Kunyu Biosciences Unveils a New Paradigm in MRD Detection with Cost-Effective, PCR-Based ctDNA Methylation Assay for Colorectal Cancer
There Seems to Be a Missing Pivot Between the Ideal and Reality of MRD Testing.
MRD Testing Opens a New Window for Cancer Patients. Clinically, small tumor lesions with a diameter of less than 1 millimeter are often difficult to detect through imaging examinations, posing a hidden risk of recurrence and metastasis. MRD testing has gained significant attention in recent years; it can identify molecular-level minimal residual disease, enabling the early identification—months or even years in advance—of the risk of tumor recurrence and metastasis, and is thus held in high expectation.
However, detecting tumor signals present in extremely low abundance within the molecular landscape poses significant challenges. The inevitable trade-off between efficiency and efficacy made by developers has left minimal residual disease (MRD) testing somewhat underutilized in clinical practice. In late April, Singlera GENOMICS released clinical study results that diverged from mainstream next-generation sequencing (NGS) platforms, instead pioneering an alternative approach to validate a high-efficiency, low-cost MRD detection solution.
As the debut of this leading cancer early-screening enterprise in the field of MRD detection, Singlera GENOMICS has applied its expertise in ctDNA methylation technology to the detection of minimal residual disease (MRD) in colorectal cancer—a path less traveled. Zhang Jiangli, Co-founder and CEO of Singlera GENOMICS, told VCBeat that the study spanned two years and enrolled over 300 patients. Using multiplex PCR-based ctDNA methylation technology, Singlera GENOMICS detected tumor recurrence and metastasis up to 20 months earlier than medical imaging.
Back in March 2021, Chang Aike®In the most critical pre-market clinical study, all data collection has been completed, and the initial hypotheses are being gradually validated. However, Dr. Liu Rui, Co-founder and CTO of Singlera GENOMICS, who led this study, remains on edge, as she is closely monitoring the results of another set of data for 39 of the patients.
Over the past three years, the Singlera GENOMICS team led by Dr. Liu Rui has extensively collected blood samples from high-risk populations in major colorectal cancer-endemic regions across China, including Jiangsu and Zhejiang, South China, and North China. At that time, screening for early-stage colorectal cancer using ctDNA methylation technology was gaining popularity. As one of the first teams in China to translate ctDNA methylation technology into clinical applications, Singlera GENOMICS developed ColonAiQ®Technology, demonstrating robust capability in capturing early signals of colorectal cancer.
Dr. Liu Rui, with a medical background, has dedicated years to advancing ctDNA methylation technology and fully understands the difficulty of interpreting extremely faint tumor signals from complex noisy data; therefore, when ColonAiQ®The technology demonstrated a sufficiently low limit of detection in early-stage colorectal cancer screening, prompting her to immediately consider the potential of applying ctDNA methylation technology for minimal residual disease (MRD) detection in colorectal cancer. The post-operative tumor market addressed by the latter represents a significantly larger unmet clinical need.
MRD, or minimal residual disease/molecular residual disease, is generally considered to be highly associated with tumor recurrence. Numerous observational studies both in China and abroad have demonstrated that if MRD is not spontaneously cleared or eliminated by the host’s immune mechanisms, but instead continues to proliferate, there is a very high probability of tumor recurrence after curative surgery.
MRD circulates freely in the bloodstream, existing in a form undetectable by the naked eye. Some recurrent or metastatic tumors that are difficult to interpret through conventional imaging examinations may be captured by MRD testing, enabling earlier detection of disease progression. Clinically, MRD monitoring was first applied to the surveillance of relapse in hematologic malignancies. In September 2018, the FDA approved ClonoSEQ Assay, the world’s first MRD detection product based on next-generation sequencing (NGS) technology, for detecting MRD in acute lymphoblastic leukemia (ALL) and multiple myeloma. It is also the first MRD test covered by insurance reimbursement systems, achieving rapid clinical adoption.
