Browsing by Author "Jassiem, Wardah"

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    Identification of insertion-induced enhancers linked to gene drivers within non-coding DNA using a pipeline for diffuse large b-cell lymphoma H3K27ac ChIP-seq data
    (University of the Western Cape, 2022) Jassiem, Wardah; Bendou, Hocine
    Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma (NHL) and incorporates a diverse range of illnesses with varying biology, clinical manifestations, and therapeutic responses. Functional insertion mutations represent the driving mechanism behind many oncologic illnesses. Research has shown that variants associated with cancer in the non-coding portion of the genome, which is enriched with enhancer elements, is greatly underappreciated. The present study designed a bioinformatics pipeline using Nextflow DSL2 to identify insertion-induced enhancers associated with DLBCL oncogenes within the non-coding genome using H3K27ac ChIP-seq data. Gapped DLBCL reads identified by bowtie were mapped to the human reference genome with bowtie2. Non-coding insertions were identified with BEDTools and verified by pBla.