Sequencing approach enables early detection of cancer

The study will be featured in a press briefing and presented at the 2017 American Society of Clinical Oncology (ASCO) Annual Meeting. This approach – using high-intensity sequencing to detect cancer from circulating tumour DNA in the bloodstream – heralds the development of future tests for early cancer detection.

The high-intensity sequencing approach used in this study has a unique combination of breadth and depth. It scans a very broad area of the genome (508 genes and more than two million base pairs or letters of the genome, i.e. A, T, C, and G) with high accuracy (each region of the genome is sequenced or "read" 60,000 times), yielding about 100 times more data than other sequencing approaches. This enormous amount of data will be instrumental in developing a blood test to detect cancer early.

This approach, however, differs from liquid biopsies, including commercial tests, which only profile a relatively small portion of the genome in patients already diagnosed with cancer for the purpose of helping monitor the disease or detect actionable alterations that can be matched to available drugs or clinical trials.

"Our findings show that high-intensity circulating tumour DNA sequencing is possible and may provide invaluable information for clinical decision-making, potentially without any need for tumour tissue samples," said lead study author Pedram Razavi, MD, PhD, a medical oncologist and instructor in medicine at Memorial Sloan Kettering Cancer Center (MSK) in New York, NY.

"This study is also an important step in the process of developing blood tests for early detection of cancer." Circulating tumour DNA is a term used to describe the tiny pieces of genetic material that dying cancer cells shed into the blood circulation.

To create a picture of the entire genomic landscape of the tumour from circulating tumour DNA, scientists "read" each tiny fragment and then piece them together as a puzzle. In the bloodstream, circulating tumour DNA is only a small subset of the total cell-free DNA, as most circulating fragments of genetic material come from normal cells.

The researchers prospectively collected blood and tissue samples from 161 patients with metastatic breast cancer, non-small-cell lung cancer (NSCLC), or castration-resistant prostate cancer.

Thirty-seven patients were excluded due to unavailability of the results of the genetic analysis of the tumour or cell-free DNA samples. For 124 evaluable patients for concordance analysis, researchers compared genetic changes in the tumours to those in circulating tumour DNA from the blood samples.

Tumour tissues were analysed using MSK-IMPACT, a 410-gene diagnostic test that provides detailed genetic information about a patient's cancer. In each blood sample, the researchers separated the plasma, the liquid part of the blood, from the blood cells.

The cell-free DNA extracted from the plasma and, separately, the genome of white blood cells were then sequenced using the high-intensity, 508-gene sequencing assay.

"Finding tumour DNA in the blood is like looking for a needle in a haystack. For every 100 DNA fragments, only one may come from the tumour, and the rest may come from normal cells, mainly bone marrow cells," said Dr. Razavi.

"Our combined analysis of cell-free DNA and white blood cell DNA allows for identification of tumour DNA with much higher sensitivity, and deep sequencing also helps us find those rare tumour DNA fragments."

Patients' tumours may have various genetic changes; there can be different changes in different parts of the same tumour, as well as in different sites where the tumour spreads in the body. For these reasons, sequencing over very broad regions of the genome is critically important to identify the multitude and diversity of genetic changes in the tumour.

In 89% of patients, at least one genetic change detected in the tumour was also detected in the blood (97% in metastatic breast cancer patients, 85% in those with NSCLC, and 84% in those with metastatic prostate cancer).

Overall, including all genomic variations present in most if not all tumour cells (clonal) as well as those present only in subsets of the cancer cells (subclonal) from tumour tissue, the researchers detected a total of 864 genetic changes in tissue samples across the three tumour types, and 627 (73%) of those were also found in the blood.

Importantly, without any prior knowledge from the analysis of tumour tissue, 76% of "actionable" mutations (genetic changes that can be matched to an approved targeted therapy or one being tested in clinical trials) detected in tissue were also detected in blood.

"Prior research in the field has primarily focused on using knowledge from tumour tissue sequencing to identify specific changes to look for in circulating tumour DNA. This approach allows us to detect, with high confidence, changes in circulating tumour DNA across a large part of the genome without information from tumour tissue," said Dr. Razavi.

While circulating tumour DNA tests targeting a smaller set of cancer genes are already available for use in routine practice to guide care, by covering a much larger number of cancer genes, this high-intensity sequencing approach may enable development of future tests for early detection of cancer.

The high-intensity sequencing approach used in this study is a research platform and is not intended to be commercially available to patients. To understand the current performance and potential of this assay, the researchers first tested it in advanced cancer, an area where circulating tumour DNA has been previously characterised.

"This study will inform development of technology for a future test that could eventually be used as a blood test for early cancer detection. In patients undergoing cancer screening, tumour tissue is not available, and we will need to detect changes in circulating tumour DNA without prior knowledge of tissue analysis results," said Dr. Razavi.

Genomic changes can differ between various areas within a tumour, as well as among the different organs where the cancer has spread. A circulating tumour DNA test provides a "summary report" of all the genomic changes in the primary tumour and metastases. In contrast, a tissue biopsy, which typically takes only a small piece of the tumour, sometimes misses key genetic changes that fuel cancer growth.

Another advantage of liquid biopsy is its ability to capture genomic changes in real time, helping guide treatment planning without the need of additional conventional tissue biopsies. Genomic changes evolve as the cancer grows and spreads.

New changes may lead to cancer recurrence or resistance to treatment. A liquid biopsy test requires only a simple blood draw. It is generally safe and convenient to repeat, allowing doctors to keep easier track of new mutations.