In recent years, researchers have been continuously attempting to apply minimal residual disease (MRD) detection in the clinical diagnosis and treatment of solid tumors. Currently, data from multiple observational clinical studies worldwide have been released, validating that among patients with various cancers—including breast cancer, esophageal cancer, gastric cancer, pancreatic cancer, lung cancer, bladder cancer, and colorectal cancer—who have undergone curative-intent treatment, those who are MRD-positive have a significantly higher risk of recurrence than those who are MRD-negative. Furthermore, if a patient’s MRD status remains positive after adjuvant chemotherapy, they are considered to be at high risk for recurrence.
For a long time after market launch, mainstream MRD testing could only be performed using high-throughput NGS platforms. Due to the complex procedures and lengthy turnaround times, most MRD testing was confined to top-tier hospitals with the strongest clinical diagnostic and therapeutic capabilities. In extreme cases, patients might miss critical testing windows because precise detection protocols involve protracted initialization processes such as whole-genome sequencing of tissue samples, blood validation, and locus screening, thereby significantly diminishing the clinical value of MRD testing.
New clinical studies are on the horizon. If ColonAiQ can be directly used®The detection of MRD through multiplex PCR using a fixed combination of genetic loci undoubtedly represents a significant step forward in the precise diagnosis and treatment of cancer. However, this near-ideal approach has no precedent to follow. Once clinical research on MRD testing is initiated, the follow-up period will be at least 18 months, making the R&D risks self-evident.
Thus, during the early stages of technology development, Dr. Liu Rui specifically collected matched preoperative and postoperative blood samples from 39 colorectal cancer patients to test ColonAiQ.®In addition to its application in early diagnosis of colorectal cancer, the technology has been expanded for clinical use. Further experimental results from 39 participants validated Dr. Liu Rui’s initial hypothesis; among them, seven patients unfortunately experienced postoperative recurrence, and six of these individuals had their postoperative blood samples analyzed using ColonAiQ.®Platform testing showed positive ctDNA methylation, while postoperative blood samples from other individuals did not detect levels exceeding the ColonAiQ threshold.®ctDNA methylation signals at the platform threshold. In other words, ColonAiQ®The technology enables risk stratification for recurrence in patients with colorectal cancer.
This result greatly excited Dr. Liu Rui, as it may bring a disruptive new approach to MRD detection. She promptly engaged the clinical expert team collaborating with Singlera GENOMICS to design a larger-scale study on colorectal cancer MRD using PCR-based blood ctDNA methylation detection. Professors Cai Guoxiang and Wang Zheng, among others in the clinical expert team, are leading authorities in the field of colorectal cancer in China. They have long collaborated with Singlera GENOMICS on clinical studies of ctDNA methylation detection and are highly familiar with ColonAiQ.®In terms of technical performance, there is also a desire for more practical MRD detection methods to be used in clinical practice. New clinical studies were quickly initiated, enrolling over 300 patients with colorectal cancer and beginning a two-year follow-up period.
In April 2023, the findings of this study were published in JAMA Oncology. The study enrolled 299 patients with stage I–III colorectal cancer who underwent curative-intent surgery. Blood samples were collected one week before surgery, one month after surgery, and at each follow-up point during postoperative adjuvant therapy, using ColonAiQ®Conduct dynamic blood-based ctDNA testing. Studies have found that ctDNA testing can early predict the recurrence risk in colorectal cancer patients, whether preoperatively or in the early postoperative period. Integrating ctDNA with clinical features holds promise for further optimizing risk stratification and improving recurrence prediction.
This is the world’s first study on PCR-based ctDNA methylation MRD detection, which identified tumor recurrence up to approximately 20 months earlier than conventional imaging examinations. Commenting on the results of this exploratory study, Dr. Liu Rui described them as “very fortunate,” noting that they provide a critical foundation for future clinical trials. Zhang Jiangli also stated that there is still a long way to go before MRD testing is widely adopted in clinical practice, with each step requiring robust clinical data support. “However, it is predictable that within the next 2–3 years, research on ctDNA methylation-based MRD detection may flourish across multiple fronts.”
