CAMBRIDGE, Mass.—One of the challenges of treating cancer is that cellular biology has run amok in tumors. To try to bring a sense of control to this chaos, researchers at the Dana Farber Cancer Institute (DFCI), 454 Life Sciences and other research centers performed detailed sequencing experiments to identify subtle but significant cancer-associated mutations. They presented their analysis in Nature Medicine.
As DFCI's Dr. Roman Thomas, lead author of the paper, explains, tumor heterogeneity is a significant problem because key genetic signals can be lost in a noise of normal or extraneous sequencing information generated from impure samples. "If all of the exciting successes of genomic medicine are to be a success for the actual patients, it needs to be ensured that accurate molecular diagnosis can be made for every single patient—regardless of the quality of the tumor specimen," he says.
The researchers used 454's massively parallel sequencing-by-synthesis approach to identify cancer-related mutations that existed at 0.2 percent abundance. Furthermore, the method allowed them to identify mutations previously missed by the more traditional Sanger sequencing method and to analyze formalin-fixed paraffin-embedded (FFPE) tumor samples.
"Most clinically available cancer specimens are FFPE samples, which impose particular problems to classical sequencing," Thomas says. "However, 454 sequencing was reliably able to detect mutations in such specimens allowing for analysis of this clinically widespread source of patient material."
As Dr. Michael Egholm, 454's VP of molecular biology, explains, the experiments were made feasible by 454's emulsion PCR process and massive sequencing throughput. "If we sequence 1,000 'clones' and two percent are from tumors, then we have 20 reads from the tumor—more than enough to figure out what is going on there," he says.
Egholm suggests that this analysis could be performed using conventional amplification and sequencing technology, but the study could take months to complete instead of a day or two using the 454 method and it would be prohibitively expensive.
Thomas and Egholm are also looking beyond the current experiments, and both see a role for this technology as a companion diagnostic for disease therapeutics, a concept heavily touted by the FDA lately.
Thomas strongly believes that the possibility to provide rapid, sensitive and accurate mutation diagnosis is key for the advancement of the concept of molecularly targeted therapy. In his opinion, the current work shows how the application of highly sensitive molecular diagnostics enables mutation diagnosis in settings where such analyses were not possible before.