multipl
ClinicalTrials.gov study NCT03679936. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
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Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
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Data from: Diagnostic yield in epileptic encephalopathies is improved by genome sequencing and re-analysis
<p><b>Objective:</b> To assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE).</p> <p><b>Methods: </b>We performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray (CMA), and either research ES (n=15) or diagnostic MGP (n=15).</p> <p><b>Results</b>: 8 diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants which now had additional evidence for pathogenicity. 11 diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n=10) involved genes not included in the panel, particularly in individuals with post-neonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features and/or multi-organ involvement. 42% of diagnoses were autosomal recessive or X-chromosome linked.</p> <p><span><span><b>Conclusion:</b> WGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n=3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel non-coding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.</span></span></p>
Data from: Diagnostic yield in epileptic encephalopathies is improved by genome sequencing and re-analysis
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Expression data of whole genome and circRNA from new diagnostic AML patients (with or without EMI) and healthy volunteers
GEO Series GSE116618. Homo sapiens. 24 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer
GEO Series GSE246110. Homo sapiens. 100 samples. Type: Other.
Expression data of whole genome from new diagnostic AML patients (with or without EMI) and healthy volunteers
GEO Series GSE116616. Homo sapiens. 12 samples. Type: Expression profiling by array.
Whole genome-derived tiled peptide arrays detect pre-diagnostic autoantibody signatures in non-small cell lung cancer
GEO Series GSE128077. Homo sapiens. 174 samples. Type: Protein profiling by protein array.
An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects non-invasive diagnostic markers for gliomas
GEO Series GSE132118. Homo sapiens. 222 samples. Type: Methylation profiling by high throughput sequencing.
Study of the Diagnostic Value of "Rapid" High Throughput Genome Sequencing Analysis in Diagnostic Emergency Situations
ClinicalTrials.gov study NCT03956069. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Functional Genomics of Rare Genetic Diseases: Realization of Innovative Tools With High Diagnostic Power
ClinicalTrials.gov study NCT04152876. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Pan-genome Analysis of Neuroblastoma by Comparative Genomic Hybridization and Correlation With Pathology for the Diagnostic and the Prognostic Classification
ClinicalTrials.gov study NCT02864563. IPD Sharing: YES. 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.