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Full-Text Articles in Bioinformatics
Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer, Zuhal Ozcan
Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer, Zuhal Ozcan
Dissertations & Theses (Open Access)
Comprehensive genomic and transcriptomic characterization of tumors has uncovered enrichment for distinct aneuploidy and expression patterns, demonstrating the utility of molecular based classification of cancers and their subtypes. Existing cohorts with transcriptomic profiling from next-generation sequencing contain an untapped potential to also relate genomics with rich clinical phenotypes. Yet, derivation of somatic copy number and expression profiles from analyses of RNA has remained elusive. Further, DNA analysis in these cohorts is not always feasible due to limited tissue availability or financial constraints. Here, we present a statistical approach that overcomes these challenges using haplotype information to aid detection of somatic …
An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan
An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan
Dissertations & Theses (Open Access)
Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and is associated with significant morbidity and mortality. To date, the majority of work in the field has focused on genomic alterations such as mutations and copy number alterations. However, the clinical success of targeted therapies that exploit known genomic alterations, such as EGFR mutations, has remained mixed. Over the past decade, the importance of epigenetic regulators has come to the forefront, with the realization that many of these genes are mutated in cancer. Despite this realization, the role of epigenetics in regulating tumorigenesis, progression and …