Conference Coverage

Multiomics blood test outperforms other tests for colorectal cancer screening



– A blood-based test that integrates data from multiple molecular “omes,” such as the genome and proteome, performs well at spotting early-stage colorectal cancer, the AI-EMERGE study suggests.

Dr. Girish Putcha. chief medical officer, Freenome, South San Francisco Susan London/MDedge News

Dr. Girish Putcha

At a specificity of 94%, the multiomics test had a sensitivity of 94% for detecting stage I and II colorectal cancer. Moreover, the test netted better sensitivity than a fecal immunochemical test (FIT), a circulating tumor DNA (ctDNA) test, and a carcinoembryonic antigen (CEA) test.

These findings were reported in a poster session at the 2020 GI Cancers Symposium, which is sponsored by the American Gastroenterological Association, American Society of Clinical Oncology, American Society for Radiation Oncology, and Society of Surgical Oncology.

“Today, about a third of age-appropriate adults are not up to date with colorectal cancer screening,” lead study investigator Girish Putcha, MD, PhD, chief medical officer of Freenome in San Francisco, noted at the symposium. “A noninvasive blood-based screening test having high sensitivity and specificity for colorectal cancer generally, but especially for early-stage disease, could help improve adherence and ultimately reduce mortality.”

Dr. Putcha and colleagues evaluated a blood-based multiomics test in 32 patients with colorectal cancer of all stages and 539 colonoscopy-confirmed negative control subjects.

The test uses a multiomics platform to pick up both tumor-derived signal and non–tumor-derived signal from the body’s immune response and other sources. The test uses machine learning, and entails whole-genome sequencing, bisulfite sequencing (for assessment of DNA methylation), and protein quantification methods.

At 94% specificity, the test had a 94% sensitivity for spotting stage I and II colorectal cancer, 91% sensitivity for stage III and IV colorectal cancer, and 91% sensitivity for colorectal cancer of any stage. By location, sensitivity was 92% for distal tumors and 88% for proximal tumors.

The multiomics test outperformed a ctDNA test, a CEA test, and a FIT. At a specificity of 96% for both tests, the multiomics test yielded a higher sensitivity than a commercially available FIT stool test (OC-Auto FIT, Polymedco) for stage I and II disease (100% vs. 70%), stage III and IV disease (100% vs. 50%), and any-stage disease (100% vs. 67%).

When set at 100% specificity, the multiomics test outperformed a commercially available plasma ctDNA test (Avenio, Roche) set at 75% specificity. The multiomics test yielded a higher sensitivity for stage I and II disease (94% vs. 38%), stage III and IV disease (91% vs. 55%), and any-stage disease (90% vs. 47%).

At a specificity of 94% for both tests, the multiomics test yielded a higher sensitivity than plasma CEA level for stage I and II disease (94% vs. 18%), stage III and IV disease (91% vs. 45%), and any-stage disease (91% vs. 31%).

“Although there were many exciting aspects to this study, the test’s ability to detect cancers without loss of sensitivity for early-stage cancers was striking to me,” said Michael J. Hall, MD, of Fox Chase Cancer Center in Philadelphia, who was not involved in this study. “The loss of sensitivity in early tumors has been a limitation of other tests – FOBT [fecal occult blood test], FIT – so if this is replicable, this is exciting.”

Dr. Hall added that the need for only a blood sample would be a plus in screening healthy people. “When we consider the discomfort and inconvenience of colonoscopy, mammogram, and prostate cancer screening, and how they lead to reduced uptake of screening, the attractiveness of a noninvasive blood-based screening only increases further,” he elaborated.

Although the study was small for a colorectal cancer screening assessment, “the preliminary results presented in the poster were certainly compelling enough to support more research,” Dr. Hall said.

Dr. Putcha said that the test will be validated in a prospective, multicenter trial of roughly 10,000 participants at average risk, expected to open later this year. Further research will also help assess the test’s performance among patients with inflammatory bowel disease, for whom false-positive results with some available screening tests have been problematic.

The current study was sponsored by Freenome. Dr. Putcha is employed by Freenome and has a relationship with Palmetto GBA. Dr. Hall disclosed relationships with Ambry Genetics, AstraZeneca, Caris Life Sciences, Foundation Medicine, Invitae, and Myriad Genetics, and he shares a patent with institutional colleagues for a novel method to investigate hereditary colorectal cancer genes.

*This story was updated on Feb. 4, 2020.

SOURCE: Putcha G et al. 2020 GI Cancers Symposium, Abstract 66.

Next Article: