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166 results for “CNV”
Cancer cell line CNV samples
<p>This tab separated file includes all cancer cell line samples used for cell line heterogeneity analysis.</p> <p>Columns: sample ID, original NCIT code, cellosaurus ID, bins.</p> <p>All bins, duplications (1) and deletions (2), are merged while keeping their original order. Bin size: 5 Mb.</p> <p>This dataset belongs to the publication: https://doi.org/10.1101/2024.05.15.594310</p> <p> </p>
TCGA KIRC CNV preprocessed by Polewko-Klim
<p>The TCGA KIRC CNV dataset preprocessed by Polewko-Klim, Aneta, originally for the purposes of analysis in the conference paper: "Analysis of Ensemble Feature Selection for Correlated High-Dimensional RNA-Seq Cancer Data", ICCS 2020, Springer.</p> <p>The decision variable is set to vitality status (1 for dead). There are 172 dead and 341 alive patients (513 patients in total).</p> <p>The first column in each file is the identifier of the sample (patient).</p> <p>The dataset includes 21106 copy number variation variables.</p> <p>KIRC = kidney renal clear cell carcinoma<br> CNV = copy number variation</p>
USP8 and TP53 drivers are associated with CNV in a corticotroph adenoma cohort enriched for aggressive tumors
<p><b>Context:</b> Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropic hormone (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown.</p> <p><b>Objective</b><strong>:</strong> To investigate genomic drivers of corticotroph tumors at risk for aggressive behavior.</p> <p><b>Design:</b> Whole-exome sequencing of patient-matched corticotroph tumor and normal DNA from a patient cohort enriched for tumors at risk for aggressive behavior.</p> <p><b>Setting:</b> Tertiary care center.</p> <p><b>Patients:</b> 27 corticotroph tumors from 22 patients analyzed. 12 tumors were macroadenomas, of which 6 were silent ACTH tumors, 2 were Crooke's cell tumors, and 1 was a corticotroph carcinoma.</p> <p><b>Intervention:</b> Whole-exome sequencing.</p> <p><b>Main outcome measure:</b> Somatic mutation genomic biomarkers.</p> <p><b>Results:</b> We found recurrent somatic mutations in USP8 and TP53 genes, both with higher allelic fractions than other somatic mutations. These mutations were mutually exclusive, with TP53 mutations occurring only in USP8-wildtype (WT) tumors, indicating they may be independent driver genes. USP8-WT tumors were characterized by extensive somatic copy number variation compared to USP8-mutated tumors. Independent of molecular driver status, we found an association between invasiveness, macroadenomas, and aneuploidy.</p> <p><b>Conclusions: </b>Our data suggest that corticotroph tumors may be categorized into a USP8-mutated, genome-stable subtype versus a USP8-WT, genome-disrupted subtype, the latter of which has a TP53-mutated subtype with high level of chromosome instability. These findings could help identify high risk corticotroph tumors, namely those with widespread CNV, that may need closer monitoring and more aggressive treatment.</p>
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in DLBCL, MCL, T-NHL, and BL, as well as pre-assembled CNV gene list
<p>A complete list of variants which passed filtering described in supplemental methods, that were found in both PDX model sample and patient’s sample from which it was derived (S1A) and variants which were gained (S1B) or lost (S1C) during PDX model derivation. Gene lists for filtration of variants in genes of special interest are included in the table (S1D). Gene list for filtration of CNV changes in genes of special interest is included in the table (S1E). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, Patient AF - Allele frequency in the patient’s sample, Patient Depth – Read depth in patient’s sample, PDX AF- Allele frequency in PDX model sample, PDX Depth - Read depth in PDX sample, DLBCL - Diffuse Large B-cell lymphoma, MCL - Mantle Cell Lymphoma, TCL - T-cell lymphoma, BL – Burkitt Lymphoma, and CNV - Copy Number Variation.</p>
Data from: House mouse Slx and Sly CNV and expression data
