RNA Next-Generation Sequencing Offers More Accurate, Less Invasive Analysis for Lung Cancers

PHILADELPHIA (November 18, 2022)—Genetically targeted therapy can make treatment for lung cancer much more effective, but testing to identify specific gene fusions involved in the disease remains a challenge. However, a new study by researchers at Fox Chase Cancer Center demonstrates that RNA next-generation sequencing (RNA-NGS) can offer results that are more accurate and comprehensive while using smaller tissue samples.

Although the test isn’t new, it’s only recently that the technology has improved to the point where it’s viable for clinical use, said corresponding author Shuanzeng “Sam” Wei, MD, PhD, an associate professor in the Department of Pathology and medical director of the Clinical Genomics Laboratory at Fox Chase. He said the findings provided further evidence to support updating clinical guidelines to recommend RNA-NGS testing for lung adenocarcinoma.

“The national guidelines right now don’t have a definitive recommendation for the use of RNA-NGS for detecting gene fusions,” said Wei, who conducted the study with colleagues in the Department of Pathology. “But our platform is now much better than it was previously and RNA-NGS is just much more sensitive.”

Lung adenocarcinoma is the most common form of lung cancer in the United States, representing about 40% of all cases. Fusion genes can play a major role in the development of the disease, and when they appear, they can be targeted with specific therapies.

Most current testing protocols, including FISH and PCR, can only test for one fusion gene at a time, with tests usually focusing on the most common candidates. However, RNA-NGS testing can search for as many as 507 fusion genes with a single test.

“Even if you don’t know the partner gene, you can still get a positive result,” Wei said.

In addition, RNA-NGS can deliver accurate results with just a tiny sample of cells drawn from a fine needle aspiration of the tumor. In contrast, conventional testing methods require a tissue biopsy—a much larger sample extracted through an invasive procedure.

“The benefit for the patient is that the operation is small and causes minimal injury, compared to a core biopsy,” Wei said. For the study, researchers used RNA-NGS to analyze 120 lung adenocarcinoma tumor cytology samples. They then used traditional testing methods, including DNA-NGS, FISH, and chromosomal microarray analysis, to verify the results.

The RNA-NGS testing had an overall success rate of 93% at detecting gene fusion. The older testing methods were less accurate and sensitive. Of the 22 samples analyzed for fusion genes using FISH, half of the tests failed because the samples did not contain enough material. Some of the positive results detected by FISH turned out to be false positives.

Even though RNA-NGS testing is easier to use and more accurate than traditional methods, the technology is not yet widely accessible. Fox Chase has one of the few comprehensive platforms available for clinical use in the United States. However, Wei said he expects the test to become more common in the coming decade.

The researchers plan to continue refining the technology by gathering data on its use in testing for different types of cancers, including sarcomas.

The study, “Cell Block-Based RNA Next Generation Sequencing for Detection of Gene Fusions in Lung Adenocarcinoma: An Institutional Experience,” was published in Cytopathology.

Fox Chase Cancer Center (Fox Chase), which includes the Institute for Cancer Research and the American Oncologic Hospital and is a part of Temple Health, is one of the leading comprehensive cancer centers in the United States. Founded in 1904 in Philadelphia as one of the nation’s first cancer hospitals, Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. Fox Chase is also one of just 10 members of the Alliance of Dedicated Cancer Centers. Fox Chase researchers have won the highest awards in their fields, including two Nobel Prizes. Fox Chase physicians are also routinely recognized in national rankings, and the Center’s nursing program has received the Magnet recognition for excellence six consecutive times. Today, Fox Chase conducts a broad array of nationally competitive basic, translational, and clinical research, with special programs in cancer prevention, detection, survivorship, and community outreach. It is the policy of Fox Chase Cancer Center that there shall be no exclusion from, or participation in, and no one denied the benefits of, the delivery of quality medical care on the basis of race, ethnicity, religion, sexual orientation, gender, gender identity/expression, disability, age, ancestry, color, national origin, physical ability, level of education, or source of payment.

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