Epigenetics technology developer Base Genomics said today it was launched with an $11 million oversubscribed seed funding round, with proceeds intended toward commercializing a liquid biopsy based on DNA methylation sequencing.

Base Genomics said the blood test will be designed to apply Base Genomics’ TET-assisted pyridine borane sequencing (TAPS) technology, developed at the Ludwig Institute for Cancer Research Branch at the University of Oxford, with an initial focus on detecting early-stage cancer and minimal residual disease.

TAPS is a novel chemical reaction designed to convert methylated cytosine to thymine under mild conditions.

As noted by Chunxiao Song, Ph.D., a co-inventor of TAPS at the Ludwig Institute on its website, the two major epigenetic modifications in human DNA are 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), both derived from cytosine, which play crucial roles in biological processes ranging from gene regulation to normal development. Changes in the abundance and location of 5mC and 5hmC are associated with various diseases, with abnormal patterns of 5mC and 5hmC being hallmarks of cancer.

“One of my key aims is to sequence 5mC and 5hmC in circulating cell-free DNA from the blood for non-invasive early cancer detection,” Song explained. “However, before we can do that, we need the right tools.”

According to Base Genomics, TAPS is designed to detect 5mC and 5hmC directly without affecting unmodified cytosines. That differs from the industry standard technology of bisulfite sequencing since TAPS does not degrade DNA or reduce sequence complexity through indirect detection, leaving significantly more DNA available for sequencing. As a result, the company says, TAPS can generate significantly more information from a given sample.

“TAPS could replace bisulphite sequencing as the new standard in DNA epigenetic analysis and could have wide applications in academic research and clinical diagnostics,” Song stated.

TAPS also better retains sequence complexity, cutting sequencing costs in half and enabling simultaneous epigenetic and genetic analysis, Base Genomics added.

“The ability to sequence a large amount of high-quality epigenetic information from a simple blood test could unlock a new era of preventative medicine,” Base Genomics founder and CEO Oliver Waterhouse said in a statement. “In the future, individuals will not just be sequenced once to determine their largely static genetic code, but will be sequenced repeatedly over time to track dynamic epigenetic changes caused by age, lifestyle, and disease.”

Oxford Sciences Innovation, the investment firm created to spin out companies based on science and technologies developed at the University of Oxford, led the funding round, which included participation by undisclosed “investors with industry expertise in genomics and oncology.”

Waterhouse was previously at Oxford Sciences Innovation as an Entrepreneur in Residence, as well as a founding team member at Zinc VC, before joining Base Genomics.

Waterhouse heads the company’s leadership team of scientists and clinicians, which includes Song and another co-inventor of TAPS at the Ludwig Institute, Yibin Liu, Ph.D.; CTO Vincent Smith, Ph.D., a specialist in genomic product development and former Illumina VP; and Anna Schuh, M.D., Ph.D., Head of Molecular Diagnostics at the University of Oxford and Principal Investigator on over 30 clinical trials.

“In order to realize the potential of liquid biopsies for clinically meaningful diagnosis and monitoring, sensitive detection and precise quantification of circulating tumor DNA is paramount,” Schuh said. “Current approaches are not fit for purpose to achieve this, but Base Genomics has developed a game-changing technology which has the potential to make the sensitivity of liquid biopsies a problem of the past.”

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