SNP Genotyping of Cancer Cell Lines via CCLE and Creation of a Web-Based Tool for Data Exploration

The Cancer Cell Line Encyclopedia (CCLE) is a pivotal resource in cancer research, providing comprehensive genomic datasets, including Whole Exome Sequencing (WES), Whole Genome Sequencing (WGS), and RNA sequencing (RNA-seq), across a broad panel of tumor-derived cell lines. In this thesis, a web-based tool was developed to enable efficient exploration and querying of genomic analyses performed on the CCLE dataset. Specifically, all common single nucleotide polymorphisms (SNPs) were genotyped, and copy number variations (CNVs) were systematically annotated. In addition, the ancestry of the cell lines was inferred, and SNP allele frequencies were compared with those from human populations in the 1000 Genomes Project, providing a framework for assessing the genetic representativeness of these in vitro models.