Despite the significant discoveries that have been made in recent years, the specific mechanisms that cause cancer largely remain a mystery. Part of the hurdle to understanding cancer progression is simply a matter of numbers. Repositories are filled with thousands of tumor samples that might hold the answers, but the DNA inside these formalin-fixed, paraffin-embedded (FFPE) tissues is so degraded that it is unusable. Instead, scientists have had to rely on fresh-frozen tissue samples, which are less abundant.
To address this challenge, Dr. Annalisa Astolfi and her team at the University of Bologna developed a way to isolate and sequence FFPE DNA from tumor samples. Using a quality check (QC) method, they can screen FFPE samples and use only high-quality DNA for sequencing. The data generated using this method are comparable to data from fresh-frozen samples, opening new doors for cancer researchers who want to analyze archival FFPE tumors. “We can now investigate tumor samples more deeply with sequencing, enabling us to search for novel somatic mutations in rare tumors,” Dr. Astolfi said. “We were surprised to perform exome sequencing on FFPE samples so successfully!”
Already, the team has used sequencing to identify inactivating mutations in the SDH
gene that are associated with gastrointestinal stromal tumors. They plan to apply their method to different cancer types to understand “how the genetic basis of tumors might influence reactions to therapeutic drugs, and how the molecular background of rare tumors differs from common tumors.” They hope that this information will provide a better understanding of the factors that cause cancer.