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Showing 1 to 20 of 43 for “"Copy Number Alterations"”.

  1. Prevalence and prevention of large-scale somatic copy number alterations

    Knouse, Kristin AnnMassachusetts Institute of Technology2017

    … of megabases, as occurs with sub-chromosome copy number variants (CNVs) or whole-chromosome aneuploidy, is almost always associated with embryonic lethality or severe disease. However, while large-scale genomic imbalance has adverse consequences at the organismal level, both CNVs and …

    mit Repository record

  2. Evolution and vulnerabilities of somatic copy number alterations in cancer

    Gibson, William J., Ph. D. Massachusetts Institute of TechnologyMassachusetts Institute of Technology2015

    … of endometrial cancers, whereas BAF complex alterations occur late. We identified novel recurrent alterations in primary tumors, including mutations in the estrogen receptor cofactor NRIPJ in 12% of patients. Phylogenetic analyses in cases with multiple metastases indicated these metastases …

    mit Repository record

  3. INSIGHTS INTO THE SELECTION AND FUNCTION OF COPY-NUMBER ALTERATIONS DURING CANCER EVOLUTION

    ALFIERI, FABIOUniversità degli Studi di Milano2025

    … instability, including large- and small-scale alterations, such as copy-number alterations (CNAs) or single-nucleotide mutations, respectively. Those alterations play a critical role in tumor development, genetic diversity, and resistance to therapies. This thesis explores the selection and …

    milano Repository record

  4. Statistical Modeling Approaches For The Inference of Cancer Mechanisms

    Huang, Licai2024

    … accounting for impure tumor samples and copy number alterations. eQTL analysis is a powerful tool for understanding the genetic basis of complex traits. However, existing methods do not account for copy number alterations in tumor cells, resulting in increased false positive discoveries. …

    uthsc Repository record

  5. The role of dosage sensitive genes in aneuploid phenotypes

    Bonney, Megan EllisMassachusetts Institute of Technology2016

    … aneuploid phenotypes are the consequence of copy number changes of a few especially harmful genes that may be present on the extra chromosome, or are caused by copy number alterations of many genes that confer no observable phenotype when varied individually. We used the proliferation defect …

    mit Repository record

  6. Functional In Vivo Screen Identifies Pygo2 As A Putative Gene to Promote Prostate Cancer

    Pan, Xiaolu2019

    … cancer is correlated with rampant chromosomal copy number alterations, highlighting the potential function of genes with copy number gains and losses in driving prostate cancer progression. To identify putative genes promoting prostate cancer, an <em>in vivo</em> tumorigenesis screen was …

    uthsc Repository record

  7. Genetic differences in lung adenocarcinoma cells from patients of African and European ancestry

    Diseko, KaraboDepartment of Integrative Biomedical Sciences (IBMS)2024

    … comprehensive comparisons of gene expression, copy number alterations, and mutation frequencies between the two ethnic cohorts. Key genetic disparities between the two groups were discerned, including 371 significantly differentially expressed (SDE) genes, a higher incidence of copy number …

    cape-town Repository record

  8. OPTIMISATION AND THERAPEUTIC-TARGET-DISCOVERY ORIENTED ANALYSIS OF CRISPR-CAS9 SCREENS

    VINCETI, ALESSANDROUniversità degli Studi di Milano2024

    … Key challenges include addressing biases from copy number alterations and distinguishing between core-fitness and context-specific fitness genes. Identifying context-specific genes is crucial for personalized cancer treatments. Additionally, cancer dependency datasets derived from CRISPR-Cas9 …

    milano Repository record

  9. Temporal examination of DNA methylation profile reprogramming in the promoter region of PGC-1α during the progression of insulin resistance and type 2 diabetes mellitus in rodent models

