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MGI Unveils 'Extreme Throughput' Sequencing Platform at AGBT to Enable $100 Human Genome

MARCO ISLAND, Florida – MGI, the instrument subsidiary of China's BGI Group, on Wednesday announced a new ultra-high-throughput sequencing platform that can produce human genomes at $100 in consumables costs when running at scale.

During the last conference talk of the Advances in Genome Biology and Technology annual meeting – a spot traditionally reserved for the presentation of novel technology and occupied for the second time in a row by MGI – CSO Rade Drmanac’ described the new platform, called DNBSeq Tx (the x stands for "extreme throughput"), and showed some limited performance data.

The platform is the result of an effort to enable "genomics for all" and make it "unlimited and affordable," he said.

"The scale of the MGI technology and the unique sequencing detection methods that accompany it may add a new consideration to the sequencing options," said Shawn Levy, CSO of genomics at HudsonAlpha Discovery, who runs a high-throughput sequencing lab, in an email. "It will be interesting to see how the new technology develops in the US market."

"This could be the opening of a liberating paradigm of ubiquitous genomics that will change our understanding of health and disease," said Chris Mason, associate professor at Weill Cornell Medicine who has expertise in several sequencing technologies, in an email. "The data show extraordinary promise."

The system, which is more of a sequencing factory than a self-contained instrument and consists of several components, spatially uncouples the fluidics from the imaging and uses large, open slides instead of flow cells to carry the DNA nanoball (DNB) arrays. A robotic arm in the center moves the slides around between several fluidic dipping stations and fluorescent imagers. In the US, the Tx will only run with the antibody-based CoolMPS sequencing chemistry that MGI first described a year ago and published in a preprint posted on BioRxiv last week, while in China and other locations, the system can run either MGI's traditional chemistry or the CoolMPS chemistry.

Last week, MGI announced that it will start shipping its sequencing systems in the US in April, a move that has been opposed by Illumina, which has been in patent litigation with MGI and BGI and is seeking a preliminary injunction from a court to block MGI's US launch.

Drmanac said the company has been working on the Tx system for three years. With its robotic arm, it resembles the Revolocity system from Complete Genomics, which Drmanac cofounded and which BGI acquired in 2013. BGI canceled the commercialization of the Revolocity, which was Complete Genomics' most high-throughput sequencing system at the time, in 2015.

The Tx, several of which are already up and running at the China National GeneBank, according to Drmanac, has an output of up to 70 terabases per run, or 20 terabases per day, and a run time of 3.5 days. It can process up to eight independent slides, each of which can produce data for up to 150 human genomes at 30X coverage.

Much of the cost savings allowing for the $100 genome result from the slide architecture. The Tx slides are four times bigger than the flow cells for the T7, the high-throughput sequencer that MGI announced a year ago and launched last fall, and the DNBs are paced twice as densely on the arrays as they are on the T7 arrays, which results in sixfold consumables savings.

Drmanac presented some early performance data comparing the Tx to the DNBSEQ-400 for whole-genome sequencing, showing that the SNP and indel accuracy is similar for both systems. In an interview, he said that MGI plans to generate sequencing data for a "Genome in a Bottle" standard sample this year and make the data available on its website.

The system will be sold together with automation solutions for sample and library preparation, specifically the APL-S for DNA extraction from blood that can run 200,000 to 600,000 samples per year and the APL-L for library preparation that can process 300,000 to 500,000 samples per year. It will also come with a computing system called zTron for primary data analysis from FASTQ to VCF files that can handle 10,000 to 100,000 samples per year.

In principle, the Tx can churn out on the order of 100,000 human genomes at 30X coverage per year, and it would take 50 of the systems to sequence all newborns in the US each year, Drmanac said. Alternatively, it could be used to run a million oncology tests with cell-free DNA or 100 million single-cell transcriptomes. Another potentially useful application would be shallow human genome sequencing at 2X coverage, the cost of which would be less than $10 per genome, he added.

MGI plans to build the Tx to custom order and wants to target large population genomics projects that aim to analyze millions of genomes. The company has not yet determined a list price, Drmanac said, which might also differ between customers since the system will be adapted to their specific needs.

Until pricing information for the system is available, "it is difficult to evaluate if $500 or even $100 per genome in sequencing reagents costs is a significant movement from current and mature technology," Levy said. However, Drmanac maintained that amortized over hundreds of thousands of genomes, the instrument price will add only a little to the total cost per genome.

Going forward, sequencing with MGI systems could become even cheaper by reducing the diameter of the DNBs to 100 nm instead of 200 nm, Drmanac said, which is possible because of the strong signal from the antibodies used in the chemistry, allowing the DNBs to be packed even more densely on the array.