Genomics in the AWS Cloud

CHAPTER 12Cancer Genomics

In this chapter, we discuss the analysis of somatic mutations, which are mutations we develop across our life span. By far, the most studied somatic mutations are the mutations found in cancerous tumors, so we named this chapter “Cancer Genomics.” However, the workflow presented in this chapter could also be applied to any tissue in the body, such as the analysis of your sun-damaged skin (provided you are willing to submit yourself to a punch skin biopsy) or the analysis of a benign polyp of your cat.

Somatic Genomes

As we age, our genome accumulates mutations and diverges from our birth genome. As mentioned in Chapter 2, our birth genome, derived from the fusion of the germ cells of our parents, is called our germline genome. Across our life span, our cells acquire mutations through replication errors or environmental factors such as UV rays, tobacco, toxins, or viruses. These acquired mutations are called somatic mutations, and by definition they affect only certain cells of our body.

This is the fundamental difference: germline mutations affect all our cells, whereas somatic mutations are present only in some cells of our body. Organs that accumulate more somatic mutations are those most exposed to environmental mutagens or with a high cellular turnover, like the skin, lung, gastrointestinal tract, liver, and blood. In contrast, cells of the brain and muscles, for example, are less prone to mutations.

Somatic mutations can also develop while in ...