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New “Ultra-Mild” Sequencing Method Fixes Long-Standing Flaws in Cancer DNA Methylation Tests

Matthew — Wed, 12 Nov 2025 22:03:39 GMT

Re-engineered bisulfite chemistry overcomes decades-old limitations in methylation sequencing

Cambridge, MA - Traditional bisulfite sequencing damages DNA, while enzyme-based alternatives are inconsistent. A novel methylation analysis method, called UMBS-seq, was published this week in Nature Communications. UMBS-seq achieves both accuracy and gentleness, unlocking more reliable cancer biomarker detection. The method, which was initially developed by researchers at The University of Chicago, will be made commercially available to cancer diagnostic test developers by Ellis Bio early next year.

Ellis Bio and UChicago Announce Breakthrough Ultra-Mild Bisulfite Sequencing Technology

Matthew — Tue, 14 Oct 2025 13:09:03 GMT

CAMBRIDGE, Mass. —

Ellis Bio Inc., a genomics biotechnology company, announced the publication of a new bioRxiv preprint from the laboratory of its scientific founder, Professor Chuan He of The University of Chicago (UChicago)/Howard Hughes Medical Institute (HHMI), describes the Ultra-Mild Bisulfite Sequencing (UMBS) method. UMBS is the foundation of Ellis Bio’s SuperMethyl™ Max Bisulfite Conversion Kit, which provides highly accurate methylation detection while minimizing DNA damage.

Following the SuperMethyl™ Max kit’s early-access launch at the ADLM 2025 Conference, Ellis Bio is highlighting the scientific foundation of its technology and the upcoming joint poster with The University of Chicago at the American Society of Human Genetics (ASHG) conference in Boston. Concurrently, Professor He will also present at the Epigenetics Society International Conference in Chicago.

Breakthrough in Methylation Detection

UMBS represents a significant advance in DNA methylation detection. The new bisulfite formulation and protocol developed in Professor He’s laboratory provide an exceptionally gentle, enzyme-free cytosine conversion method that maintains DNA integrity.

In the bioRxiv preprint, the UChicago team demonstrates that UMBS consistently achieves 99.8% C-to-T conversion efficiency, outperforming both conventional bisulfite and enzymatic approaches. The method supports robust, high-fidelity detection of 5-methylcytosine (5mC) from challenging low-input clinical samples such as cell-free DNA (cfDNA) and FFPE-derived DNA, making UMBS ideal for applications in biomarker detection and epigenetic profiling research where sensitivity and DNA preservation are critical.

From Academic Discovery to Commercial Translation

Ellis Bio holds the exclusive global license to the UMBS technology from The University of Chicago and has integrated it into its SuperMethyl™ Max research-use-only bisulfite kit. The kit’s optimized UMBS chemistry provides enzymatic-level DNA preservation without the complexity of enzyme-based reactions. SuperMethyl™ Max boasts a simple two-to-three-hour workflow, up to six times fewer false positives, and high-yield performance across multiple sample types.

“UMBS is an excellent example of how fundamental chemical insight can simplify complex workflows while improving analytical performance,” said Diana West-Szymanski, Ellis Bio Operations Lead. “We are proud to translate this innovation from Professor He’s laboratory into a reliable and accessible research tool.”

Joint Presentation and Future Outlook

At ASHG 2025, authors from Professor He’s research group and Ellis Bio will present a joint poster (#4037T) featuring UMBS technology and performance data. Ellis Bio will also exhibit at booth #461, The Methylation Station™, where team members will discuss SuperMethyl™ Max and other products. At the Epigenetics Society International Conference in Chicago, Professor He will give a keynote talk, and Ellis Bio will host an exhibitor table for attendees interested in its bisulfite kits.

“Our partnership with the University of Chicago demonstrates how academic research can drive innovation in the biotechnology industry,” said Ruitu Lyu, PhD, co-author on the UMBS preprint and incoming CTO at Ellis Bio. “UMBS sets a new standard for low-input DNA methylation detection, and SuperMethyl™ Max brings this capability into everyday research.”

