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1,023 results for “copy number”
Association of copy number alterations with the immune transcriptomic landscape in cancer
<p>This repository contains supplementary materials for the research paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:</p> <ul> <li>00_code: code to reproduce the analysis</li> <li>01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets</li> <li>02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs</li> <li>03_ica_immune_tc: identified immune-TCs, list of immune gene sets</li> <li>04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets</li> <li>05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs</li> <li>06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset</li> <li>07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample</li> <li>08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs</li> <li>09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology </li> <li>10_projection_spatial_transcriptomics: activity of CNA-TC and immune-TC for each spot in spatial transcriptomic datasets from 10xGenomics</li> <li>11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune-TCs for 13 immunotherapy response datasets with predictive performance</li> </ul>
Data from: Canine mammary tumours are affected by frequent copy number aberrations, including amplification of MYC and loss of PTEN
Background: Copy number aberrations frequently occur during the development of many cancers. Such events affect dosage of involved genes and may cause further genomic instability and progression of cancer. In this survey, canine SNP microarrays were used to study 117 canine mammary tumours from 69 dogs. Results: We found a high occurrence of copy number aberrations in canine mammary tumours, losses being more frequent than gains. Increased frequency of aberrations and loss of heterozygosity were positively correlated with increased malignancy in terms of histopathological diagnosis. One of the most highly recurrently amplified regions harbored the MYC gene. PTEN was located to a frequently lost region and also homozygously deleted in five tumours. Thus, deregulation of these genes due to copy number aberrations appears to be an important event in canine mammary tumour development. Other potential contributors to canine mammary tumour pathogenesis are COL9A3, INPP5A, CYP2E1 and RB1. The present study also shows that a more detailed analysis of chromosomal aberrations associated with histopathological parameters may aid in identifying specific genes associated with canine mammary tumour progression. Conclusions: The high frequency of copy number aberrations is a prominent feature of canine mammary tumours as seen in other canine and human cancers. Our findings share several features with corresponding studies in human breast tumours and strengthen the dog as a suitable model organism for this disease.
Data from: Screen for mitochondrial DNA copy-number maintenance genes reveals essential role for ATP synthase
The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome-wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA-intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives included many proteins of the cytosolic proteasome and ribosome (but not the mitoribosome), three proteins involved in vesicle transport, some other factors involved in mitochondrial biogenesis or nuclear gene expression, > 30 mainly uncharacterized proteins and most subunits of ATP synthase (but no other OXPHOS complex). ATP synthase knockdown precipitated a burst of mitochondrial ROS production, followed by copy number depletion involving increased mitochondrial turnover, not dependent on the canonical autophagy machinery. Our findings will inform future studies of the apparatus and regulation of mtDNA maintenance, and the role of mitochondrial bioenergetics and signaling in modulating mtDNA copy number.
A Family Study of Copy Number Variations in Patients With Autism Spectrum Disorder
ClinicalTrials.gov study NCT02228876. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Investigation of the HDAC4 Copy Number Variation and Its Effect on Gene and Protein Expression in Patients With ASD
ClinicalTrials.gov study NCT03670381. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of DNA Copy Numbers Variations and Gene Expression Profile of Bone Marrow Plasma Cells From MGUS and SMM.
ClinicalTrials.gov study NCT01079429. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Investigation of Copy Number Variations and Genetic Variants in POI
ClinicalTrials.gov study NCT05327283. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Development of a NIPTT for Detecting Copy Number Variations
ClinicalTrials.gov study NCT04774640. IPD Sharing: NO. Countries: 1. Publications: 0.
Periodontal Pathogens and Atherom Plaque The Number of Mitochondrial DNA Copies
ClinicalTrials.gov study NCT07165054. IPD Sharing: NO. Countries: 1. Publications: 0.
Copy Number Variation in Prenatal Diagnosis
ClinicalTrials.gov study NCT04561440. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Osimertinib Combined With Savolitinib in the Treatment of NSCLC With Low Copy Number MET Amplification
ClinicalTrials.gov study NCT07322783. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Association of Copy Number Variations in the SMN Genes With Acute Kidney Injury After Heart Surgery
ClinicalTrials.gov study NCT04317196. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Association of Uremic Sarcopenia and Mitochondrial Copy Number and Its Clinical Correlates
ClinicalTrials.gov study NCT03929458. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Copy Number Variation in CHRNA7 Gene in Migraine and Gene Expression
ClinicalTrials.gov study NCT04912752. IPD Sharing: NO. Countries: 1. Publications: 0.
Copy Number Variations, Inflammatory Cytokines and the Risk of Dementia
ClinicalTrials.gov study NCT00878280. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Mitochondrial DNA Copy Number and Leukocyte Telomere Length as Biomarkers in Type 2 Diabetic Patients
ClinicalTrials.gov study NCT05684406. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Mutation Analysis and Copy Number Changes of KRAS and BRAF Gene in Taiwanese Cases of Biliary Tact Adenocarcinoma
ClinicalTrials.gov study NCT01588860. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Developmental Control of Gene Copy Number by Repression of Replication Initiation and Fork Progression
GEO Series GSE31900. Drosophila melanogaster. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array; Genome variation profiling by genome tiling array; Expression profiling by high throughput sequencing.
Genetic Copy Number Variants in Sib Pairs Both Affected with Schizophrenia
GEO Series GSE16930. Homo sapiens. 20 samples. Type: Genome variation profiling by array.
Copy number variation profiling of gastric tissues: Cancer Samples vs. Matched Adjacent Noncancerous Samples
GEO Series GSE33428. Homo sapiens. 27 samples. Type: Genome variation profiling by genome tiling array.
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