Researchers at Karolinska Institutet in Sweden have developed a cheap method that can identify highly heterogeneous tumors that tend to be very aggressive—and, therefore, need to be treated more aggressively. The new technique was presented today in Nature Communications.
A common feature of cancer cells is “copy number alterations,” or CNAs. CNAs are a variation in the number of copies of specific genes that arise in somatic cells. Even within the same tumor, different cells may carry different CNAs. Tumors with many CNAs are typically very aggressive and tend to reform more often, even after harsh treatments. Now, researchers have developed a genomic method named CUTseq that can assess the number and type of CNAs in many different parts of the same tumor at a much lower cost than existing technologies.
“I expect that CUTseq will find many useful applications in cancer diagnostics,” says co-senior author Nicola Crosetto. “Multi-region tumor sequencing is going to be increasingly used in the diagnostic setting, in order to identify patients with highly heterogeneous tumors that need to be treated more aggressively. I believe that our method can play a leading role here.”
The method works with DNA extracted from multiple biopsies and even from very small portions of thin tissue sections—the type of sample that pathologists commonly rely on to make a diagnosis of cancer under the microscope. By tagging the DNA extracted from multiple regions of the same tumor sample with unique molecular barcodes, a comprehensive picture of the heterogeneity of CNAs in a tumor can be obtained with a single sequencing experiment.
But applications of CUTseq are not only limited to cancer diagnostics. “For example, CUTseq could be used as a platform for cell line authentication and to monitor genome stability in large cell line repositories and biobanks,” says co-senior author Magda Bienko. “It could also be applied in ecology, as an alternative to other reduced representation genome sequencing methods, such as RAD-seq, to assess biodiversity in a cost-effective way.”