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ShareScore release 0.9.0
Dataset results
257 results for “exome”
Fast Exome for Diagnosis of Congenital Conditions in Infants Under 12 Months of Age Hospitalized in Intensive Care Unit
ClinicalTrials.gov study NCT03831035. IPD Sharing: Not stated. Countries: 1. Publications: 29.
Whole-exome Sequencing in Childhood Obesity
ClinicalTrials.gov study NCT02418377. IPD Sharing: NO. Countries: 1. Publications: 3.
What Benefit of a Full Analysis of Exome? Routine Care Study in Patients With Solid Tumors
ClinicalTrials.gov study NCT02840604. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Whole Exome Screening of Newborns
ClinicalTrials.gov study NCT05325749. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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
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HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution
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Schistosoma mansoni raw genotype calls from exome data
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Data from: Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses
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Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species
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Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
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Data from: Unique features of germline variation in five Egyptian familial breast cancer families revealed by exome sequencing
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Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as genotyping platform in Norway spruce
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Data from: Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform
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Evaluation datasets and pre-computed scores for: "CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations"
<p>CAPICE is a computational method for predicting the pathogenicity of SNVs and InDels.</p> <p>This new repository added index for CAPICE v1.0 (build37) precomputed files.</p> <p><strong>Repository description:</strong></p> <p>1) "paper_datasets.tar.gz" contains all datasets used in the CAPICE paper;</p> <p>2) "capice_v1.0_build37_indels.tsv.gz" contains the precomputed scores for InDels in genome build 37</p> <p>3) "capice_v1.0_build37_indels.tsv.gz.tbi" contains the index for file"capice_v1.0_build37_indels.tsv.gz"</p> <p>4) "capice_v1.0_build37_snvs.tsv.gz" contains the precomputed scores for all possible SNVs in genome build 37</p> <p>5) "capice_v1.0_build37_snvs.tsv.gz.tbi" contains the index for file "capice_v1.0_build37_snvs.tsv.gz"</p> <p> </p>
Data from: Exome-chip association analysis of intracranial aneurysms
Objective: To investigate to what extent low-frequency genetic variants (with minor allele frequencies <5%) affect the risk of intracranial aneurysms (IA). Methods: 1056 IA patients and 2097 population-based controls from the Netherlands were genotyped using the Illumina HumanExome BeadChip. After quality control (QC) of samples and single nucleotide variants (SNVs), we conducted a single variant analysis using Fisher's exact test. We also performed the variable threshold (VT) and the sequence kernel association tests (SKAT) at different minor allele count (MAC) thresholds of ±5 and ±0 to test the hypothesis that multiple variants within the same gene are associated with IA risk. Significant results were tested in a replication cohort of 425 IA patients and 311 controls, and results of the two cohorts were combined in a meta-analysis. Results: After QC, 995 IA patients and 2080 controls remained for further analysis. The single variant analysis comprising 46,534 SNVs did not identify significant loci at the genome-wide level. The gene-based tests showed a statistically significant association for FBLN2 (best p=1x10-6 for the VT test, MAC±5). Associations were not statistically significant in the independent but smaller replication cohort (p±0.57), but became slightly stronger in a meta-analysis of the two cohorts (best p=4.8x10-7 for the SKAT, MAC>1). Conclusion: Gene-based tests indicated an association for FBLN2, a gene encoding an extracellular matrix protein implicated in vascular wall remodeling, but independent validation in larger cohorts is warranted. We did not identify any significant associations for single low-frequency genetic variants.
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.
Identification of Genes Involved in Juvenile Idiopathic Arthritis by Wholel Exome Sequencing
ClinicalTrials.gov study NCT02067962. IPD Sharing: Not stated. Countries: 0. Publications: 1.
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International Brain Laboratory public data
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OpenNeuro
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