TAPS aims for gold (standard)

OXFORD, U.K.—Base Genomics Ltd. has raised $11 million in an oversubscribed seed round to further develop and launch the commercialization of TAPS, a liquid biopsy technology which may set a new gold standard in DNA methylation detection.

The technology was invented at the Ludwig Institute for Cancer Research at Oxford University, and the funding round—led by Oxford Sciences Innovation—will accelerate the development of the DNA methylation-based blood test, unlocking opportunities in preventative medicine and patient monitoring.

According to the Ludwig Institute, Dr. Chunxiao Song developed a method called TAPS (TET-assisted pyridine borane sequencing) to tackle the issue of DNA sensitivity. The standard way of measuring DNA methylation, bisulphite sequencing, can cause severe degradation of the DNA sample, thus lowering the amount of DNA available for detection and compromising the test’s sensitivity. Song’s TAPS technology, initially focusing on developing a blood test for early-stage cancer and minimal residual disease, overcame the significant drawbacks of the existing industry standard for mapping DNA methylation.

The Ludwig Institute states that TAPS was found to retain the DNA in a sample and retain sequence complexity.

“Base Genomics' technology, TAPS, produces significantly more data and higher-quality data at half the sequencing cost when compared to the current gold standard method, bisulfite sequencing (protocol),” Oliver Waterhead, Base Genomics founder and CEO, tells DDN.

“TAPS overcomes the two significant problems with bisulfite sequencing, which degrades DNA (meaning that a significant amount of the DNA you are trying to analyze is lost) and reduces sequence complexity (meaning that data quality is compromised),” Waterhead says.

“TAPS, therefore, allows epigenetics to be studied in more detail and in new contexts, such as single-cell and long-read sequencing,” Waterhead continues. “It also enables a vast array of clinical opportunities. For example, in the detection of early-stage cancer from liquid biopsy, the name of the game is to achieve sufficient sensitivity by getting as much information as possible out of a sample.”

Although major companies continue to use the bisulphite sequencing method, Waterhead believes that there is a significant market for TAPS. As he puts it, “The market is the whole population above a certain age where it is prudent to routinely screen individuals. TAPS generates far more information from the precious DNA in a liquid biopsy sample, and has the potential to diagnose Stage I and Stage II cancers with high sensitivity and specificity.”

Base Genomics is currently producing TAPS and applying the technology on liquid biopsy samples from oncology patients at different stages of disease, and is working toward creating a liquid biopsy test for the detection of early-stage cancer and minimal residual disease, and toward commercializing those tests, Waterhead says.

Although the focus with TAPS right now is testing across cancer types, the technology also is applicable to other diseases, Waterhead notes: “For example, there are DNA methylation biomarkers for the detection of Alzheimer's disease, and TAPS will be able to detect these with higher sensitivity than the existing methods. TAPS will also be able to find new biomarkers, and has the potential to enable the discovery of new drug targets.”

Adds Base Genomics’ chief medical officer, Anna Schuh, who is also head of the Molecular Diagnostics Department at the University of Oxford: "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. Current approaches are not fit 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."

“Genomic technologies with the power, simplicity and broad applicability of TAPS come along very infrequently, with the potential to have an impact on epigenetics similar to that which Illumina’s SBS chemistry had on next-generation sequencing,” concluded Vincent Smith, Base Genomics’ chief technology officer and a former Illumina vice president.