We Comment on Coverage of Colorectal Cancer Non-Invasive Biomarker Screening Tests

Policy, Testimony & Briefings

October 10, 2025

Re: National Coverage Analysis (CAG-00440R)
Request for Public Comment on Coverage of Colorectal Cancer Non-Invasive Biomarker Screening Tests

The National Center for Health Research (NCHR) appreciates the opportunity to provide comments in response to the Centers for Medicare & Medicaid Services (CMS) request for input on the coverage of colorectal cancer (CRC) non-invasive biomarker screening tests, including multi-target stool RNA (mt-sRNA) assays, and on the review of sensitivity and specificity cut points.

NCHR is a nonprofit think tank committed to bridging the gap between scientific evidence and public policy with the goal of improving the health and safety of patients and consumers. Our mission is to ensure that medical products and technologies are not sold in the U.S. unless they are proven safe and effective based on rigorous, independent evidence, with particular attention to how benefits and risks differ across diverse patient populations, including older adults who make up the majority of Medicare beneficiaries.

We recognize the need for more convenient CRC screening. However, FDA approval of the multi-target stool RNA (mt-sRNA) screening test ColoSense does not in itself establish clinical effectiveness in Medicare populations. The FDA’s Summary of Safety and Effectiveness Data (P230001) for ColoSense noted uncertainty regarding the test’s sensitivity, requiring a post-market study of 12,500 participants to confirm accuracy. We agree on the need for such a study, but it should be completed and analyzed prior to Medicare making a coverage decision. We describe the research evidence and shortcomings below.

Background and Context

ColoSense, the multi-target stool RNA (mt-sRNA) test, was assessed in the pivotal CRC-PREVENT trial (Barnell et al., 2023) of 8,289 participants, demonstrating analytical validity and 94% sensitivity for colorectal cancer (CRC). However, the FDA’s Summary of Safety and Effectiveness Data (SSED; PMA P230001) identified several limitations in the study design and performance interpretation. According to the SSED, “there is a chance that as many as 24.3% of patients with colorectal cancer may be missed by this test” based on the lower bound of the 95% confidence interval. The FDA therefore required Geneoscopy to conduct a post-approval study of 12,500 participants to confirm real-world sensitivity and specificity. The protocol for this post-market study was originally accepted on May 3, 2024, and the current protocol was accepted on September 9, 2024, but the study appears to have not begun according to fda.gov and there is no NCT registration number for the post-market study posted to ClinicalTrials.gov. 

 

This lack of an active or publicly registered required post-approval study raises substantial concerns about transparency, regulatory compliance, and readiness for coverage in the Medicare population. A study of 12,500 patients followed for 2 years will take years to complete, and yet the company hasn’t even started the research yet. Without post-market validation data, CMS cannot reasonably determine whether ColoSense performs as well as existing CMS-covered tests such as Colorguard, the multi-target stool DNA test.

 

Furthermore, ColoSense’s existing data reported a specificity of 85.6%, which is substantially lower than that of Cologuard Plus (91%), suggesting it would result in an increased false-positive burden and downstream colonoscopy demand (Exact Sciences, 2025). These unresolved issues reinforce the need for the FDA’s required post-market study to be appropriately completed before any national coverage determination is made.

 

The Role of Stool-Based RNA Colorectal Cancer Screening Tests

Stool-based RNA colorectal cancer screening tests expand early-detection options beyond colonoscopy and traditional fecal tests. These assays analyze RNA biomarkers shed by cancer cells into stool, identifying colorectal cancers and precancerous lesions through simple at-home sample collection (Barnell et al., 2023; Barnell et al., 2025).

Unlike other stool-based tests, the mt-sRNA test, ColoSense, eliminates the need for patients to swab or scrape their stool. Instead, the patient deposits a sample into a container and mails it to a lab for technician-handled analysis (Barnell 2025). This could potentially increase adherence among patients who are uncomfortable with other stool-based tests and unwilling or unable to undergo colonoscopy. 

