IP Profile: Compositions and methods for polynucleotide extraction and methylation detection, Johns Hopkins School of Medicine, US

The invention features methods and compositions for methylation detection, as well as a novel method for polynucleotide extraction and sodium bisulfite treatment.

Organization: Johns Hopkins School of Medicine, Baltimore, MD, US
Inventors: Tza-Huei Wang, Vasudev Bailey, Stephen Baylin, James Herman, Hetty Carraway, Hariharan Easwaran, Yi Zhang, and Brian Keeley, John Hopkins School of Medicine, US
Primary Market: Molecular Biology, Biosensors, Molecular Diagnostics
Technology Contact: S. Volko, Johns Hopkins Technology Transfer

IP Profile Courtesy of Johns Hopkins School of Medicine, US


DNA methylation contributes to carcinogenesis by silencing key tumor suppressor genes. Current methods to detect DNA methylation can be expensive, cumbersome and involve three separate independent processes including isolating DNA from the biosamples followed by treating the DNA with sodium bisulfite and finally setting up a Methylation-Specific PCR (MSP) to analyze the methylation status.

The size of the academic DNA methylation market this year was estimated to considerably exceed US $216 million in 2008 (NIH/NSF grant data). More than 23 large companies are involved in methylation based diagnostics. Since methylation-based markers are a relatively new discovery, we expect the market size to grow at a rapid rate.

Methylation-on-beads (MOB) extraction and bisulfite treatment and MS-qFRET detection are novel methods that combine the aforementioned three processes into a single tube step with the help of silica superparamagnetic beads (SSBs), wherein all steps are implemented without centrifugation or air drying. MS-qFRET uses quantum dots (QDs) that serve as both a FRET donor as well as a nanoconcentrator to capture fluorescently labeled target amplicons and determine methylation status via fluorescence resonance energy transfer (FRET). MS-qFRET is able to detect as little as 15 pg of methylated DNA in the presence of a 10,000-fold excess of unmethylated alleles.

MOB and MS-qFRET have both been extensively tested on various clinical samples including whole blood, tumors, serum and sputum and have consistently shown better performance than commercially available technologies. Both technologies would be ready to be packaged and marketed together, or separately. The technology could be beneficial to any biomarker or molecular biology company. It could easily find a place with companies that sell kits for methylation detection. Reliable detection offers great promise for use in cancer risk assessment, early cancer diagnosis, prognostic assessment of tumor behavior, and responsiveness to therapy. We are currently talking to companies about licensing the technology and are open to questions/ interest.

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