AACR Annual Meeting 2021: Facilitating Early Cancer Detection with Liquid Biopsy
Cancer is the second leading cause of death globally, accounting for nearly 10 million deaths each year. Late-stage diagnosis is a major contributor of cancer-related mortality, as patients diagnosed with advanced cancer have fewer treatment options and a greater likelihood of death. Early detection of cancer may, therefore, help reduce cancer-related mortality around the world.
Screening programs for breast, colorectal, and cervical cancers have demonstrated the power of early cancer detection. The widespread implementation of regular mammograms, colonoscopies, and Pap/HPV tests over the past several decades has allowed physicians to detect cancers prior to the onset of symptoms, reducing late-stage diagnoses and dramatically decreasing mortality rates.
Despite these successes, easy screening methods are currently unavailable for some of the world’s deadliest cancers, including those of the lung, liver, and stomach, among others. Adding to the problem is that many cancers often go unnoticed due to the lack of obvious symptoms during earlier stages of the disease. As a result, patients with such cancers tend to be diagnosed only after their cancer has spread to other organs, when the risk of death is greatest. A simple, noninvasive screening method for various cancers could allow physicians to catch cancer in its early stages, when survival rates are much higher. A recent study published in the AACR journal Cancer Epidemiology, Biomarkers & Prevention predicted that incorporation of a multicancer early detection test in usual care would reduce late-stage diagnosis by 78 percent and reduce cancer mortality by 26 percent.
Liquid biopsy is being explored as a potential tool to facilitate the early detection of cancer. Requiring only a simple blood sample, a liquid biopsy-based multicancer early detection test could provide a much-needed noninvasive screening method to detect multiple types of cancer. The AACR Annual Meeting 2021 showcased some of the latest advances in this burgeoning field.
How is cancer detected from liquid biopsies?
Researchers have explored diverse strategies for detecting cancer from liquid biopsy samples, including analyzing circulating tumor cells (CTCs), proteins, and/or cell-free DNA shed from tumors. Each of these methods has shown potential, but challenges remain. CTCs comprise an extremely low proportion of cells within the blood, which makes enrichment and analysis of these cells difficult. An alternative method is to search for somatic mutations in cell-free DNA; however, typical sequencing methods are error-prone, and there is vast heterogeneity of somatic mutations between individual patients and different cancer types.
In recent years, researchers have examined the utility of cell-free DNA methylation patterns for early cancer detection. DNA methylation is a modification on DNA that can guide gene expression, and multiple studies have suggested that abnormal DNA methylation may be indicative of cancer. Searching for abnormal methylation patterns in cell-free DNA could, therefore, allow for early detection of a wide range of cancers using a noninvasive blood sample. Compared to somatic mutation analysis, this method has higher sensitivity due to the presence of multiple methylation sites within a single gene. Furthermore, DNA methylation patterns are relatively consistent between different types of cancer, making this method more widely applicable.
A DNA methylation-based early detection
test by GRAIL Inc.
Three presentations from this year’s Annual Meeting discussed a multicancer early detection test developed by GRAIL Inc., which utilizes machine learning and cell-free DNA from liquid biopsy samples to search for abnormal patterns of DNA methylation. Each of these presentations shared results from the Circulating Cell-free Genome Atlas (CCGA) study, a prospective, multicenter, case-control study that enrolled approximately 10,500 participants with cancer and approximately 4,500 participants without cancer.
Gregory Alexander, PhD, senior director of biostatistics at GRAIL, presented data from the CCGA study on the potential of their early detection test to be used for cancer screening. Alexander noted that the test had 100 percent specificity, meaning that no false positives were found. Furthermore, the test correctly identified the site of cancer origin for all 50 different cancer types tested. Similar results were presented during last year’s AACR Virtual Annual Meeting I.
New results presented this year included an examination of the test’s technical aspects, including how other substances in blood samples might impact the accuracy of the test. According to Alexander, potential interfering substances, such as hemoglobin, bilirubin, triglycerides, and genomic DNA had no impact on cancer detection or tissue origin identification. Analysis of the test’s limit of detection demonstrated that it was able to detect cancer as long as the cancer-specific variant comprised at least 0.11 percent of the sample, and the test was found to have 100 percent repeatability and reproducibility.
“Together, these data demonstrate [that] the analytical robustness of this test is sufficient to support its routine clinical use as a complementary tool alongside other currently available cancer screening options,” Alexander noted.