<p>A remarkable gene copy number (CN) arms race system has recently been described in laboratory mice, where <em>Slx;Slxl1</em> and <em>Sly</em> genes compete over transmission by altering fertilisation success of X and Y chromosome-bearing sperm, respectively. Here, we focus on this system in nature, where natural selection can counter CN/gene product escalation. Our model is house mouse subspecies hybridising in Europe. In some regions, Y chromosomes of the Eastern subspecies have introgressed onto Western genomic backgrounds, accompanied by sex ratio distortion in favour of males, consistent with the inbred-lines suggested mechanism: overabundance of SLY protein expressed by invading Y chromosomes. We take <em>Slx</em> as representative of the X side of this arms race and measure <em>Slx|Sly</em> CN and expression across an 'Invasion' transect where Ys introgress and a 'Control' transect with negligible introgression. Since we found similar <em>Slx|Sly</em> ratios in both transects, <em>SLY</em> overabundance is unlikely to explain the introgression. However, <em>Slx</em> CN is relatively low in the introgression area, suggesting <em>Slx</em> is less able to combat <em>Sly</em> effects here. Further, deterministic changes in <em>Slx;Sly</em> expression proportions versus CN proportions suggest standing variation for trans regulation of <em>Slx|Sly</em> is being co-opted in nature where their arms race reduces population fitness.</p>
A Proof-of-Concept Study of Faricimab (RO6867461) in Participants With Choroidal Neovascularization (CNV) Secondary to Age-Related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT02484690. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Data from: House mouse Slx and Sly CNV and expression data
Open the record for dataset details and reuse information.
USP8 and TP53 drivers are associated with CNV in a corticotroph adenoma cohort enriched for aggressive tumors
Open the record for dataset details and reuse information.
SEQC2 CNV benchmark sets
Open the record for dataset details and reuse information.
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in 25 MCL patients at diagnosis compared to relapse, as well as a CNV genelist
<p>Supplemental Table 1 shows a complete list of variants which passed filtering described in supplemental methods, that were found in both diagnostic samples and relapsed samples (i.e., shared variants, sheet 1A), variants that were newly detected – N/D (sheet 1B) or newly undetected – N/U (sheet 1C). Gene lists for filtration of variants and CNV changes in genes of special interest are included in the table (sheet 1D). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, DG_AF – Variant Allele frequency in the diagnostic sample, DG_Depth - Read depth in the diagnostic sample, REL_AF - Variant Allele frequency in the relapsed sample, REL_Depth - Read depth in the relapsed sample, SNV - Single Nucleotide Variant, and CNV - Copy Number Variation. </p>
nCNV-seq: nanopore-based CNV analysis tool for brain tumor classification & grading
<p>An available glioma test-dataset designed for nCNV-seq analysis and its corresponding database</p>
Reinterpretation of CNV With Unknown Significance: a 5-year Retrospective Analysis
ClinicalTrials.gov study NCT04575350. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Intravitreal Bevacizumab for the Treatment of CNV in VKH Disease - A Prospective Study
ClinicalTrials.gov study NCT02015351. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Ranibizumab to Treat Choroidal Neovascularization (CNV) in Patients With Pseudoxanthoma Elasticum (PXE)
ClinicalTrials.gov study NCT00510965. IPD Sharing: Not stated. Countries: 1. Publications: 1.
CNV in AMD Analyzed by OCT Angiography Under IntravitreaL Eylea (COCTAEyl)
ClinicalTrials.gov study NCT03803631. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
A Dose Escalation Trial of an Intravitreal Injection of Sirna-027 in Patients With Subfoveal Choroidal Neovascularization (CNV) Secondary to Age-Related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT00363714. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Brolucizumab for CNV Associated With Pathologic Myopia
ClinicalTrials.gov study NCT04976244. IPD Sharing: NO. Countries: 1. Publications: 1.
PHP Home Preferential Hyperacuity Perimeter for the Detection of Choroidal Neovascularization (CNV)
ClinicalTrials.gov study NCT00359008. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Study Evaluating the Efficacy of Aflibercept for the Treatment of Inflammatory CNV in Young Patients (ALINEA).
ClinicalTrials.gov study NCT02556229. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Ranibizumab for the Treatment of Choroidal Neovascularisation (CNV) Secondary to Pathological Myopia (PM): an Individualized Regimen
ClinicalTrials.gov study NCT01037348. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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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.
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.