Science has published THE genome of breast and colorectal cancers. Not the whole genome, mind you, but just 13,023 protein coding genes. The researchers identified mutations associated with cancers, but I'm not sure if they looked outside of the protein coding sequences (I have yet to read the paper, and I'm not sure when I'll get around to it). Nobel Intent has a review of the paper.
When I first heard about this project I wondered what exactly they'd be doing. The fact that this study only looked at 11 cancers for each tissue is somewhat surprising. What I'd really like to see is a study that can tie together DNA sequence changes (protein coding, non-translated transcribed sequences, and cis-regulatory regions), gene expression profiles, and chromosomal aberrations. Without all three, I think you're missing out on major aspects of cancer genetics.
I think Orac needs to chime in on this one.
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