%0 Journal Article
%T Cancer genomics identifies determinants of tumor biology
%A Elaine R Mardis
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-5-211
%X Whole-genome sequencing and analysis of tumor and matched normal genomes with next-generation sequencing platforms has begun to illuminate commonly mutated genes and transcript-level events that contribute to the underlying tumor biology. To elucidate the role of frequent somatic mutations, the mutant proteins have been biochemically characterized and the results interpreted in terms of the selective advantages these variants may confer on the tumor. Certain somatic alterations have demonstrable prognostic value for specific tumor types in which they commonly occur, although their downstream metabolic signatures may obviate genotyping to identify their mutational status. The metabolic signature is a direct result of the mutation's impact on a given protein/enzyme; therefore, rather than performing sequencing to detect whether a mutation is present, metabolic profiling may be more straightforward, cheaper, and have a lower error rate, for example. New insights into the relationship between a primary tumor and its fatal metastatic disease are also beginning to emerge from genomic comparisons, with the fine detail afforded by next-generation sequencing enabling these comparisons.The transcriptomes of cancer cells also have their own unique somatic complexities, which often result from structural perturbations to the genome, but can be due to transcription-level events such as alternative splicing, RNA editing or transcript fusion. These types of alterations may explain certain aspects of tumor biology and may also be corroborated by cytogenetic phenomena. In this review, I will describe some tumor-specific alterations that were discovered as a result of analyses of unbiased genome or transcriptome sequencing data (unbiased sequencing does not select for portions of the genome or transcriptome in advance, and the entire genome or transcriptome is therefore surveyed) and then illustrate how these discoveries were pursued further to reveal insights into tumor biology that
%U http://genomebiology.com/2010/11/5/211