Algorithms and applications of next-generation DNA sequencing : ChIP-Seq, database of human variations, and analysis of mammary ductal carcinomas

Next Generation Sequencing (NGS) technologies enable Deoxyribonucleic Acid (DNA) or Ribonucleic Acid (RNA) sequencing to be done at volumes and speeds several orders of magnitude faster than Sanger (dideoxy termination) based methods and have enabled the development of novel experiment types that would not have been practical before the advent of the NGS-based machines. The dramatically increased throughput of these new protocols requires significant changes to the algorithms used to process and analyze the results. In this thesis, I present novel algorithms used for Chromatin Immunoprecipitation and Sequencing (ChIP-Seq) as well as the structures required and challenges faced for working with Single Nucleotide Variations (SNVs) across a large collection of samples, and finally, I present the results obtained when performing an NGS based analysis of eight mammary ductal carcinoma cell lines and four matched normal cell lines.Science, Faculty ofGraduat