Microarray Diagnostics

The benefits of microarray technology-rapidity, precision and abundance-are well developed in areas like biomedical research but are only beginning to take hold in the clinical lab. Many tests to assist in garnering the most specific and accurate information about a patient from a sample are in development; to date only a few are commercially available.

Because microarrays have the potential to answer clinical questions that require a large number of genes to provide a robust answer, this type of diagnostic is likely to expand for a variety of applications, explains Shawn Becker, MD, vice president of Marketing and Reimbursement for Pathwork Diagnostics.

Cancer diagnostics is reaping the benefits of microarray technology, as high-resolution scanning of tumor genomes and gene expression analysis provide laboratorians with specific information about the origin of a patient's cancer. Patients with undifferentiated tumors can present serious challenges. A microarray could be used to assess the gene expression profile of a tumor of unknown origin and compare it to expression patterns of a number of known tumors.

Dr. Becker explains, "The first step in beginning standard-of-care, tumor-specific therapy per National Comprehensive Cancer Network Clinical Practice Guidelines is to identify the tissue of origin. Targeting therapy to specific tumor types can also allow patients to avoid the toxicity of broader, and in some cases, ineffective chemotherapy." The accuracy enabled by this microarray diagnostic also may offer the benefit of earlier diagnosis and therapy.

Array comparative genomic hybridization (CGH) technology allows the clinical laboratory to provide a high-resolution copy number scan of the entire human genome using a DNA-based approach that circumvents the cell culture problems associated with traditional cytogenetics," explains Shelly Gunn, medical director at Combimatrix Molecular Diagnostics Inc. Microarray-based CGH offers more information than chromosome-based CGH and is the standard of care for genomic analysis of patients with congenital abnormalities.

Remaining hurdles must be overcome for the clinical lab to be able to fully reap the benefits that microarray technology can offer. RNA degradation in formalin-fixed paraffin-embedded tissues has presented a technical challenge in implementing broader use, Dr. Becker explains, making it a challenge to generate robust and reproducible data for many genes simultaneously. But microarrays capable of using FFPE have come to market, opening the door for future advancements.

Due to the vast amount of data produced by microarrays, the need remains to determine how best to harness and make use of all the information. But in many cases, says Gunn, "the technology is ready for clinical use, and the biggest remaining obstacle is a lack of awareness by physicians and patients that this powerful tool is available to them."

Kelly J. Graham is assistant editor.