Introduction 

2023 continued to see advancements in methylation technology. This year saw a dynamic mix of established entities and emerging innovators in the field, marking their presence with novel product launches, securing regulatory approvals, and driving robust research initiatives. These efforts collectively strengthened the evidence for the role of methylation as a potential biomarker and diagnostic tool for cancer. This summary highlights some significant contributions and milestones achieved by key players in the methylation domain, underscoring the technology's growing impact in diagnostics.

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Figure 1. Timeline of Select Events in 2023

To interact, hover over an event “dot” to see the company name, event title, date and a link to the corresponding press release

Key Takeaways

• Products: The year witnessed a surge in methylation product launches, with nine companies unveiling offerings, signifying an increase from the previous year. These innovations predominantly encompassed Next-Generation Sequencing (NGS)-based methylation methods, followed by Polymerase Chain Reaction (PCR)-based methods.
• Research: Research efforts remained robust, retaining its status as the category with the most activity from the year prior; numerous companies presented pivotal study results, further validating both existing and prospective methylation technologies
• Approvals: The FDA granted approvals to four companies for their methylation-based products, indicating a growing recognition of the technology’s clinical relevance
• M&As: Three key mergers and acquisitions occurred this year including Agilent’s acquisition of Avida Biomed, Freenome’s acquisition of Oncimmune, and Genetron Health’s merger with their parent company to become private
• Partnerships: Twelve companies announced strategic partnerships, spanning clinical applications to validation studies, underlining the sector's collaborative nature
• Funding: Precede, EarlyDx, Previse, and Adela all secured funding this past year

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Trends

We continue to see an effort to move away from bisulfite conversion. Notably, Pentabase developed EpiDirect, a method for the direct analysis of DNA methylation, that does not require pretreatment of DNA. PentaBase has commercialized this approach into their EpiDirect MGMT assay which detects and quantifies methylation in the MGMT region of brain tumor samples. 

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Additionally, methylation continues to expand outside of cancer, with developments in cardiology, neurology, and aging. On the cardiology front, CardioDiagnostics launching another epigenetic-informed product, PrecisionCHD, for early detection of Coronary Heart Disease is another step towards the increased clinical presence of methylation in the space. imited diagnostic strides were made in aging, but firms in the arena continued to lay the groundwork for future commercial development, including partnerships from longevity company, Gero, which uses methylation signatures to explore the idea of biological age. The use of methylation analysis in neurology continues to be developed primarily in a research context with limited commercial assays. Of note, Pentabase is leveraging their bisulfite free qPCR-based methylation analysis in their EpiDirect MGMT assay, designed for assessing the MGMT region of brain tumors. 

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The methylation space also saw some significant legal strife this past year with the acquisition of GRAIL by Illumina challenged in both the U.S. and Europe. As of early 2024, Illumina has announced that they will divest GRAIL after facing mounting pressure. This blockbuster legal battle highlighted some of the challenging market dynamics that come from balancing both innovation and competition in diagnostics. 

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Key Product Developments

Biomodal (formerly Cambridge Epigenetix) commercially launched their “duet multiomics” solution, designed to simultaneously sequence both genetics and epigenetics in a single workflow. The single-base resolution sequencing technology leverages liquid biopsy of cell-free DNA, and is compatible with any sequencer. 

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Previse (formerly Capsulomics) launched Esopredict which delivers risk predictions over a 5-year horizon, identifying alterations in DNA methylation levels across four genes by using a sample of Barrett’s esophagus cells. Esopredict provides a result report termed Esoscore which informs the future risk of developing esophageal cancer in patients with Barret’s esophagus. 

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Predicine announced their PredicineALERT MRD assay at AACR 2023. PredicineALERT leverages methylation profiling of cell-free DNA for tumor-naive detection of MRD. 

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Cardio Diagnostics launched PrecisionCHD, an epigenetic-genetic blood test for the early detection of coronary heart disease. PrecisionCHD is the second clinical test leveraging the firm’s AI-driven Integrated Epigenetic-Genetic Engine, following the Epi+Gen CHD risk assessment test which was launched in 2021. 

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Lucid Diagnostics laboratory, LucidDX Labs, launched the second installment of their EsoGuard esophageal DNA test, EsoGuard 2.0. The second generation of EsoGuard promises enhanced assay performance, DNA yield, and lower associated costs. 

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Eone-Diagnomics Genome Center (EDGC) announced in September 2023 that they are on the cusp of launching their OncoCatch-E test. The blood-based next generation multi-cancer early detection test is set to detect colorectal, lung, breast, and gastric cancers in its launch year with hopes to expand screening to include 10 cancer types and potentially non-cancer applications such as Alzheimers. The test identifies the presence and source of cancer through an algorithm-driven analysis of methylation patterns across 65,000 sites in circulating tumor DNA. 

