Overcoming the Challenge of Using Formalin-Fixed-Paraffin-Embedded (FFPE) Tissues for Large Scale Cancer Genome Sequencing Studies
Mentors: Fernando Viloria and Kristin Ardlie
Studies involving sequencing DNA of cancer cells typically utilize DNA isolated from fresh frozen tissues. While ideal, these samples can be difficult to obtain. Pathology departments routinely store samples that are formalin-fixed-paraffin-embedded (FFPE) tissues that have been treated with formaldehyde and embedded in wax.
Betsy and her mentors investigated 161 FFPE tissues to determine if DNA from these samples can be used in cancer genome sequencing research. Betsy prepared stained microscope slides of 95 of these samples for further examination by pathologists, and she isolated DNA from 66 of these samples. She then assayed the quality of the DNA using PicoGreen, Quality Gel, and Quality-Control-PCR methods. DNA yields were lower than those from equivalent fresh frozen tissues, and samples showed varying levels of degradation and PCR amplification. The samples Betsy isolated will next be tested for their performance in sequencing, to determine the feasibility of using these samples in cancer genome discovery projects.
Betsy, a Newton South High School Senior, investigated the use of DNA isolated from Formalin-Fixed-Paraffin-Embedded Tissues for cancer genome sequencing.