The rapidly expanding portfolio of tumor markers facilitates earlier diagnosis and targeted therapies.

About 1.5 million people in the United States are diagnosed with cancer each year, and 500,000 to 600,000 people die annually, according to the National Cancer Institute. Many are questioning why these statistics are still so high in a time of unprecedented scientific breakthroughs that should be leading to new diagnostics, therapies, and cures.

According to Amit Kumar, PhD, CEO and president of CombiMatrix Molecular Diagnostics Inc, Mukilteo, Wash, the key to success lies in a paradigm shift in the way the industry looks at cancer and in the way it is treated. Kumar says the industry spends upward of $20 billion every year in therapeutic drug research for cancer—and very few of the reputed wonder drugs make it through the government approval process. When a drug does make it through, it usually works on a very small percentage of cancer patients.

Very little is spent on ways to diagnose and detect cancer earlier, when it can be treated more efficiently, effectively, and inexpensively to prevent advanced cancer and increase the chance of survival, Kumar explains.

“Our philosophy is that there should be a shift,” Kumar says. “We should be spending money on diagnostic techniques because that will make a huge impact on the patient and on the health care economy.”

In the vanguard, CombiMatrix has turned its expertise in microRNA technology to develop a noninvasive test for the early detection of cancer, expected to launch in 2010. The test measures the drawn blood for specific microarray markers to distinguish if a patient has cancer, and then it specifically identifies the organ where the cancer exists. Current studies focus on prostate, colon, ovarian, breast, and lung cancers, as these five cancers comprise roughly 85% of all solid tumors in the United States.

Using a comprehensive microRNA (miRNA—a recently discovered type of nucleic acid) built on its CustomArray platform, the study by Dominic Suciu, PhD, a senior scientist at CombiMatrix, revealed that the miRNA expression patterns in blood from patients with cancer were dramatically different from those of patients without cancer.

Cancer Gene Microarrays

Developing a noninvasive blood test for cancer is not new, but success has eluded researchers. The blood is very good at cleaning its contents of cancer DNA proteins and tumor cells, so when these proteins and cells spill out and circulate in the blood, the enzymes clean them out, leaving concentrations that are too low to detect. MicroRNA is more stable in the blood because it comes from the so-called “junk” portion of the gene, and cancer cells each have different microRNAs.

In December of last year, CombiMatrix introduced the first prostate array-based test, simply called the Prostate Cancer Microarray Test. Based on peer-reviewed studies that identified several genetic tumor markers that enable a more precise stratification of the risk profile of cancer patients, the test comprises probes for specific positions that a given gene occupies on a chromosome.

These loci have copy number gains and losses that have been shown to correlate with the risk of recurrence and metastasis in patients after their prostate surgery. These additional probes are a further enhancement of the CMDX solid tumor array platform design that enables whole-genome tumor profiling, or genomic grading, while also providing information about the copy-number status of specific disease-associated loci

“This groundbreaking test provides a valuable new tool that allows physicians to determine which of the patient’s genes have certain specific copy variations that indicate the aggressiveness or indolence of the gene,” Kumar explains. “Based on this information, the physician and patient can make an informed decision about the benefits and risks of whether or not to treat prostate cancer, and, if so, in what manner.”

Also on the cutting edge of microarray gene expression profiling is the High Throughput Genomics (HTG) quantitative nuclease protection assay (qNPA™) plate system, an automated assay that allows researchers to quickly and accurately measure gene-expression levels of mRNA and miRNA in cells, blood, saliva, and tissues with minimal hands-on time. The method enables gene-expression measurement without the need for RNA isolation, reverse transcription, or amplification—each of which is technically difficult and required in the traditional formalin-fixed paraffin-embedded tissue method (FFPET). In addition, results obtained with FFPET are often less than reliable because of technical sample variation. HTG’s method use of short 50-mer probes enables hybridization and leads to more precise and reproducible results.

According to B.J. Kerns, vice president of strategic marketing and business development at High Throughput Genomics, the translational medical tool can interrogate a number of different markers in genes that are relevant for particular oncology patient populations to help predict their sensitivity to drugs. This will help the physician and patient decide whether a drug should be used or not.

“I have talked with surgical oncologists who are very disappointed in what research has done for their patients to date,” Kerns says. “They say we have spent so much on genomic research, and while this has resulted in a greater understanding of cancer, the research hasn’t been translated yet into clinical utility. There is nothing out there today that is better than a decade ago.”