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HKG Epitherapeutics has developed epiCervix, an epigenetic biomarker-based test to screen patients for cervical cancer. epiCervix uses next-generation sequencing to screen for changes in methylation patterns across four cancer-associated genes. 

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Vesica Health announced that they are preparing to relaunch AssureDx, the bladder cancer detection test initially created by MDxHealth. The test is designed to aid in decision making for patients with hematuria, or blood in the urine. The startup licensed the AssureDx assay from MDxHealth which had largely stalled the assay to focus on its prostate cancer portfolio. 

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PentaBase has developed a qPCR-based method, EpiDirect, for the direct analysis of DNA methylation without pre-treatment of DNA. The company is commercializing their technology into their EpiDirect MGMT assay to assess 5-methylcytosine (5mC) levels in the MGMT region of brain tumor samples. 

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Research

There were a significant number of presentations and research publications in the past year with much of the research remaining focused on early cancer detection as well as MRD. Five companies announced pivotal or final results of studies that could lead to further product approvals and advancements in the methylation analysis space. However, research strides were made across the board with 20 companies publishing or presenting research this past year. 

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CellMax Life announced results at ASCO for their FirstSight blood test which demonstrated 92% overall sensitivity for colorectal cancer, and a regional (stages I-III) sensitivity of 89%. The results also indicated advanced adenomas (AA) were detected with a 53% sensitivity at 91% specificity, increasing to 66% for adenomas with high-grade dysplasia and 69% for large adenomas ≥3cm in size.

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Universal DX presented data from their 1,000-patient multi-cohort study which indicated 93% sensitivity for colorectal cancer (stages I and II), and 54% specificity for advanced adenoma at 92% specificity.

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Exact Sciences presented new long-term patient outcomes in MCED breast cancer recurrence. Long-term analyses from the Detecting Cancers Earlier Through Elective mutation-based blood Collection and Testing (DETECT-A) study showed that all patients diagnosed and treated for Stage I or II cancers remained cancer-free over four years later. This was the first large, prospective, interventional study to screen for multiple cancers with a blood-based MCED test. Additionally, Exact presented results from their BLUE-C study which showed that Cologuard demonstrated 94% overall sensitivity for colorectal cancer at 91% specificity, and 93% sensitivity for stages I-III. BLUE-C demonstrated an improvement on DeeP-C, the FDA registrational trial for Cologuard, including a 30 percent lower false positive rate.

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GRAIL announced further final results of their MCED PATHFINDER study. In the study, the Galleri test identified a cancer signal in 1.4% of participants, 38% of whom were diagnosed with cancer (true positives). GRAIL also presented validation data on a novel prognostic test in stage 1 lung cancer. The study leveraged a plasma-based targeted methylation assay which demonstrated an analytical specificity of 96.9% and 100% accuracy to detect a signal at ctDNA input of 2ng. 

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Guardant Health presented additional information from their ECLIPSE study which showed that the Shield test achieved overall sensitivity of 83% and 90% specificity in colorectal cancer, including 55% sensitivity at stage I and 100% sensitivity at stages II-IV. Guardant also shared first results from their PEGASUS trial, one of the first prospective studies to employ liquid biopsy. Initial results indicated that 34% of patients with a positive liquid biopsy result following surgery had their cancer return, while only 10% of patients with a negative result experienced a return of cancer. 

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Additionally, Guardant provided an update on their COBRA study which aimed to evaluate the efficacy of using MRD testing in patients with stage II colon cancer following surgery with a planned final readout of the study set for 2026. However, in early 2024, they announced the study had halted due to not meeting its endpoints. It was found that the use of chemotherapy did not increase the rate of ctDNA clearance among patients who had detectable ctDNA after surgery compared with patients who did not receive chemotherapy. The research remains to be presented at ASCO 2024. 

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Key Approvals

Nucleix’s Bladder EpiCheck received FDA 501(k) clearance for monitoringNon-Muscle Invasive Bladder Cancer (NMIBC) Recurrence

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China-based BurningRock received FDA Breakthrough Device Designation for its OverC Multi-Cancer Detection Blood test in early 2023.

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Promis Diagnostics’ EarlyText BCD received FDA Breakthrough Device Designation for Bladder cancer detection. 

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Singlera’s liquid biopsy (LBx) assay also received FDA Breakthrough Device Designation.

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Conclusion

2023 was a testament to the burgeoning potential and diverse applications of methylation in diagnostics. The industry's trajectory, marked by innovative products, strategic growth, and impactful research, sets a promising course for the future of methylation-based diagnostics.With multiple new products and a torrent of research developments in 2023, the space is rife with progress and innovation, even in a year that was largely uncertain for novel tool and technology development at large. Looking ahead, we anticipate further milestones and developments and look forward to our continued tracking of methylation and the discussions it brings.