UC San Diego

Determining DNA sequence has been a principle tool for several methods in biology research. From whole genome sequencing to RNA expression assays to several types of immunoprecipitation experiments, sequencing DNA has been a staple detection technique. Recent advances in sequencing and detection of DNA has revealed many new possibilities, and problems, with regards to data analysis. Here, I present a study analyzing a novel detection technology and sequencing method. These are both important contributions for not only providing new insights for utilizing a more sensitive detection technique, but also creating a method which enables any researcher to quickly analyze the unheralded amount of sequence data now being produced, soon be available to everyone. Chapter 2 focuses on the current uses and analysis of a novel DNA detection technique called DNA Selection and Ligation (DSL). By taking advantage of the more sensitive and specific DSL strategy, any assay that is dependent on DNA detection is improved. In this chapter, I show how DSL can be used to modify the standard chromatin immunoprecipitation (ChIP)- on-chip assay (termed ChIP-DSL), in both the promoter- specific and tiling cases. Additionally, I show how the ChIP-DSL method gives promising results for a high- throughput version of the chromatin conformation capture (3C) assay, which is used to measure if two regions of DNA are interacting. Chapter 3 concentrates on next-generation sequencing, more specifically on the Illumina Genome Analyzer (GA). After describing the details of how the sequencing is performed and analyzed, I discuss the current flaw in these datasets, and propose a solution to the problem, the Genome Ontology. I then give several examples where the Genome Ontology is helpful in extracting knowledge from these incredibly large datasets. Chapter 4 describes numerous future directions of my own work as well as several of my observations that resulted from working with these next-generation sequencing datasets