How can I get my tumor genome sequenced?

I suppose every year—strike that, every week—we learn about a new method, therapy, treatment, test or other indication that some researchers somewhere have uncovered the key to understanding and ‘curing’ cancer. However, some recent developments suggest that, in fact, that key could actually be in development as we speak.

Remember the race to sequence the entire human genome? It was Craig Venter vs the US Government, and even though Venter deserved most of the credit, the two teams agreed to make it a mutual achievement, and the first human genome was sequenced in 2003. The promise of this breakthrough was that it was going to be the answer to understanding and conquering a host of diseases.

A decade later, and the sequenced genome has failed to deliver on that promise.

Or has it?

Maybe, instead of sequencing the human genome, we were sequencing the wrong organism. Emerging research says yes—we should be sequencing the inhuman genome, otherwise known as a cancer cell. The first tumor was sequenced in 2008,

In August 2010, the journal Genome Biology published a case report of a 78-year-old man who had a salivary gland tumor (tongue tumor) that was proving resistant to treatment—namely, to the targeted treatment Tarceva (erlotinib). The man consented to have his tumor’s genome sequenced, and it was discovered that the signalling pathways expected in such a tumor and therefore exploited by Tarceva were largely absent, which explained why the Tarceva failed. However, sequencing revealed other signalling pathways, ones exploited by Sutent (sunitinib) and Nexavar (sorafenib), drugs used against GI cancers and kidney cancers, respectively. Consequently, treatment was initiated and although the man eventually died, the drugs were shown to have significant activity against his tumor.

In sum, a tumor on the tongue wasn’t tongue cancer at al.

More recently, the Journal of the American Medical Association published two related papers. One of them sought to determine “whether whole-genome sequencing can identify cryptic, actionable mutations in a clinically relevant time frame.” They were able to complete sequencing in 7 weeks’ time, and since the results of the sequencing indicated a different diagnosis than initially determined, the patient’s original treatment plan (initially for acute myeloid leukemia) was changed to reflect what was learned through sequencing.

It’s all a part of personalized medicine. Since there is no such thing as the same two cancers—which is the foundation for anatomically based cancer treatment—identifying the chromosomal transcriptions and genetic mutations of each person’s individual cancer and applying treatments known to exploit the present signalling pathways makes more and more sense. Sure it’s a bit expensive now, but the price will come down as labs capable of sequencing begin competing for business.

Here’s the problem: What do you, as a recently diagnosed cancer patient, have to do to get your tumor genome sequenced so that your treatment has a better chance of working? Who do you have to ask? Will insurance pay for it?

I’m gonna try to find out. Check back later.

SOURCES

Jones SJ et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010;11(8):R82.

Link DC et al. Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML. JAMA. 2011;305(15):1568-1576

Welch JS et al. Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene. JAMA. 2011;305(15):1577-1584.