Liquid biopsy for the win in cancer

SOUTH SAN FRANCISCO, Calif.—Twist Bioscience Corp., a company enabling customers to succeed through its offering of high-quality synthetic DNA using its silicon platform and next-generation sequencing (NGS), recently announced the launch of the Twist NGS Methylation Detection System, an end-to-end sample preparation and target enrichment solution for identifying methylated regions in the human genome.

DNA methylation plays a key role in many biological processes including cancer. When present on a single nucleotide, a methyl group can alter genetic behavior without changing the DNA sequence. Analyzing these methylation patterns provides unique understanding of disease pathology, including the ability to screen for cancer earlier using blood samples known as liquid biopsies.

“Methylation is one of the most interesting and informative epigenetic modifications due to its wide-reaching effects, but historically it has been difficult to study efficiently,” said Dr. Emily M. Leproust, CEO and co-founder of Twist Bioscience. “In partnership with New England Biolabs [NEB], we’ve developed a state-of-the-art system to identify and accurately evaluate methylation patterns that enable our customers to create better tests and/or conduct research more efficiently. In addition, the superior results produced through this system provide incentive for our customers using SNP microarray technology to switch to using Twist products plus sequencing.”

DNA methylation appears in consistent patterns across the genome, making it possible to assess multiple loci for a more specific and sensitive test. In cancer methylation, patterns appear early, providing an attractive approach for screening through revolutionary liquid biopsy tests, which are designed to detect a wide range of tumors from a single blood sample.

Despite the promise of methylation detection, the approach presents many challenges, including the preparation of the blood sample and the need for multiple probes for each sequence of interest. For many years, bisulfite sequencing was considered the gold standard in methylation detection. While this method provides a quantitative readout with high throughput and single-base pair resolution, bisulfite treatment can degrade DNA samples substantially and result in specific areas not being detected, particularly for tests with a small relative volume of target DNA for study, as in liquid biopsies. 

In addition, effective methylation detection requires four different DNA probes for every target sequence of DNA, a substantial undertaking for complex diagnostic tests. In order to overcome these challenges, Twist has partnered with NEB, which has developed a novel, enzyme-based alternative to sodium bisulfite treatment, EM-seq, for preparation of samples for methylation analysis.

“We developed Enzymatic Methyl-seq, or EM-seq, using a combination of enzymes to achieve highly efficient and gentle conversion of 5mC and 5hmC for downstream identification using next generation sequencing,” said Theodore Davis, executive director of the Applications and Product Development division at NEB. “Application of EM-seq to target enrichment workflows enables efficient analysis of methylation status in defined regions of the genome, with utility across a broad spectrum of areas that can impact human health. We are delighted to partner with Twist to expand the utility of EM-seq.”

The Twist NGS Methylation Detection System begins with NEB’s EM-seq for preparation of enzymatically converted libraries, and includes the Twist Methylation Enhancer, Universal Blocker and FastHyb as well as the Twist NGS Custom Methylation Panels. The custom panels, a key component of the product, include DNA probes to capture all four potential sequences at a given site: methylated, unmethylated, sense, and antisense. 

In addition, Twist works with customers to create custom content unique to a particular area of focus, allowing flexibility not found using static array designs. This unique feature of the Twist System facilitates exploration of dynamic and cell-specific methylation targets or poorly understood targets found in more elusive noncoding regions at single base pair resolution.