NEW YORK – Semiconductor-based genomics technology startup AxBio is working toward the commercial launch of a long-read, single-molecule nanopore sequencer that promises low cost and high data accuracy for low-throughput applications in research and diagnostics.
Earlier this month at the Precision Medicine World Conference in Santa Clara, California, the company, which maintains operations in the US and China, publicly showcased its AxiLona AXP-100 sequencing platform for the first time, aiming to attract collaborators for an early-access program later this year.
In 2022, the firm raised $100 million in a Series B financing round led by AstraZeneca-CICC investment fund, a joint healthcare fund of AstraZeneca and Chinese private equity firm CICC Capital, as well as by Yunfeng Capital, a Chinese VC firm.
AxBio's sequencing technology combines aspects of Pacific Biosciences' and Oxford Nanopore Technologies' respective long-read technologies.
Like PacBio, it relies on sequencing-by-synthesis, utilizing a proprietary DNA polymerase that has been engineered to incorporate special nucleotides that have been modified with unique functional groups corresponding to each base. To increase accuracy, the technology also employs circular consensus sequencing, where a single-stranded DNA template is read several times over in a circle.
Similar to Oxford Nanopore, the company uses protein nanopores and a high-density CMOS sensor chip array to determine the base sequence by detecting changes in the electrical properties across the pore, a variation of alpha-hemolysin. But in the case of AxBio, those changes are not caused by DNA being pulled through the pore. Instead, the functional groups on the nucleotides transiently interact with the pore, changing its electrical properties as they get incorporated into the nascent DNA strand by the polymerase, which is physically tethered to the nanopore. The company is not revealing further details about its technology at this time.
Last year, a team led by Peter Belenky, an associate professor of molecular microbiology and immunology at Brown University, demonstrated the use of AxBio's nanopore platform for microbial 16S rRNA sequencing.
In a paper published in Frontiers in Microbiomes, the researchers tried out the AxBio technology as part of a mouse study to understand how diet influences the gut microbiome's response to antibiotics.
For that study, they sequenced PCR-amplified 16S rRNA from several hundred mouse fecal samples on the Illumina MiSeq and a subset of 11 samples in addition on the AxiLona AXP-100. "The potential of this technology is that it can produce full-length 16S rRNA reads with acceptable Q scores," they wrote, adding that they wanted to test the technology as part of their project. "As this platform was in development, we were limited to testing 11 samples due to instrument availability, and we do not view this as a complete platform validation, but rather as an effective test run," they added.
Notably, the researchers detected species from a total of 368 microbial families using AxBio sequencing, whereas Illumina sequencing only detected 35 families in the same sample subset. "We attribute the discrepancies that we observed in the family-level identifications to the longer read length, and therefore, heightened discrimination between closely related families with reduced error," they wrote.
Specifically, they were able to use the nanopore sequencing data to determine the top 30 most abundant families in treated and untreated mice, followed by a closer look at the species level. "While this analysis did not have sufficient [sample size] to conduct statistical analysis, it did demonstrate that AxBio AXP100 long-read sequencing can be used to conduct species-level analysis," they concluded.
16S rRNA microbiome sequencing is only one of several applications AxBio is pursuing for its sequencer. According to Nikolay Sergeev, AxBio's VP of applications, the firm is also considering metagenomics, as well as pharmacogenomic testing and genetic disease diagnostics. In particular, it is eyeing tests for genetic repeat disorders and is currently working toward approval of a fragile X syndrome test from China's National Medical Products Administration (NMPA), he added.
According to printed marketing material from AxBio, the AxiLona AXP-100 instrument can generate up to a million reads per run with read lengths up to 100 kilobases and greater than 99 percent accuracy from consensus sequencing. It has a throughput of up to 100 Gb per run with run times of less than four hours. The instrument is about the size of a small desktop printer and weighs less than 7 kg.
The underlying semiconductor sensor chip currently boasts 1 million signal acquisition channels with chips carrying 10 million channels currently under development.
Along with the sequencer and chemistry kits, AxBio has developed an automated library preparation system called AxiLona Auto Lib Prep, a liquid handling robot that can process up to eight samples at a time, and AxiLona AXP Sys data analysis software.
While AxBio is not releasing pricing information at this time, it claims that both the instrument price and cost per Gb of data will be "significantly lower" than that of other sequencing platforms.
During a talk at PMWC, Hui Tian, AxBio's CEO, said he cofounded the company in Silicon Valley in 2016 together with Igor Ivanov, AxBio's chief operating officer. Besides its Santa Clara location, the firm has an R&D center in Shenzhen and a synthetic chemistry center in Tianjin. All of AxBio's platforms are manufactured in a GMP facility near Shanghai that has ISO 13485:2016 accreditation.
Most of AxBio's approximately 130 employees work in R&D, Tian said, and more than half have advanced degrees. Tian, who holds Ph.D. and M.S. degrees from Stanford University and undergraduate and M.S. degrees from Tsinghua University, is a physicist and electrical engineer by training and a former VP of Roche Sequencing as well as a former VP of nanopore sequencing firm Genia, which Roche acquired in 2014. Many AxBio employees hail from the sequencing industry including Roche and MGI, he said, as well as from the semiconductor industry.
According to Tian, AxBio conducted a mutagenesis and enzyme screening program to design its own polymerase for the sequencer. To reach low cost, it uses an "industry-leading" 12-inch wafer and narrow chips, he added, which allows for the production of more chips per wafer than other designs.
Besides the nanopore sequencer, AxBio has also developed a microarray platform called AxiLona EL-100 Microarray Analyzer and a real-time PCR platform called AxiLona FL-100 Multiplexed Nucleic Acid Analyzer.
The microarray platform uses oligonucleotide probes attached to the surface of electrochemical sensors and can detect up to 54 targets per assay in 15 minutes. According to the firm, the instrument is "well suited for on-site and point-of-care testing." The PCR instrument delivers results within 1.5 hours and has "significantly lower instrument and single-test costs than targeted sequencing," according to AxBio.
The Microarray Analyzer, which already has the CE mark, could be especially useful for infectious disease diagnostics, Tian said.
Finally, the company has developed a so-called "strip tester," he said, a handheld device to measure proteins and other analytes at the point of care with high sensitivity. A potential first application could be noninvasive glucose testing, he added, using saliva instead of blood.