Among various solid tumors, research on minimal residual disease (MRD) in colorectal cancer has been at the forefront. “Colorectal cancer is a typical example, as its genomic characteristics are strongly associated with the onset and progression of the disease,” explained Dr. Liu Rui. “In this sense, developing MRD detection products for colorectal cancer holds significant clinical value.” In the aforementioned study published in JAMA Oncology, Singlera GENOMICS found that one month after radical resection, colorectal cancer patients who were ctDNA-positive had a 17.5-fold higher risk of recurrence compared to those who were ctDNA-negative.
Meanwhile, a wealth of clinical research data has emerged, propelling MRD testing into the spotlight as a key update in clinical guidelines for various solid tumors. Clinical guidelines for colorectal cancer in the United States, Europe, and other regions have increasingly incorporated MRD testing into their considerations, with the European Society for Medical Oncology (ESMO) having developed detailed clinical recommendations for MRD testing procedures.
In China, the 2022 CSCO Clinical Guidelines for Colorectal Cancer explicitly noted that studies had shown dynamic ctDNA monitoring helps provide early warning of postoperative recurrence and metastasis. However, due to a lack of relevant interventional clinical trial data, the guidelines at that time emphasized that there was still controversy over whether dynamic ctDNA monitoring should be routinely used in postoperative follow-up to guide treatment. In April 2023, the CSCO Clinical Guidelines for Colorectal Cancer were updated, further clarifying and expanding the clinical value of MRD. During this period, an interventional clinical study on MRD conducted in Australia yielded key data. Based on these findings, the latest guidelines state that ctDNA testing plays an important role in predicting recurrence risk, assessing minimal residual disease, thereby providing earlier indication of tumor recurrence, and enabling precise risk stratification for stage II colon cancer patients to guide chemotherapy application.
"Clinically, since the recurrence rate for patients with stage I and stage IIa colorectal cancer is only 5%–10%, clinicians often do not arrange adjuvant chemotherapy for these patients after surgery. 'We found that even among the clinically low-risk population with stage I and stage IIa disease, there are a small number of MRD-positive patients, two-thirds of whom experienced tumor recurrence within two years,' Dr. Liu Rui told VCBeat. 'These patients may be unique, with different levels of tumor invasiveness or residual disease. Although current MRD test results cannot yet influence routine diagnosis, they may help clinicians take a more comprehensive view of the patient’s condition and adjust treatment plans in a timely manner.'"
Furthermore, in the clinical management of patients with intermediate- to advanced-stage cancer, overtreatment and undertreatment often coexist. This is because devising chemotherapy regimens tailored to individual patients is a complex endeavor that requires clinicians to make comprehensive judgments based on their diagnostic and therapeutic experience, taking into account the patient’s specific disease status and tolerance. Appropriate minimal residual disease (MRD) testing undoubtedly provides clinicians with an additional dimension of information to support decision-making.
In PCR-based studies of ctDNA methylation for minimal residual disease (MRD) detection in colorectal cancer, the research team stratified patients with stage III colorectal cancer into different subgroups based on clinical recurrence risk assessment [high-risk (T4/N2) and low-risk (T1-3N1)] and adjuvant therapy duration (3 vs. 6 months). The analysis revealed that among high-risk subgroup patients who were ctDNA-positive, those receiving six months of adjuvant therapy had a lower recurrence rate. In contrast, among low-risk subgroup patients who were ctDNA-positive, there was no significant difference in therapeutic efficacy between different durations of adjuvant therapy. Furthermore, ctDNA-negative patients demonstrated significantly better prognosis and longer recurrence-free survival (RFS) compared to ctDNA-positive patients.
In this sense, the integrated application of ctDNA with clinical features holds promise for further optimizing risk stratification and improving recurrence prediction.
“Of course, as a brand-new biotechnology, MRD testing is still in its early stages of development. ‘At the current stage, relying solely on MRD test results to guide clinical treatment carries significant risks,’ pointed out Dr. Liu Rui.” To evolve from an innovative biotechnology into a mature clinical tool, MRD testing must navigate multiple stages, including proof of concept (such as large-scale multicenter validation and randomized controlled trials [RCTs]), regulatory review, and market education.
