Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
138
datasets available to search
ShareScore release 0.9.0
Dataset results
138 results for “Exome Sequencing”
Scalable mixed model approaches for set-based association studies on large-scale categorical data analysis and its application to 450k exome sequencing data in UK Biobank
<p>The ongoing release of large-scale sequencing data in the UK Biobank allows for identifying associations between rare variants and complex traits. SAIGE-GENE+ is a valid approach to conducting set-based association tests for quantitative and binary traits. However, for ordinal categorical phenotypes, applying SAIGE-GENE+ with treating the trait as quantitative or binarizing the trait can cause inflated type I error rates or power loss. In this study, we propose a novel method for rare-variant association tests, POLMM-GENE, in which a proportional odds logistic mixed model was used to characterize ordinal categorical phenotypes while adjusting for sample relatedness. POLMM-GENE fully utilizes the categorical nature of phenotypes and thus can well control type I error rates while remaining powerful. In the analyses of UK Biobank 450k whole exome-sequencing data for 5 ordinal categorical traits, POLMM-GENE identified 54 gene-phenotype associations.</p>
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
NIPD of CFTC by WGA Coupled to Mini-exome Sequencing
ClinicalTrials.gov study NCT03743948. IPD Sharing: NO. Countries: 1. Publications: 0.
Exome Sequencing Study in Cardiomyopathy to Identify New Risk Variants
ClinicalTrials.gov study NCT03754101. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
A Study of Consent Forms for Whole Exome and Whole Genome Sequencing
ClinicalTrials.gov study NCT01927770. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Whole Exome Sequencing in CKD Hypertension
ClinicalTrials.gov study NCT03718585. IPD Sharing: NO. Countries: 1. Publications: 25.
Contribution of High-throughput Exome Sequencing in the Diagnosis of the Cause Fetal Polymalformation Syndromes
ClinicalTrials.gov study NCT02512354. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparison of the Non-invasive Approach and Fetal Exome Sequencing in Prenatal Diagnosis When Fetal Ultrasound Signs Are Discovered
ClinicalTrials.gov study NCT05182242. IPD Sharing: NO. Countries: 1. Publications: 1.
Exome Sequencing in Autistic Spectrum Disorder
ClinicalTrials.gov study NCT01059201. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Whole Exome Sequencing and Whole Genome Sequencing for Nonimmune Fetal/Neonatal Hydrops
ClinicalTrials.gov study NCT03911531. IPD Sharing: YES. Countries: 1. Publications: 6.
Adult Patients With Undiagnosed Conditions and Their Responses to Clinically Uncertain Results From Exome Sequencing
ClinicalTrials.gov study NCT03605004. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Whole-exome Sequencing in Childhood Obesity
ClinicalTrials.gov study NCT02418377. IPD Sharing: NO. Countries: 1. Publications: 3.
Evaluation of the Diagnostic Contribution of High-throughput Exome Sequencing for Patients With Convulsive Encephalopathy of Unknown Etiology: Pilot Study to Improve Genetic Counselling
ClinicalTrials.gov study NCT03652246. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Whole-Exome Sequencing (WES) of Cancer Patients
ClinicalTrials.gov study NCT02127359. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata
Open the record for dataset details and reuse information.
Data from: Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses
Open the record for dataset details and reuse information.
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Open the record for dataset details and reuse information.
Data from: Unique features of germline variation in five Egyptian familial breast cancer families revealed by exome sequencing
Open the record for dataset details and reuse information.
Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single nucleotide polymorphisms (SNPs), of which 1,590,653 high confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype restricted non-synonymous SNPs that are predicted to impact protein function in genes that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17,228 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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.