Epigenetics company Base Genomics has launched with a team of leading scientists and clinicians with the aim of setting a new gold standard in DNA methylation detection. The company has closed an oversubscribed seed funding round of US$11 million to accelerate development of its TAPS technology, initially focusing on developing a blood test for early-stage cancer and minimal residual disease. The funding round was led by Oxford Sciences Innovation.
DNA methylation is an epigenetic mechanism involved in gene regulation and has been shown to be one of the most promising biomarkers for detecting cancer through liquid biopsy. The existing industry standard for mapping DNA methylation degrades DNA and reduces sequence complexity, however, limiting scientific discovery and clinical sensitivity. Base Genomics’ new technology, TAPS, overcomes these issues and generates significantly more information from a given sample, creating new opportunities in research and clinical application.
Dr Anna Schuh, CMO, Base Genomics, commented: “In order to realize the potential of liquid biopsies for clinically meaningful diagnosis and monitoring, sensitive detection and precise quantification of circulating tumour DNA is paramount. 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.”
First developed at Ludwig Institute for Cancer Research Branch at the University of Oxford, TAPS is a novel chemical reaction that converts methylated cytosine to thymine under mild conditions. Unlike the industry standard technology, bisulfite sequencing, TAPS does not degrade DNA, meaning that significantly more DNA is available for sequencing. TAPS also better retains sequence complexity, cutting sequencing costs in half and enabling simultaneous epigenetic and genetic analysis.
Dr Vincent Smith, CTO, Base Genomics said: “[TAPS] has the potential to have an impact on epigenetics similar to that which Illumina’s SBS chemistry had on Next Generation Sequencing.”
Base Genomics is led by a highly experienced team of scientists and clinicians, including Dr Smith, a world-leader in genomic product development and former Illumina VP; Dr Schuh, Head of Molecular Diagnostics at the University of Oxford and Principal Investigator on over 30 clinical trials; Drs Chunxiao Song and Yibin Liu, co-inventors of TAPS at the Ludwig Institute for Cancer Research, Oxford; and Oliver Waterhouse, previously an Entrepreneur in Residence at Oxford Sciences Innovation and founding team member at Zinc VC.
Waterhouse, founder and CEO, Base Genomics, said: “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. 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.”

Modern science and data sharing converged to underpin a study led by the Translational Genomics Research Institute (TGen), an affiliate of City of Hope, that identified a gene associated with a rare condition that results in physical and intellectual disabilities of children.

The results suggest that rare variants in the gene DDX6 are associated with a significant disruption in the development of the central nervous system, governing such basic skills as the ability to walk and talk.

“One of the most powerful revelations of this study is the identification of pathogenic mutations in DDX6; a gene not previously linked to childhood disorders and one which appears to play a key role in early brain development,” said Chris Balak, a research associate in TGen’s Neurogenomics Division, and the study’s lead author.

Balak zeroed in on DDX6 by comparing the sequencing results from a 5-year-old Arizona girl who was seen at TGen’s Center for Rare Childhood Disorders (the Center) with those identified in large population databases and to the genomes of her parents, who are healthy. Following this revelation, and preliminary findings posted on a website shared by investigators worldwide, TGen identified four similar cases: two in the U.S., and one each in France and the Netherlands.

These children’s conditions were characterized by intellectual disability, developmental delay, speech and feeding difficulties, low muscle strength with difficulties walking, mild-to-moderate cardiac anomalies, and specific facial features.

“Something we are quite proud of with this work is our combined effort with other physi-
cians and scientists in Europe to demonstrate that changes in this gene cause this rare syndrome in multiple patients,” said Dr. Matt Huentelman, TGen Professor of Neruogenomics, Scientific Director of the Center, and one of the study’s senior authors. “Collectively, our clinical and laboratory data describe a new brain development syndrome caused by genetic changes in DDX6.”
TGenwww.tgen.org/news/2019/august/15/tgen-identifies-ddx6-linked-to-disabilities/