The Feb. 24 issue of the journal Science Translational Medicine, published by the American Association for the Advancement of Science (AAAS), will include the discovery of a new technique in genome sequencing that led scientists to develop a way to trace cancer by identifying biomarkers present at specific kinds of tumors in different patients.
This technique, dubbed Personalized Analysis of Rearranged Ends (PARE), involves sequencing whole genomes of a patient’s tumor, developing biomarkers that are only found in the patient’s tumor, and using the biomarker to monitor residual and recurrent tumors, which is essential to evaluating the effectiveness of treatments such as radiation, chemotherapy, and surgery.
“Whole genome sequencing refers to a group of technologies whose goal is to identify the precise sequence of all of the genes in a cell,” Dr. Bert Vogelstein of the Johns Hopkins Kimmel Cancer Center said in a video provided by the center.
For 20 years, scientists have known that tumors are caused by genetic alterations, but many alterations were not identified because “each cancer in each patient is different from any other cancer in any other patient,” said Vogelstein.
“This kind of technology might seem familiar to people who watch crime shows on TV, because on those shows, you put someone’s DNA into a machine, and you get their sequenced cell. But that really was science fiction up until a couple years ago, and in the last few years there have been more than a hundred cancers in which all of the genes have been sequenced.”
It was found that tumor cells often have genomes in which sections of the DNA are rearranged.
"In sequencing individuals' genomes in the past, we focused on single-letter changes, but in this study, we looked for the swapping of entire sections of the tumor genome," said Vogelstein in a press release. "These alterations, like the reordering of chapters of a book, are easier to identify and detect in the blood than single-letter changes."
Since these rearrangements are known to occur only in cancer cells, they are ideal biomarkers for detecting cancer. DNA sheds from tumors into the bloodstream. Therefore, by taking blood samples from patients after a surgery, amplifying the DNA in the samples, and detecting the biomarkers, doctors can determine if a patient’s cancer has been cured or if it is recurring.
“One of the biggest obstacles for physicians to treat cancer is how to monitor our patients,” said Dr. Luis Diaz, professor at Johns Hopkins University, at a press conference.
"Eventually, we believe this type of approach could be used to detect recurrent cancers before they are found by conventional imaging methods, like CT scans," Diaz said in a press release.
Currently, a genome scan costs about $5,000, and a CT scan costs about $1,500. However, CT scans are not able to detect cancer on small scales like PARE can, and the researchers believe the cost for PARE will become affordable.
“There's still a lot of work to be done to translate this approach and make it widely accessible to patients. However, we are optimistic that this will happen within the next two years,” said Diaz.