In a plenary talk about cancer genomics at the annual meeting of the American Association for Cancer Research (AACR; Philadelphia) in Denver, the association's 100th, Eric Lander, founding director of Broad Institute, said he hopes to see complete cancer genome analyses become a routine part of research within five years and a standard of care for patients in 10 years. Lander specified that this goal was a "hope" rather than a prediction – which some might consider too lofty.

But a sampling of data from the AACR conference reveals plenty of progress down the personalized medicine path.

One presentation that garnered attention was that of Daniel Von Hoff, a scientist at Translational Genomics Research Institute (Phoenix), who is using molecular profiling to drive treatment decisions for 66 relapsed and refractory cancer patients, resulting in improved progression-free survival for 18 patients. Von Hoff collected tumor samples from patients with various kinds of metastatic disease who had failed an average of about four prior therapies, although some patients had failed as many as 13 treatments.

The samples were analyzed using Target Now, an oncology testing service marketed by Caris Diagnostics (Irving, Texas). Through DNA microarray and immunohistochemical analyses, the service was able to identify biomarkers in all patients pointing to the potential utility of various approved drugs. Of the 66 patients treated according to the biomarker analysis, 18 patients (27%) had a clinically significant improvement in progression free survival. Additionally 47 patients (71%) experienced tumor shrinkage, and six patients (9%) experienced dramatic tumor shrinkage.

Other presentations at the conference focused on new ways to identify cancer biomarkers and diagnose cancer.

Life Technologies Corp. subsidiary Applied Biosystems (Carlsbad, California) touted its SOLiD System as a tool for identifying methylation patterns across the genome, which may serve as new cancer biomarkers.

Meanwhile researchers from the University of Southern California (Los Angeles) and the California Institute of Technology (Pasadena) presented data on a new membrane microfilter device to capture and characterize circulating tumor cells in blood samples. The device, which separates tumor cells from normal blood cells based on size, captured tumor cells from blood in 92.9% of patients samples, while the current gold standard CellSearch from Johnson & Johnson (New Brunswick, New Jersey) caught the cancer in 45.6% of the samples. The researchers said the microfilter device is about three to five years from clinical use.

Also working on blood tests to detect cancer is Celera (Alameda, California), which presented data on biomarker panels for the detection of lung, prostate and colon cancer. Celera said its colon cancer test distinguished proximal and distal lesions with 90% sensitivity and 93% specificity, outperforming the standard fecal occult blood test. In lung cancer, the company's test showed 94 percent sensitivity and 93% specificity and distinguished malignant cases from benign lung disease.

For now, most cancer biomarkers are used primarily to monitor disease progression and treatment rather than for diagnosis.

Genentech's (South San Francisco, California) Herceptin (trastuzumab) for breast cancer and Novartis AG's Gleevec (imatinib) for chronic myeloid leukemia and gastrointestinal stromal tumors are prescribed according to the results of biomarker-based companion diagnostic tests. Additionally, DxS Ltd. (Manchester, UK) is seeking FDA approval of a companion diagnostic to detect KRAS mutation status in colorectal patients considering Amgen's (Thousand Oaks, California) Vectibix (panitumumab).

Last fall, biomarker data offered new hope for AstraZeneca's (London) EGFR-inhibitor Iressa (gefitinib), which received accelerated approval for lung cancer only to be yanked off the market when it failed to show survival benefit in a confirmatory trial.

A Phase III study of the drug in an enriched population of 1,217 Asian patients expected to be responsive to EGFR inhibitors demonstrated that Iressa monotherapy significantly improved progression-free survival (PFS) compared to chemotherapy in front-line NSCLC patients with EGFR-activating mutations. In patients without the EGFR mutation, the chemotherapy group had significantly better PFS.

So while Iressa couldn't beat placebo in past studies, in the right patients, it beat standard-of-care chemotherapy.

New cancer funds to speed research

In another report from the AACR meeting, John Niederhuber, director of the National Cancer Institute (NCI), said that additional funding expected for the institute ought to speed cancer research. After several years of flat budgets, the NCI will receive a nearly 3% budget increase this fiscal year and $1.3 billion from the economic stimulus package, offering a "chance to enhance and to change cancer science," he said.

Niederhuber noted that cancer researchers have not been immune from the effects of the economic downturn. "Scientists everywhere have felt the strain of NCI budgets that, for four years, have received no increase," he said. "You have felt the strain of the up-front downward negotiation of your grants, on average, some 17% to 21%. We have all worried that the pace of cancer research is becoming imperiled and that biomedical research will no longer attract the best and the brightest."

However, he said, the ARRA stimulus funds will now give cancer researchers "the chance to be visionary" and "move cancer research from the accumulation of scientifically exciting genomic data to a new way of approaching prevention, diagnosis and therapy and to ensure access to our latest science for all."

He said that NCI is taking a series of steps to increase the support for research project grants (RPG), particularly the investigator initiated R0I. The so-called RPG payline – the line of demarcation between grants that are funded and not funded, based solely on peer review – will be "rising considerably," he said.

3-D fluidic device built to 'sort' nanomaterials

The need to determine the differentiating characteristics of nanomaterials of different sizes was the driver for the development of a new, 3-D nanofluidic device by researchers at the National Institute of Standards and Technology (NIST; Gaithersburg, Maryland) and Cornell University. Based on the development of microfluidic and other nanofluidic devices, the researchers took the concept and added an additional dimension to the traditional flat, 2-D architecture of these devices, according to Samuel Stavis, PhD, a National Research Council Research Associate at NIST.

As described in their paper, published online in the journal Nanotechnology, Vol. 20, these chambers, Lilliputian but significantly more complex than conventional 2-D devices, were created using a photolithographic process, the prototype system pointing the way to future tools for manipulating and measuring different sizes of nanoparticles in solution, Stavis said.

He told BB&T that future applications of 3-D nanofluidic devices have "high impact" potential and include the separation and measurement of complex nanoparticle mixtures for drug delivery, gene therapy and nanoparticle toxicology; and the isolation and confinement of individual DNA strands for analysis.