Genotyping techniques to address diversity in tumors.

Array-based genotyping platforms have during recent years been established as a valuable tool for the characterization of genomic alterations in cancer. The analysis of tumor samples, however, presents challenges for data analysis and interpretation. For example, tumor samples are often admixed with nonaberrant cells that define the tumor microenvironment, such as infiltrating lymphocytes and fibroblasts, or vasculature. Furthermore, tumors often comprise subclones harboring divergent aberrations that are acquired subsequent to the tumor-initiating event. The combined analysis of both genotype and copy number status obtained by array-based genotyping platforms provide opportunities to address these challenges. In this chapter, we present the basic principles for current array-based genotyping platforms and how they can be used to infer genotype and copy number for acquired genomic alterations. We describe how these techniques can be used to resolve tumor ploidy, normal cell admixture, and subclonality. We also exemplify how genotyping techniques can be applied in tumor studies to elucidate the hierarchy among tumor clones, and thus, provide means to study clonal expansion and tumor evolution.