Molecular Analysis Used to Identify Specific Cancers

A method has been described that identifies cancer-causing rearrangements of genetic material called chromosomal translocations quickly, accurately, and inexpensively.

The technique developed combines microarray technology, which can look for thousands of translocations in a single test, with a novel antibody that is used to detect the presence of the translocation.

Scientists at the University of Utah (Salt Lake City, UT, USA) developed a new approach, called antibody detection of translocations (ADOT), to identify Ewing's sarcoma and which avoids the shortcomings of current techniques. The technique is applied to frozen or formalin fixed paraffin embedded (FFPE) primary tumor samples. Ribonucleic acid (RNA) is extracted, followed by microarray hybridization and antibody detection. Reverse-transcriptase polymerase (RT-PCR) chain reaction was performed using iScript SYBR green RT-PCR kit (Bio-Rad; Hercules, CA, USA).

Total RNA from tumor cells or tissues was hybridized on the array. Bound RNA was detected with a monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion. Many cancers result from chromosomal translocations in tumor cells. Hundreds of cancer-causing translocations have been discovered, but current methods for detecting them have significant shortcomings. The investigators were able to detect specific translocation from three out of four FFPE samples. The method is much better with real-life specimens than the current standard techniques. ADOT is capable of detecting known or unknown translocations in biological samples, including those most commonly encountered during the diagnostic work-up of a patient. ADOT bears promise as a discovery tool for identifying fusion transcripts in cancers, as well as a diagnostic tool for patients with translocation-associated tumors.

Stephen L. Lessnick, MD, PhD, a lead author of the study, said, "We're moving past the age when a pathologist looking through the microscope at a tumor sample is the best way to diagnose what type of cancer it is. The molecular tests currently available are slow, inefficient, and expensive, and one of the biggest issues is that you need high-quality tumor samples, not always available in the clinical setting, to do them. With this method, there's potential to develop a single array that could test for every known cancer-causing translocation simultaneously. Currently, a clinician has to decide beforehand which specific cancer to test.” The study was published online on March 15, 2012, in the journal European Molecular Biology Organization (EMBO) Molecular Medicine.

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