Liquid Biopsy Enables Whole-Exome Sequencing of Metastatic Tumors in Nearly Half of Patients

November 6, 2017
Liquid Biopsy Enables Whole-Exome Sequencing of Metastatic Tumors in Nearly Half of Patients
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Researchers at the Broad Institute of MIT and Harvard, Koch Institute at MIT, Dana-Farber Cancer Institute (DFCI), and Massachusetts General Hospital have just released data demonstrating that nearly 90% of a tumor's genetic features can be detected in blood samples using whole-exome sequencing, and that the method can be effectively applied in up to 49% of patients with advanced cancer. Findings from the new study, published today in Nature Communications  (“Scalable Whole-Exome Sequencing of Cell-Free DNA Reveals High Concordance with Metastatic Tumors”), are a window into cancer's genome and have a range of potential applications.

"Our ultimate hope is to use blood biopsies to exhaustively search for and characterize even the smallest remnants of tumors," explained co-lead study investigator Viktor Adalsteinsson, Ph.D., group leader at the Broad Institute. "And, as tumors evolve in more advanced stages of cancer, developing resistance or becoming metastatic, we might access timepoints that could be pivotal in deciding which therapies are right for that patient."

The ability to detect and analyze cancer DNA from a patient's blood sample is emerging as a promising alternative to invasive surgical biopsies, which can be difficult, painful, and costly—especially when tumors have appeared in locations that are challenging to access. Liquid biopsies are poised to overcome many of these issues. They have the potential to allow doctors to track the progress of disease and treatment in real-time and to help researchers understand how tumors resist treatment with far greater resolution.

Compiling a whole exome from DNA fragments currently requires at least 10% tumor DNA in a blood sample, but the fraction of tumor DNA in the blood can vary wildly from patient to patient. Because of this variation, the research team first desired an unbiased approach for detecting and measuring levels of cancer DNA before attempting whole-exome sequencing. While many current blood biopsy methods detect tumor DNA by screening for mutations in known cancer-related genes, these targeted sequencing events can often miss cancers without those mutations.

In the current study, the scientists developed a tool called ichorCNA that can analyze DNA fragments for mutation patterns nearly universal in cancer genomes and, as a result, capture cancers with both known and unknown mutations. Moreover, the researchers focused on detecting stretches of DNA that have either fewer or greater copies in cancer cells, in contrast to healthy cells. The research team tested and refined ichorCNA on 1439 blood samples collected prospectively from 520 metastatic breast or prostate cancer patients

Using this approach, the researchers found that in 33% to 49% of the metastatic breast and prostate cancer patients, depending upon whether one or multiple blood samples were examined, tumor DNA made up greater than 10% of the cell-free DNA in their blood—enough to make whole-exome sequencing of cell-free DNA feasible.

"Our study has demonstrated that we can get a cancer whole exome reliably from blood; that it reflects the matched tumor biopsy—and that it can be done for a significant fraction of patients with metastatic cancer," noted Dr. Adalsteinsson. "This validation suggests that we can use blood biopsies for large-scale genomic characterization of disease in patients with metastatic cancer."

To determine whether this sequencing of cell-free tumor DNA could offer the same level of insight into cancer genetics as a tissue biopsy could, the team compared surgically obtained tumor biopsies to data collected from the whole-exome sequencing of cell-free DNA from a group of 41 patients. The researchers found that genetic data from blood whole-exome sequencing and tissue biopsies matched significantly across some genetic features, such as clonal somatic mutations (88% match) and copy number alterations (80% match).

These results support cell-free DNA whole-exome sequencing from blood samples as a potential substitute for metastatic tumor biopsy sequencing for many patients.

"It unlocks the potential for a lot of studies that we couldn't do before," remarked co-senior study investigator Gad Getz, Ph.D., a Broad Institute member and director of the Cancer Genome Computational Analysis group at Broad, associate professor of pathology, and director of bioinformatics at the Massachusetts General Hospital Cancer Center and department of pathology. "The technology will allow us to track the dynamics of cancer and understand the evolution of drug resistance, or the development of the metastatic state, in a way that isn't possible through surgical biopsies."

This new study improves the analysis pipeline for blood biopsies and allows it to be performed at an expanded scale. The researchers are actively applying their work to thousands of patients with metastatic cancer who may otherwise not have their tumors biopsied.

"We are excited about using blood biopsies to understand metastatic breast cancer, drug resistance, and tumor evolution, and to get a snapshot of the metastatic setting in patients who might not have available tissue from a metastatic biopsy," concluded study co-author Nikhil Wagle, M.D., an associate member at the Broad Institute, deputy director of the Center for Cancer Precision Medicine at DFCI, and leader of the Metastatic Breast Cancer Project. "With the Blood Biopsy Team's latest results, it was clear that this technology had reached the right point for us to incorporate into the Metastatic Breast Cancer project."