However, the potential for increased adherence is valuable only if verified with real-world data.

Sensitivity and Specificity of Current Non-Invasive CRC Screening Tests

There are several FDA-approved stool-based CRC screening tests that are covered by Medicare.  The goal of stool-based CRC screening tests is to be non-invasive and more convenient than colonoscopies, with the understanding that positive results will require additional testing with a colonoscopy.  They therefore must balance high sensitivity to detect early cancers and advanced adenomas, as well as adequate specificity to prevent unnecessary colonoscopies and associated risks.

The fecal immunochemical test (FIT) is the most widely used stool-based screening tool. It detects hidden (occult) blood in stool by identifying human hemoglobin proteins using specific antibodies. FIT is simple, inexpensive, and can be done annually at home. However, while it is highly specific (~94%), its sensitivity for early cancers (~74%) and advanced adenomas (~23%) is lower than that of multi-target molecular stool tests, leading to more missed precancerous lesions (Imperiale et al., 2014; Lin et al., 2016; Knudsen et al., 2021; US Preventive Services Task Force (JAMA 2021).

The currently approved multi-target stool DNA (mt-sDNA) test, marketed as Cologuard, combines molecular DNA markers with a fecal immunochemical test (FIT) to detect occult blood and DNA mutations associated with colorectal cancer (CRC) and advanced adenomas. In the DeeP-C trial (Imperiale et al., 2014), Cologuard achieved 92.3% sensitivity for CRC, 42.4% for advanced adenomas, and 86.6–89.8% specificity, outperforming FIT alone (73.8% CRC sensitivity, 23.8% advanced adenoma sensitivity, 94% specificity) (Eckmann et al., 2020).

In contrast, ColoSense, a multi-target stool RNA (mt-sRNA) test, uses RNA rather than DNA biomarkers. However, the ColoSense test is not based solely on RNA biomarkers; it combines three components, which are a fecal immunochemical test (FIT) that detects hidden blood in stool, a panel of RNA transcripts shed by tumor or precancerous cells, and a patient factor (smoking status) to generate an overall test score. This means that the mt-sRNA assay, ColoSense, builds upon, rather than replaces, the traditional FIT methodology. However, the FDA’s performance audit identified several limitations in the CRC-PREVENT trial of ColoSense, so the agency required a post-market study to provide real-world accuracy and safety (FDA, 2023; P230001C). 

It is important to note that when the RNA portion of the ColoSense test was analyzed separately, it performed only slightly better than random chance with an Area Under the Receiver Operating Characteristic (AUROC) value of 0.58–0.62 (An AUROC of 0.5 indicates no diagnostic value, while 1.0 indicates perfect accuracy.). This indicates that most of the test’s diagnostic power likely comes from the FIT component rather than the RNA markers themselves. This raises clear questions about the added clinical value of the RNA component and reinforces the importance of continued evidence development before granting full Medicare coverage (Barnell et al., JAMA 2023; Supplement 3, eFigure 3). 

Taken together, these data indicate that while ColoSense is promising, it has not demonstrated that it as effective or superior to the existing CMS-covered mt-sDNA (Cologuard) or FIT tests. 

Patient-Centered Considerations

Expanding coverage for non-invasive colorectal cancer screening options has been found to improve participation among older adults and those with comorbidities who face challenges with colonoscopy preparation, sedation, or access to endoscopy facilities (Cooper et al., 2013; Lin, 2014; Kwok et al., 2023). These at-home stool tests, including the fecal immunochemical test (FIT), multi-target stool DNA (mt-sDNA; Cologuard), and multi-target stool RNA (mt-sRNA; ColoSense) can reduce logistical and procedural barriers to screening. For rural, minority, and socioeconomically disadvantaged populations, mail-based stool tests may help overcome transportation and access barriers (Sepassi et al., 2024; CDC, 2025; Redwood et al., 2023). However, these tests complement, rather than replace colonoscopy, which remains the diagnostic gold standard for detecting and removing precancerous lesions.