About the bioRxiv Preprint

The preprint available on bioRxiv this week is entitled “Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA,” and is authored by Professor Chuan He’s team, including Qing Dai, Tanner Baldwin, Ruitu Lyu, Bryan Daniels, Yiding Wang, and others.

Exciting Innovations at ADLM 2025

Matthew — Thu, 24 Jul 2025 20:07:53 GMT

Explore how Ellis Bio is revolutionizing DNA methylation analysis with their groundbreaking bisulfite conversion kits at ADLM 2025.

Ellis Bio unveils SuperMethyl™ Max kit for low-input DNA methylation workflows

Matthew — Thu, 15 May 2025 20:32:14 GMT

New bisulfite chemistry delivers high-yield recovery and NGS compatibility for challenging epigenomic applications

Introducing SuperMethyl™ - Fast Bisulfite Conversion Kit

Matthew — Wed, 07 May 2025 18:08:21 GMT

CAMBRIDGE, Mass. —

Chicago, IL – Ellis Bio, a new biotech company spun out from The University of Chicago, officially launches this week with a mission to revolutionize epigenomics research. Founded by Professor Chuan He, the John T. Wilson Distinguished Service Professor and an HHMI Investigator, Ellis Bio derives its name from Ellis Avenue, which intersects several of The University Chicago's prestigious research labs, including that of Professor He. Ellis Bio aims to bridge pioneering academic discoveries with transformative tools for researchers worldwide.

The company’s first product, the SuperMethyl™ - Fast Bisulfite Conversion Kit was launched at the Chicago Biomedical Consortium’s 2024 Chicago BioCapital Summit. This advanced kit achieves over 99.5% methyl conversion in less than 10 minutes—a significant improvement over competitors’ methyl conversion incubation times.

“The SuperMethyl - Fast kit provides researchers with a fast and reliable solution for bisulfite methyl conversion,” said Dr. Ruitu Lyu, Scientific Advisor at Ellis Bio. “As the demand for methylation biomarker discovery grows, particularly in fields like early cancer detection, our kit is poised to accelerate methylation workflows and drive epigenetic research.”

Ellis Bio is driven by Professor He’s pioneering contributions to epitranscriptomics and epigenetics, which were recognized with the Wolf Prize in Chemistry and membership in the American Academy of Arts and Sciences. With a focus on translating academic research into practical solutions, Ellis Bio is positioned to lead innovation in epigenomic technologies, enabling researchers to push the boundaries of biomarker discovery and therapeutic development.

The company’s operations in Chicago reflects its commitment to staying near the center of both its scientific origins and the supportive resources that the Polsky Center for Entrepreneurship and Innovation, Chicago Biomedical Consortium, and other Chicago biotech ecosystem partners. With the SuperMethyl™ - Fast kit, Ellis Bio is poised to set new standards in DNA methylation analysis, supporting the rapid evolution of epigenomics research.

https://www.biospace.com/press-releases/ellis-bio-launches-to-transform-epigenomics-research-with-supermethyl-fast-kit-debut

https://www.biopharmadive.com/press-release/20241108-ellis-bio-launches-to-transform-epigenomics-research-with-supermethyl-flash-1/

The Top 5 Tips for Conducting DNA Methylation Experiments

Matthew — Thu, 27 Mar 2025 18:06:23 GMT

DNA methylation is a crucial epigenetic modification that plays a significant role in gene regulation, development, and disease progression. In this blog post, we discuss 5-methylcytosine (5mC), which is the most commonly studies epigenetic mark. Researchers studying DNA methylation must take careful steps to ensure high-quality, reproducible results. Here are the top five tips to optimize your DNA methylation experiments.

Chicago Biocapital Summit at Fulton Labs

Matthew — Wed, 06 Nov 2024 22:37:50 GMT

We are excited to launch our new and innovative bisulfite conversion kit at the Chicago Biocapital Summit at Fulton Labs!

Stop by the Hall of Inventions on November 7th to learn about Ellis Bio's groundbreaking science that will transform epigenomics research.

Founded by Professor Chuan He, the John T. Wilson Distinguished Service Professor at UChicago and HHMI Investigator, Ellis Bio develops cutting-edge reagent kits based on innovations from Professor He’s laboratory.

Register here: https://lnkd.in/ex6rBtPA