Eric Klein, MD, chairman of the Glickman Urological & Kidney Institute at the Cleveland Clinic, presented results from a separate validation sub-study of CCGA. The validation cohort included 4,077 individuals, of whom 2,823 had cancer and 1,254 did not have cancer. In this cohort, the early detection test had 99.5 percent specificity and 51.5 percent sensitivity. Sensitivity of the test increased with stage, ranging from 16.8 percent for stage 1 tumors to 90.1 percent for stage 4 tumors. The test detected cancer across more than 50 different cancer types and correctly predicted the site of tissue origin in 88.7 percent of cases.
“The test performed with high specificity and high accuracy of signal origin prediction, which could help direct the follow-up diagnostic work-up,” said Klein. “These data support the foundation for population-scale clinical implementation of this test.”
The cell-free DNA methylation liquid biopsy test developed by GRAIL may also have diagnostic value, according to Alan Bryce, MD, chair of hematology and medical oncology at the Mayo Clinic. Bryce presented results from a sub-study of CCGA that evaluated the test in a subgroup of participants who presented with symptoms indicative of cancer. Bryce and colleagues found that the test accurately identified 66.4 percent of the 518 cancer cases and 99.5 percent of the 398 non-cancer cases included in the sub-study. As in the study presented by Klein, the test’s sensitivity increased with tumor stage. Prediction of the cancer’s tissue origin was 91.7 percent accurate. “These findings support further clinical development of this important multicancer detection test that could accelerate the diagnostic resolution of symptomatic individuals,” Bryce concluded.
Exact Sciences test relies on DNA methylation and protein analysis
In another presentation during the meeting, Hatim Allawi, PhD, MBA, vice president of research and technology development at Exact Sciences, discussed a multicancer early detection test developed by Exact Sciences. Like the test from GRAIL, the test developed by Exact Sciences relies on detection of abnormal DNA methylation in cell-free DNA; however, unlike the above test, it also examines the presence of known cancer-associated proteins (CEA, CA-125, CA19-9, CA15-3, and AFP). Twenty-six DNA methylation markers were analyzed, which included tissue-specific and universal markers.
Allawi and colleagues found that their method correctly identified 86 percent of the 257 participants without cancer and 95 percent of the 180 patients with cancer, representing six different cancer types (lung, esophageal, stomach, pancreatic, liver, and ovarian cancers). Sensitivity of the test varied among different cancers, ranging from 78 percent for lung cancers to 90 percent for ovarian and pancreatic cancers.
“[This was] a truly successful early feasibility study that showed that methylated DNA markers have excellent coverage for multicancer detection,” said Allawi, adding that their multi-marker approach of proteins and DNA methylation markers enhanced performance of the test. Allawi noted that future work will aim to improve the method and may include refinement of the marker panel and employment of next-generation sequencing.
CancerRadar by Early Diagnostics examines features of cell-free DNA and plasma
The AACR Annual Meeting 2021 featured a third liquid biopsy-based multicancer early detection test, called CancerRadar, which was developed by Early Diagnostics and presented by Xianghong Jasmine Zhou, PhD, a professor of pathology and laboratory medicine at the University of California at Los Angeles.
This early detection test combines cell-free DNA methylation data with other features, including cell-free DNA fragment size, copy number variations, and microbial composition. In contrast to the Exact Sciences test, CancerRadar analyzes all methylation sites across the genome, rather than focusing on the methylation patterns of specific genes. This test also utilizes a cost-effective protocol that allows it to avoid deep sequencing while achieving 12 times greater coverage compared to the conventional method of whole genome bisulfite sequencing, Zhou explained.
Zhou and colleagues determined that CancerRadar correctly identified 85.9 percent of cancer cases—including 80.9 percent of early-stage cancers—out of 275 cancer samples. The test correctly identified 99 percent of the 204 non-cancer samples. Furthermore, CancerRadar accurately identified the cancer’s tissue origin 91.5 percent of the time across all tumor stages and 89.1 percent of the time for early-stage cancers.
“We developed a cost-effective methylome profiling protocol, specifically tailored for cell-free DNA,” Zhou summarized, adding that “CancerRadar showed excellent performance in early cancer detection.”
While further validation is needed, these studies highlight the potential of liquid biopsy-based methods to screen for a broad range of cancers using a noninvasive method. Beyond its use in screening and early detection, liquid biopsy may also have implications for the diagnosis, treatment, and management of cancer.
To learn more about additional applications of liquid biopsy, be sure to visit the recently launched AACR Stories, The Faces and Voices Behind the Science, page on liquid biopsy. The site features a discussion with prominent cancer researcher Victor Velculescu, MD, PhD, and highlights recent research advances on this topic.