Risks, Limitations, Concerns, and Data Gaps

  1. Disproportionate inclusion of smokers may bias the results.
    The ColoSense CRC-PREVENT trial incorporated smoking status as a variable in its composite scoring algorithm, alongside the fecal immunochemical test (FIT) and RNA biomarkers. The FDA’s Summary of Safety and Effectiveness Data (PMA P230001, 2024) reported that 34.3% of participants were classified as current or former smokers, a prevalence nearly three times higher than the U.S. adult current smoking rate average of approximately 12% (CDC, 2024). Because smoking is a known risk factor for colorectal neoplasia, this overrepresentation may have artificially inflated test sensitivity in a high-risk cohort. Moreover, the company does not explain why their study sample included so many smokers, and whether the study participants may not be representative of the general population or of the Medicare population in other ways as well. In addition, since smoking behavior was self-reported and some participants declined to disclose their status, the accuracy of this variable is uncertain and the proportion of smokers may have been even higher. 
  2. False positives increase the downstream burden of colonoscopy.
    While stool-based screening tests aim to reduce unnecessary colonoscopies, their value depends on whether they perform at least as well as existing noninvasive options. ColoSense (mt-sRNA) demonstrated a specificity of 85.6% in the CRC-PREVENT trial, lower than the FDA-approved and CMS-covered Cologuard (mt-sDNA) test, which achieved about 91% specificity and 92% sensitivity for colorectal cancer in the DeeP-C study (Imperiale et al., 2014). Since ColoSense (mt-sRNA) data do not indicate that this RNA-based approach is at least as accurate or that it meaningfully improves real-world adherence, it may not be as beneficial as the ColoGuard test. Moreover, higher false positives increase downstream colonoscopy burden, so any new stool test with more false positives must demonstrate substantial added value to justify coverage. 
  3. Trial performance may not reflect real-world Medicare outcomes.
    Adherence and follow-up rates observed in clinical trials are likely to be substantially higher than those seen in community or Medicare populations. Consequently, real world evidence of ColoSense compared to Cologuard would provide important information that is currently lacking. Continuous monitoring providing real world evidence of adherence, false-positive rates, and follow-up colonoscopy completion is essential to validate test performance.

For all the reasons specified in #1-3, the composite model’s performance may not reflect the accuracy of the test for a representative sample of patients of any age or health status, and certainly not those in the Medicare population. CMS should therefore interpret ColoSense’s published accuracy metrics with caution and require independent validation of the model without the smoking variable before considering coverage.

  1. FDA-Mandated post-approval study is pending; CMS should wait.
    The FDA mandated a post-approval study to confirm the safety and effectiveness of ColoSense, enrolling 12,500 participants to assess performance across diverse populations (FDA PMA P230001C, 2024). Although the protocol was accepted on September 9, 2024, the FDA database currently lists the study as “Study pending” with no posted study information and no NCT number assigned on clinicaltrials.gov. The reporting schedule on the FDA website notes that progress reports have been submitted on time, but no links or public summaries of these reports are available. At present, the only registered clinical trial related to ColoSense is the pivotal CRC-PREVENT study (NCT04739722).

This FDA requirement of a post-approval study for ColoSense and the lack of evidence that the company has started recruited patients adds to the concerns about ColoSense’s trial findings and limits CMS’s ability to assess its performance in Medicare-age populations to make an evidence-based coverage determination. Given ColoSense’s commercial availability, the timely initiation and completion of the required post-approval study may not be a high priority. A NCD could inadvertently reduce the incentive to generate the evidence necessary for regulatory and clinical validation. We strongly encourage CMS to refrain from granting coverage until the required post-market data are available and reviewed by the FDA and/or CMS.

