Global ETD Search
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Showing 1 to 20 of 22 for “"copy number aberrations"”.
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Driver genes associated to Broad Copy Number Aberrations in solid cancers
Large numerical and structural chromosomal aberrations (aneuploidy) are intrinsic features of tumour cells and cell transformation. The chromosomal aberrations are collectively called Broad Copy Number Aberrations (BCNAs) and mainly include aneuploidy (i.e. an incorrect number of one or more …
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Detection of Novel Genomic Markers for Predicting Prognosis in Hepatocellular Carcinoma Patients by Integrative Analysis of Copy Number Aberrations and Gene Expression Profiles: Results from a Long-Term Follow-Up
… (HCC) prognosis by integrative analysis of DNA copy number aberrations (CNAs) and gene expression profiles. Array comparative genomic hybridization and expression array were performed on 45 and 31 HCC samples, respectively. To identify functionally important genes, concordant results of DNA copy …
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Functional interactions of overexpressed transcripts associated to Broad Copy Number Aberrations (BCNAs) in solid cancers [Interazioni funzionali di trascritti over-espressi associati ad ampie aberrazioni del numero di copie nei tumori solidi]
L'aneuploidia è una caratteristica intrinseca delle cellule tumorali e della trasformazione cellulare. Questa tesi di dottorato indaga i meccanismi molecolari alla base dell'instabilità cromosomica e dell'espressione genica nel cancro, concentrandosi sul carcinoma colorettale e …
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Measuring ongoing chromosomal instability in single-cell DNA sequencing data
… status. Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy as a consequence. Correct estimation of the ploidy of single cell genomes is crucial for many aspects of downstream analysis, such as copy number calling and inference of cell phylogenies. …
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Integrative approaches for systematic reconstruction of regulatory circuits in mammals
… candidate regulator genes, microRNAs and copy number aberrations with biological, and possibly therapeutic, importance.
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Accurate Identification of Significant Aberrations in Cancer Genome: Implementation and Applications
Somatic Copy Number Alterations (CNAs) are common events in human cancers. Identifying CNAs and Significant Copy number Aberrations (SCAs) in cancer genomes is a critical task in searching for cancer-associated genes. Advanced genome profiling technologies, such as SNP array technology, facilitate …
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Prognostic Significance of Chromosome 9p Deletion in Clear Cell Renal Cell Carcinoma
The prognostic role of chromosomal copy number aberration in renal cell carcinoma (RCC) has been explored in several studies. Chromosome 9p deletion was reported as an independent prognostic factor in clear cell subtype (ccRCC). The findings from these studies initially appeared promising however …
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Statistical Methods For Resolving Intratumor Heterogeneity With Single-Cell Dna Sequencing
… a cell, a necessary step in the determination of copy number. In this work, software for calculating probabilities from a multinomial distribution was written to estimate the number of cells that must be sequenced (chapter 2). Two new methods were developed for predicting the number of mutations …
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A clinicopathological and molecular genetic analysis of low-grade glioma in adults
… mutation analysis, MGMT methylation analysis, copy number analysis using array comparative genomic hybridisation and identification of differentially expressed miRNAs using miRNA microarray analysis. IDH1 mutation was present at a frequency of 71% in low grade glioma and was identified as an …
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A Pan-Cancer Single-Cell Analysis of Intratumoral Copy Number Diversity and Evolution
… is a hallmark of human cancers, with many copy number aberrations (CNAs) being associated with disease progression. Previous studies have revealed extensive inter-patient heterogeneity (IPH) in copy number profiles. However, the extent of intratumoral heterogeneity (ITH) and its …
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Genomic aberrations as determinants of immune infiltrates in high grade serous ovarian carcinoma
… role in HGSOC tumourigenesis leave imprints of copy-number aberrations (CNA) in the patient’s genome. These CNA can be summarised into seven copy number (CN) signatures, each associated with a specific mutational process. To identify mutational process associated with determining the immune …
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Multi-omic characterisation of Barrett’s oesophagus reveals a molecular continuum in the progression to oesophageal adenocarcinoma
… heterogeneous with regards to mutational load, copy-number aberrations (CNAs) and structural variants (SVs). Mutational signatures are laid down early and persist regardless of progression status. Hence, Cosmic signature 17 (T:A>G:C in a CTT context), the hallmark of OAC, is visible in indolent, …
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Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing
… are acquired during tumor initiation. Although copy number aberrations have been extensively studied in relation to aneuploidy and TNBC initiation, little is currently known regarding the timing and impact of single nucleotide variants (SNVs) contributing to these early transformative genomic …
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Contribution of Ectodomain Mutations In Epidermal Growth Factor Receptor to Signaling In Glioblastoma Multiforme
… involving primary sequence variations and copy number aberrations of genes involved in key signaling pathways in glioblastoma (GBM). This dataset revealed missense ectodomain point mutations in epidermal growth factor receptor (EGFR), but the biological and clinical significance of these …
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Array based genetic profiling of chronic lymphocytic leukemia
… lymphocytic leukemia (CLL), recurrent genomic aberrations (i.e. deletions of chromosome 11q, 13q, 17p and trisomy 12) are important for prognostication. Deletion of 13q as single aberration is associated with the best prognosis, whereas del(11q) and del(17p) predict a poor outcome. Recent …
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DNA G-quadruplex structures in human cancer cells
… G4s in each cancer model were associated with copy number aberrations and single-nucleotide variants, as well as common breast cancer driver regions, suggesting a link between cancer genome instability and G4 structure formation. Subsequently, to increase the versatility of G4 profiling, I …
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Biomarkers of Genome Instability and Disease Progression in Ovarian Cancer
… this disease. HGSOC is characterised by somatic copy number aberrations (CNAs) and structural variants driven by extreme chromosomal instability (CIN). Importantly, CIN is a key mediator of clonal diversity which fuels the development of treatment resistance. An increased understanding of …
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A Compendium of Genetic Drivers for Oesophageal Adenocarcinoma defines Prognostic and Therapeutic Biomarkers for use in the Clinic
… to call SNVs and indels, structural variants and copy number aberrations respectively. A suite of published tools was used to detect regions of the genome under positive selection for mutations in OAC including dNdScv, Mutsigcv, OncodriveFM and others. Copy number drivers were identified using …
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Applications of next-generation technologies in the diagnosis of haematological diseases and cancer
… single nucleotide variations (SNVs), but also on copy-number aberrations, translocations and large insertions and deletions in a single experiment. Furthermore, targeted NGS provides the capability to focus on a small number of targets simultaneously, with high accuracy and sensitivity. The …
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Differential Dependency Network and Data Integration for Detecting Network Rewiring and Biomarkers
… tasks. In the case of detecting somatic DNA copy number aberrations using bulk tumor samples in cancer research, normal cell contamination becomes one significant confounding factor that weakens the power regardless of whichever methods used for detection. To address this problem, we propose …
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