    Donnelly, Sarah RebeccaVirginia Tech2019

    … (DNA methylation) and phenotypic (mitochondrial copy number) alterations in C57/BL6 rodent models. These changes preceded overt disease onset, as classified by clinically utilized indices, which included the homeostatic model assessment for insulin resistance (HOMA-IR), the homeostatic model …

    vt Repository record

  10. The Intra-Tumour Heterogeneity Landscape of Human Cancers

    Dentro, Stefan ChristiaanUniversity of Cambridge2020

    … introduce the methods; a method to call somatic copy number alterations (Battenberg) and a method to infer subclones from single nucleotide variants (DPClust). Both are extensively validated on simulated and on real data, and I describe a rigorous quality control procedure. The methods are then …

    cambridge Repository record

  11. COMPREHENSIVE WHOLE GENOME SEQUENCING UNRAVELS THE COMPLEX GENOMIC LANDSCAPE OF NEUROBLASTOMA

    D'ALTERIO, GIUSEPPEUniversità degli Studi di Milano2024

    … i) to provide a full compendium of NBL genomic alterations (point mutations and structural variants or SVs) and ii) to investigate the correlation between germline Small Nucleotide Variants (SNVs) and the genomic instability of NBL, a well-established marker of poor prognosis. We found …

    milano Repository record

  12. Non-Invasive cancer detection: computational applications in liquid biopsy and radiomics

    Scandino, RiccardoUniversità degli studi di Trento2025

    … in breast cancer through the analysis of somatic copy number alterations (SCNAs). The panel's unique combination of elements, including genome-wide and focal single nucleotide polymorphisms (SNPs), exonic regions of key cancer-related genes, and a bespoke computational strategy, enhances the …

    trento Repository record

  13. Several consequences of aneuploidy

    Sheltzer, Jason (Jason Meyer)Massachusetts Institute of Technology2015

    … greater than 90% of tumors display chromosomal copy number alterations. Thus, understanding the consequences of aneuploidy has broad relevance for human health and development. To that end, I have studied several distinct aspects of aneuploid cell biology. In the budding yeast Saccharomyces …

    mit Repository record

  14. Accurate Identification of Significant Aberrations in Cancer Genome: Implementation and Applications

    Hou, XuchuVirginia Tech2013

    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 …

    vt Repository record

  15. Computational Analysis of Genome-Wide DNA Copy Number Changes

    Song, LeiVirginia Tech2011

    DNA copy number change is an important form of structural variation in human genome. Somatic copy number alterations (CNAs) can cause over expression of oncogenes and loss of tumor suppressor genes in tumorigenesis. Recent development of SNP array technology has facilitated studies on copy number …

    vt Repository record

  16. Identification of DNA Copy Number-Dependent Transcriptional Deregulation inHepatocellular Carcinoma (HCC)

    권, 소미2014

    … genomic profiles analysis, in which the genomic copy numbers and gene expression profiles are analyzed by the integrative way to define the chromosomal regions with both genomic copy number variation and concomitant transcriptional deregulation, is posited to provide a promising strategy to …

    ajou Repository record

  17. Investigating The Rare Aneuploid Cells in Normal Breast and Therapeutic Resistance in Triple Negative Breast Cancer Using Single Cell Genomics

    Lin, Yiyun, <p>https://orcid.org/0000-0002-9277-3048</p>2025

    … we applied single cell DNA sequencing to profile copy number alterations (CNAs) in 83,206 epithelial cells from breast tissues of 49 healthy women and single cell DNA&ATAC co-assays to 19 women. Our data shows that all women harbored rare aneuploid epithelial cells (median 3.19%) that increased …

    uthsc Repository record

  18. Characterisation of Copy Number Changes in the Progression of Barrett’s Oesophagus

    Gregson, EleanorUniversity of Cambridge2018

    … and are therefore monitored unnecessarily. Copy number changes have been shown to be important in the progression of BE to oesophageal adenocarcinoma (Li et al., 2014). Shallow whole genome sequencing (sWGS) has been established as a cost-effective method of investigating copy number changes …

    cambridge Repository record

  19. Probabilistic modelling of somatic alterations in bulk tissue and single cells using repeat DNA

    Abujudeh, SamerUniversity of Cambridge2019

    … cancer types, in which large-scale structural alterations of the genome accumulate at an increased rate. An important class of structural alterations are somatic copy number alterations (SCNAs). SCNAs have been shown to be major drivers of oncogenesis and are associated with prognosis and …

    cambridge Repository record

  20. Investigating the initiation and progression of small cell lung cancer

    Brauneis, Alison DooleyMassachusetts Institute of Technology2011

    … aberrations that occur in SCLC, we analyzed the copy number alterations in tumors and metastases arising in a mouse model of SCLC (mSCLC), driven by conditional inactivation alleles of two tumor suppressor genes, Trp53 and Rbl. We identified frequent, high-level amplification of a novel, …

    mit Repository record

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