Diagnostic Technologies

In general, all the methods to be described here can be characterized as analytic tools for the characterization of DNA, RNA, or protein, paralleling the sequence of genomic function, from archival information in DNA, its encoding in mRNA, and its translation into a functional molecule, protein (Figure 21.1). However, this simple schema, although largely correct, overlooks great complexity in the structure, organization, function, and modification of genetic information. To note only a few examples, only about 3% of the genome is associated with genes; the function of the rest is largely unknown, although there is clear evidence that this is not just "junk" DNA, as has been supposed.20 Similarly, although only 40,000 genes, more or less, are known, thousands more noncoding RNA transcripts have been detected in expressed RNA pools in cells.21 Thus, genetic and epigenetic controls over DNA replication, RNA expression, and even nuclear chromatin structure are also relevant to cancer origins, grade, and outcome, but are not explored here. Instead, we examine the proven and widely used methods for analysis of the functional genome, starting with proteins, known in aggregate as the proteome.

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