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A Chinese Genome Giant Sets Its Sights on the UItimate Sequencer

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THE WORLD’S LARGEST genetics research center isn’t at Harvard or Stanford or even the NIH. It’s a 20-mile drive from Hong Kong International Airport, in the bustling Chinese city of Shenzhen. BGI-–formerly the Beijing Genomics Institute—has sequenced the DNA of organisms big and small: millet, rice, the giant panda, 40 types of silkworm, the SARS virus, even a 4,000-year-old man named Inuk. And soon it will add a new name to its genomic guest book: Dubs, the Alaskan Malamute, and mascot for the University of Washington.

The school’s leadership will hand over a vial of husky DNA as a symbol of a new partnership between the Chinese genomics giant and UW, along with a few other US research institutions. BGI announced Wednesday the launch of a West Coast Innovation Center, co-located in Seattle and San Jose. The Seattle hub will focus on precision medicine and feature collaborations with UW, the Allen Institute for Brain Science, the Bill and Melinda Gates Foundation, and Washington State University. The San Jose facility, where BGI already has a lab and just over 100 employees, will support its ambitions to develop the next-next-generation sequencing technologies. Technologies that—up until now—have been dominated by US sequencer behemoth Illumina.

“The idea is to promote the partnership between researchers in China and the US,” says Jian Wang, BGI’s founder and chairman. “We want to work more closely to provide health care communities in both countries with new tools for preventing and fighting disease.” Some of these initial projects for the Seattle center include hunting down cancer biomarkers and mapping out an atlas of human brain cells. And there is talk of embarking on large-scale population health studies. All of which, most researchers agree, are legitimately exciting prospects for the partnership.

San Jose is where things get a little less collaborative, and a little more contentious.

Seven years ago, BGI began its bid to turn China into a DNA superpower by buying 128 of the world’s fastest sequencing machines—then the Illumina HiSeq 200. That made BGI Illumina’s biggest single customer at the time, and an overnight sequencing sensation. By 2014, it was producing at least a quarter of the world’s genomic data, more than any other institution on the planet. Today, BGI still claims to lead the world in sheer sequencing capacity. But in the last few years its aging army of machines has struggled to keep pace with newer, faster, cheaper, more powerful sequencers put out by Illumina and chief Chinese competitor, Novogene.

Instead of investing in its commercial foes, BGI decided to create the next generation of sequencing machines itself. In 2013, BGI purchased Illumina’s main competitor: Complete Genomics in Mountain View, California. Its first attempt was a flop. BGI suspended sales after just three orders. The next machine, a sequencer called the BGISEQ-500, launched in late 2015, and according to BGI, can now sequence an entire human genome for $600. That’s about 40 percent cheaper than the going street price on the Illumina platform.

Last year, the China Food and Drug Administration approved the sequencer as a medical device, allowing its use in clinical genetic testing, and BGI has already shipped it to some of its partner laboratories and other customers. Yiwu He, BGI’s global head of research, says that while it hasn’t sold any sequencers in America, the company is building up the manufacturing capacity to one day serve the US market. “It definitely has our attention,” he says.

But first, BGI will be tending to its own flock. “We’ll still be using some Illumina sequencers to meet our customers’ needs,” says He. “But down the road you’re going to see more and more BGI machines in our labs.” He wouldn’t say how soon or how big the Illumina phase-out would be, only that the San Jose R&D facility would be key to making it happen. BGI is working on a DNA-nanoball-based cluster sequencing system that the company says could drive the price of a human genome down to $200. Illumina promised a $100 genome back in January, when the company introduced its new NovaSeq machines. With BGI’s enhanced presence in California, the race isn’t just on. It’s happening right in Illumina’s backyard.

To make matters even more complicated, BGI is still an Illumina customer, even as it expands its footprint as a competitor. Jay Flatley, Illumina’s executive chairman, said the increasingly strange relationship between the two companies made it hard for him to comment on any specifics. But to the extent that BGI is pushing the field toward better informatics software and sequencing technologies, he says, its expansion can only be a good thing. “There still remains a lot of work to be done to extract clinical significance from the human genome,” Flatley says.

Both the Chinese and the US governments are investing heavily to make that happen. Last March, almost exactly a year after Obama announced a $215 million initiative to sequence 1 million Americans, China finalized its plans for a much bigger, multi-billion dollar project. Over 15 years it will pay for a trio of institutions—including BGI—to sequence the genomes of many millions of citizens. For that kind of volume, a next-next-generation sequencer would certainly come in handy.

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