First is proof of concept.From the laboratory to the clinic, MRD testing must undergo two major phases of clinical research: observational studies and interventional studies. First, extensive observational studies are conducted to clarify the association between MRD indicators defined by specific detection methods and tumor control and progression status. Subsequently, complex interventional studies are employed to validate the clinical value of MRD testing as a diagnostic tool. At present, most clinical studies on MRD testing remain in the observational phase. Interventional studies, however, face higher thresholds due to clinical ethical considerations, requiring more systematic trial designs and execution within larger organizational frameworks. Such clinical studies are just beginning to emerge worldwide.
Zhang Jiangli stated that, based on early clinical study results, Singlera GENOMICS has already begun to promote larger-scale clinical studies of MRD testing. “This is a process that requires close communication with clinical experts and continuous optimization of research and product strategies based on clinical feedback. However, we will continue to intensify our exploration efforts to test and validate the clinical value of ctDNA methylation in more diverse application scenarios.”
Next is the regulatory review of MRD testing.From a product compliance perspective, the commercialization of MRD testing is still in its early stages, whether through an IVD business model or by providing LDT services in independent clinical laboratories, with many implementation details still under exploration. “It will take at least three to five years for the MRD testing commercialization ecosystem to mature,” Zhang Jiangli told VCBeat. At present, consistent standards have not yet been established for many aspects of regulatory oversight of MRD testing products. Promoting this innovative technology for widespread clinical application requires ongoing communication and consensus-building between developers and regulators. Underpinning this process, the accumulation of application data and real-world evidence are key factors.
Finally, there is market education for MRD testing, which is also the most uncertain aspect.How can this innovative technology be integrated into clinical diagnosis and treatment workflows? What should be the defined target population? How can clinicians at all levels develop an accurate understanding of the clinical value of MRD testing? How can patient adherence be improved and accessibility optimized? Finding optimal solutions to these questions is a critical foundation for the widespread adoption of MRD testing in clinical practice, yet it poses a significant test of developers’ comprehensive product capabilities. Zhang Jiangli has given deep consideration to these issues.
He told VCBeat that Singlera GENOMICS aims to provide cost-effective MRD testing for a broad patient population, helping them efficiently address most issues throughout the entire cancer treatment journey. “Based on current clinical research data, clinical treatment for patients with Stage I–III colorectal cancer may all benefit from ColonAiQ®“With the technological benefits, we hope that most of them can access this technology as soon as possible.” In Zhang Jiangli’s view, the clinical application of MRD testing is a progressive process that unfolds from superficial to deep levels. Addressing the majority of issues faced by most patients—such as recurrence risk stratification, guidance in formulating adjuvant chemotherapy regimens, and dynamic tumor monitoring—is the solid groundwork that needs to be laid at the current stage.
In this process, the multiplex PCR platform selected by Singlera GENOMICS offers greater cost-effectiveness compared to the NGS platforms currently mainstream in MRD detection, making it a more universally applicable technological platform for clinical use. For MRD detection challenges that cannot be addressed by universal solutions, specialized cases are handled by concentrating more advanced technical resources.
Over the past three years, the large-scale demand for COVID-19 nucleic acid testing has accelerated the rapid maturation of molecular diagnostics in China. The widespread availability of PCR testing equipment across hospitals at all levels, coupled with clinical staff proficient in PCR techniques, has undoubtedly laid a solid foundation for the in-hospital implementation of ctDNA methylation-based MRD detection using multiplex PCR technology. Furthermore, in recent years, methylation detection technologies have been included in the medical service pricing catalogs in an increasing number of cities. In cities such as Shanghai and Guangzhou, these tests are even being gradually covered by medical insurance, thereby creating opportunities to expand reimbursement channels for this innovative diagnostic approach.
According to Zhang Jiangli’s plan, Singlera GENOMICS’ ctDNA methylation-based MRD test for colorectal cancer is slated for gradual commercialization following the completion of additional clinical validations. How it will reshape the market landscape for MRD testing remains to be seen over time. Nevertheless, we anticipate that this more efficient new technology will effectively help more cancer patients identify precise treatment regimens.