Abstract
Somatic analysis of the molecular features of human tumors through numerous efforts including The Cancer Genome Atlas consortium has led to unprecedented insight into the biological basis of cancer behavior. Numerous genomewide sequencing techniques have been utilized in these studies to understand DNA mutations, epigenomic alterations, and ultimately differences in protein expression profiles across various cancers. Due to the dropping costs of next-generation sequencing as well as growing power and ease of use of computational resources, researchers are able to apply these techniques to more specific cancer contexts and/or rarer tumor types. In this chapter, we describe the rationale for and details of methods used in our group for exome analysis of germ cell tumors. The methods described should also be readily applicable to genomic analysis of other tumors.
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