Recommendations

  1. Deferred Coverage Decision Pending Completion of FDA-Mandated Post-Approval Study

Based on results and concerns about the current research and the lack of any useful information about the required post-market study, CMS should not grant coverage for ColoSense, the only multi-target stool RNA (mt-sRNA) test on the market, at this time. As noted above, the FDA mandated a post-approval study enrolling 12,500 participants to confirm the accuracy, safety, and effectiveness of ColoSense (FDA PMA P230001C, 2024). Although the protocol was accepted on September 9, 2024, the FDA database currently lists the study as “pending,” with no NCT registration number and no publicly available results or progress reports. Without completion and publication of this required post-market study, there is insufficient evidence to determine whether ColoSense is as beneficial to Medicare patients as currently covered non-invasive screening options. CMS should therefore withhold national coverage until the FDA-mandated study has been completed on a representative sample and its findings peer-reviewed. This cautious approach ensures scientific integrity, regulatory consistency, and prudence before providing a national Medicare NCD “seal of approval” to a test whose effectiveness and specificity remain unproven outside a potentially biased pivotal trial due to its very large proportion of smokers.

  1. Performance Standards: Evidence-Based Benchmarks

Given that CMS already provides coverage for several convenient non-invasive stool-based tests, CMA should determine if future coverage for these or other stool-based CRC screening tests meet clear, evidence-based performance thresholds validated in Medicare-relevant populations. 

These thresholds should include:

  • CRC sensitivity: ≥ 90% preferred, ≥ 70% minimum (Imperiale et al., 2014; 2024; Barnell et al., 2023).
  • Advanced adenoma sensitivity: ≥ 40% minimum, ≥ 50–55% preferred.
  • Specificity: ≥ 85% minimum; ≥ 90% preferred.

However, analytical accuracy alone should not justify coverage. CMS should require demonstration of adherence, follow-up completion, and cancer detection stage shifts prior to any future coverage determination.

  1. Transparency and Post-Market Accountability

Prior to making a coverage determination, CMS should require Geneoscopy and other mt-sRNA screening test companies to make all FDA post-approval study protocols, enrollment progress, and data publicly available. Public dashboards or FDA-linked updates should include adherence rates, positivity rates, specificity, and follow-up colonoscopy completion, stratified by demographics. Such transparency will prevent premature coverage of unproven technologies and support equitable, evidence-based policy.

 

Conclusions 

While multi-target stool RNA (mt sRNA) testing represents a potentially useful approach to colorectal cancer screening, the current evidence is insufficient to support Medicare coverage at this time. The CRC PREVENT trial demonstrates analytical validity but lacks direct comparison with existing stool-based tests such as FIT or mt-sDNA, shows only marginal incremental value of RNA biomarkers beyond FIT, and includes population and methodological biases. Moreover, the FDA’s Summary of Safety and Effectiveness Data (P230001) acknowledges that the test (ColoSense) can miss up to 24 percent of colorectal cancers and mandated a post-approval study of 12,500 participants to confirm real world accuracy and safety. As of October 2025, this study has not been initiated, assigned a ClinicalTrials.gov (NCT) number, or publicly reported.

For Medicare coverage, new tests are reasonable and necessary if they either demonstrate significantly higher sensitivity, specificity, or adherence, or show that they are equally effective and more accessible than existing options. The current data for ColoSense show that the test may be less accurate, especially in a representative Medicare population, and there is no evidence that it meaningfully improves screening uptake.

Given these substantial evidence gaps, CMS should defer national coverage until the FDA mandated post-approval study is completed, independently verified, and vetted by FDA or CMS. Only when it is demonstrated to be at least as beneficial as the mt-sDNA test should CMS reconsider coverage. Taking this cautious, evidence driven approach will uphold CMS’s mission to ensure that coverage determinations are scientifically justified and protective of patient safety and public resources.

Respectfully submitted,
National Center for Health Research

Citations:

 

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