HTG’s qNPA uses a lysis-only, no-amplification protocol, and the 16-gene multiplexing provides a unique analysis tool with more reliable, reproducible data than other high-throughput platforms. Kerns anticipates that assays can be started in the afternoon and read the next day for around $30 per sample.

Improved gene-expression techniques, versus protein expression pattern techniques, for breast cancer patients and their physicians can help determine how their cancer should be treated.

Paired Diagnostics and Therapeutics

Invitrogen’s SPOT-Light HER2 CISH Kit, introduced in September 2008, detects HER2 gene amplification to determine if a patient should be treated with Herceptin using chromogenic in situ hybridization and bright-field microscopy. While fluorescent in situ hybridization (FISH) has long been considered the “gold standard” technique in identifying patients who would benefit from Herceptin, it is expensive and requires a fluorescent microscope and an image-capture system.

With Invitrogen’s product, all that is required is purchase of the kit, which costs $70 per specimen. Further, it does not require specialist microscopy, so the lab technician does not have to leave the office to interpret slides in the darkroom or send them out for analysis. Also, the slides may be kept permanently, which means a diagnosis may be confirmed at a later date.

Comparative studies between CISH and FISH have shown that these two techniques show excellent correlation, with concordance rates between the two ranging from 95% to 100%.

Invitrogen’s kit uses dioxigen-labeled DNA probes specific for the HER2 gene site on chromosome 17 to hybridize to the complementary nucleic acids in the breast cancer tissue. The kit contains all reagents required to perform the CISH procedure on FFPET tissues in a 2-day process separated by an overnight hybridization step. It allows HER2 gene evaluation in the context of surrounding tissue, which is difficult to evaluate in other gene-evaluation methods such as FISH. The context is helpful to gain a more complete diagnosis and to more easily identify and evaluate the tumor region to prevent false-negative readings.

In addition, since CISH can be performed in-house, labs can get results in 2 days, instead of waiting 5 to 7 days for external FISH results. In-house performance also translates into economic benefits in the form of reimbursement.

Biocare Medical provides primary antibodies, antibody cocktails, and multiplex antibody cocktails for use in traditional immunochistochemistry (ICH), which measures the level of protein overexpression to provide an assessment of the amount of Her2 receptors on the surface of breast cancer cells. According to the company, the antibodies themselves are highly specific for the epitope being sought. Because of this, they can be diluted out more than other antibodies, resulting in cost savings for the lab.

The antibodies are standardized using Biocare’s MACH detection system, based upon a micromer—compact structure—that allows a 10- to 20-fold increase in sensitivity and greatly reduces false positives. Due to advances in molecular pathology, the company is heading toward in situ hybridization, which allows for more precise testing in a shorter amount of time.

Tumor Marker Portfolios

The Elecsys Tumor Marker Portfolio from Roche Diagnostics, Indianapolis, tests for a number of markers that characterize a wide variety of cancers, from pancreatic cancer to breast and ovarian cancer to liver and colon cancers. Included are CA 19-9, CA 15-3, and CA 125 for pancreatic, breast, and ovarian cancers, respectively; and AFP and CEA for germ cell tumors and liver cancers and colorectal and other cancers, respectively.

The tumor marker portfolio offers an all-inclusive tumor marker test with broad measuring ranges and high precision to provide a single laboratory solution. Advantages are that the tests, run on serum or plasma, provide fast results in 18 minutes and can be used to screen for certain cancers and to monitor the patient’s response to therapy. Most recently, in December 2008, the company added total prostate-specific antigen (PSA) assays and free PSA assays to its menu. The Elecsys total PSA and free PSA assays are used on the Roche cobas 6000 analyzer series.

To keep up with rapidly moving oncology diagnostics, bookmark our website.

bioTheranostics, San Diego, uses its molecular cancer classification system to measure and integrate the expression of 92 genes. From its tumor reference data set, composed of primary and metastatic cancers of unknown origin, THEROS CancerTYPE ID can distinguish up to 39 different tumor types and 64 subtypes.

Approximately 3% to 5% of all cancer cases receive diagnoses of “cancer of unknown primary,” or CUP, while a large number of patients receive an “uncertain diagnosis.” Both of these diagnoses pose treatment dilemmas for the oncologist. The CancerTYPE ID provides a faster, effective, and more objective diagnostic tool that significantly reduces the number of tumors in which the primary origin is diagnosed as either “unknown” or “uncertain.” It has an overall success rate of 87% in classifying 39 cancer types, potentially decreasing time to diagnosis and increasing the success rate of cancer classification. The results help physicians to choose the most appropriate therapy for patients.

Shannon Rose is a freelance health and medical writer based in Temecula, Calif.