What if all forms of cancer could be detected by a simple blood test performed yearly in your doctor’s office? Personalized medicine, which uses information from a person’s genome to diagnose disease and select the most effective treatments, may soon make that possible. Researchers at Stanford’s School of Medicine have developed a new personalized method for detecting disease by monitoring levels of cancerous DNA circulating in the blood. "This approach could, theoretically, work for any tumor," said Dr. Ash Alizadeh, assistant professor of medicine and co-senior author of the paper appearing in Nature Medicine. "We expect it to be broadly applicable across cancers."

Circulating DNA

As cells naturally break down and die, and when they do, they release small amounts of DNA into the bloodstream which is referred to as Circulating Nucleic Acids or CNA. Cancer cells are no different from normal cells and they, too, release DNA as they die. Yet, in a person with cancer, CNA from tumor cells makes up only a small percentage of the DNA circulating within blood. "The vast majority of circulating DNA is from normal, non-cancerous cells, even in patients with advanced cancer," said Dr. Scott Bratman, a lead author of the research. "We needed a comprehensive strategy for isolating the circulating DNA from blood and detecting the rare, cancer-associated mutations."

DNA from a tumorous cell is different from the DNA of a normal cell — it has mutations in the nucleotide sequence. Some of these mutations are thought to be responsible for causing cancer, while others accumulate randomly. "Unlike Down syndrome, for example, which has a single dominant cause, for most cancers it's very difficult to identify any one particular genetic aberration or mutation that is found in every patient," Alizadeh stated in a press release.

To develop the blood test for cancer, the team of researchers began by collecting information from 407 patients with non-small-cell lung cancer and then they looked for regions in the genome with cancer-associated mutations. They identified 139 genes that are recurrently mutated in non-small-cell lung cancer. (By comparison, other blood tests that have attempted to track circulating DNA have relied on a single mutation; yet, it is unlikely that one mutation will occur in every patient with a particular cancer so tracking more than one increases the sensitivity of the test.) "We looked for which genes are most commonly altered, and used computational approaches to identify what we call the genetic architecture of the cancer," Alizadeh said. "That allowed us to identify the part of the genome that would be best to identify and track the disease." Next, the team designed and used oligonucleotides, panels of short pieces of DNA, to sequence the surrounding DNA. "By sequencing only those regions of the genome that are highly enriched for cancer mutations, we're able to keep costs down and identify multiple mutations per patient," said Dr. Maximilian Diehn, assistant professor of radiation oncology and co-senior author of the paper.

They discovered that their new technique — dubbed Cancer Personalized Profiling by deep Sequencing or CAPP-Seq for short — is sensitive enough to find the proverbial needle in a haystack; CAPP-Seq could detect just one molecule of cancerous DNA out of 10,000 healthy DNA molecules floating within the blood.  Best of all, when the researchers applied the technique to actual patients with non-small-cell lung cancer, they were able to detect disease in all of the patients with stage-2 or higher disease. Plus, they could detect cancer in half of the patients who had the earliest stage of disease (stage-1).

The researchers were delighted to discover that the levels of tumor CNA they found in patients related to the volume (or size) of their tumors. Normally, doctors can only estimate tumor size using a CT or PET scan. Importantly, too, CAPP-Seq also identified the presence in one of the patients of a mutation that confers resistance to a drug commonly used to treat non-small-cell lung cancer. If the blood test is someday used by all doctors, oncologists will be able to more effectively treat their patients.

“There are currently no reliable biomarkers available for lung cancer patients, which is the most common cancer and No. 1 cause of cancer deaths,” Diehn said. “We are very excited about our findings because a personalized, clinically useful biomarker could revolutionize how we detect and manage this devastating disease.” Best of all, the researchers believe their new approach to a cancer blood test will be applicable to many different types of tumors.

 

Source: Newman AM, Bratman SV, To J, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nature Medicine. 2014.