Methods to identify genetic and epigenetic mutations in cancer.

摘要

Human cancers are caused by genetic and epigenetic mutations. The identification of these mutations in cancer genomes has led to a better understanding of why and how cancers form and what causes them to have different clinical characteristics. Diagnostic and prognostic tests based on identifying tumor mutations are used in the clinic and targeted therapies have been developed to treat tumors with specific mutations. Breakthroughs in cancer research, especially the identification of mutations, are often enabled by new technologies. The goal of this work was to develop methods that would leverage the throughput of second-generation DNA sequencing technologies to identify genetic and epigenetic mutations in cancer. The first method, Nested Patch PCR, was designed to provide a cost-effective way to identify genetic mutations in many candidate genes across many patient samples. When applied to the study of colon cancer, this method identified a novel tumor-specific mutation in a gene known to cause colon cancer. The second method was developed to detect aberrant DNA methylation, an epigenetic mutation that often occurs in cancers. This method was developed to detect intratumor heterogeneity of aberrant DNA methylation at a single locus for many patients simultaneously. This method was applied to endometrial cancer, and enabled the identification of a subclass of patients that exhibited intra-tumor heterogeneity of MLHJ promoter methylation. The third method was developed to detect aberrant DNA methylation at many loci across many patient samples. When applied to breast and colon cancers, this method enabled the identification of several loci that exhibit tumor-specific methylation and represent strong candidate biomarkers of disease. We are witnessing the dawn of personalized medicine. An individual's genetic and epigenetic mutations will be used to predict their disease risk and prognosis, and to choose a tailored therapy that targets their specific defects. This dissertation presents three novel methods to identify genetic and epigenetic mutations in individual patients' cancers. These methods will enable the large studies that are needed to expand our understanding of cancer biology and develop diagnostic tests, prognostic markers, and targeted therapies.