This article was originally published Sept. 16.
BGI earlier this month opened [email protected], its next-generation sequencing facility at the University of California, Davis.
The facility opened with three Illumina HiSeq instruments, two of which are the 2500 version, and five of Life Technologies' Ion Proton machines, with an additional five HiSeq machines on their way, BGI and UC Davis officials told In Sequence at the BGI-sponsored International Conference on Genomics in the Americas meeting in Sacramento last week.
BGI officials also updated IS on the institute's plans for its commercial subsidiaries, BGI Tech and BGI Health, which it spun out last year (IS 10/2/2012), and discussed plans for incorporating Complete Genomics' technology into its research projects.
BGI Tech, the commercial services arm of BGI, is planning to go public, BGI Executive Director Jun Wang told IS. Wang said that he could not provide an exact timeline for this move because it will be driven in part by the shareholders. BGI sold around 40 percent of BGI Tech's shares in order to purchase Complete Genomics, a deal initiated last September and completed in March, Wang said.
BGI Tech provides whole-genome, exome, and transcriptome sequencing services on Illumina and Life Technologies machines. BGI Tech CEO Yingrui Li told IS that, aside from sequencing services, the entity has also developed its own content, such as the All-in-One capture technique that includes the whole exome, regulatory regions, the major histocompatibility complex locus, and population-based tag SNPs (IS 11/29/2011).
BGI Tech has also developed targeted, disease-specific panels for research and panels aimed at agricultural researchers focused on breeding applications for crops like maize and rice. It also offers customized bioinformatics services, Li said.
As for Complete Genomics, BGI is currently focused on integrating the technology into its own research projects, rather than into the services business of BGI Tech. One project in particular for which it plans to use Complete's sequencing technology is the Million Genomes Project, in which BGI aims to sequence one million human, one million plant and animal, and one million microbial genomes, Wang said.
Wang declined to comment further on BGI's plans for Complete Genomics. But in May, Complete Genomics CEO Cliff Reid told IS that long term, Complete Genomics would collaborate closely with BGI Health to provide sequencing services to the clinical market (IS 5/7/2013).
With regards to sequencing one million human genomes, Wang said BGI is currently working out the details and protocols for how this would be done, including how individuals would enroll. However, he said, the entire staff of BGI has already signed up.
BGI's other commercial spinout, BGI Health, has already launched a number of diagnostics within China, including its sequencing-based noninvasive prenatal aneuploidy test, dubbed NIFTY.
NIFTY uses a similar whole-genome shotgun sequencing technique as is employed by Sequenom and Illumina's Verinata Health for their respective tests. To date, BGI Health has administered more than 200,000 NIFTY tests in 22 different countries.
The test is not currently available in the US, although Wang said that BGI Health is evaluating how it would approach the US NIPT market. Key to that will be figuring out how to navigate the legal landscape. All four US companies offering noninvasive fetal aneuploidy tests are suing each other over intellectual property issues.
BGI Health's other diagnostics and screening tests include ones for autism and deafness, a carrier test for monogenic diseases, and oncology tests like EGFR testing and a gene panel to identify potential treatment options. It also has next-gen tests for HLA and HPV typing.
During a presentation at the ICG-Americas conference, Vince Gao, executive vice president of BGI Health, described one of its pipelines for testing for inherited metabolic disorders. The protocol, dubbed MS-Seq, first screens for metabolic disorders in newborns using mass spectrometry. If the test yields a positive, the sample is then tested via next-gen sequencing for diagnosis.
Sequencing for BGI Health's tests is done in accredited facilities throughout China, and Wang noted that it has collaborations with around 600 to 700 hospitals in China and a certified laboratory in each of nine provinces.
The [email protected] sequencing lab, which opened earlier this month, is a collaboration that originated three years ago, Harris Lewin, the vice chancellor of research at UC Davis, told IS. The center will support ongoing projects at UC Davis and will also develop "large signature projects that will define the relationship" between BGI and UC Davis, he said. One such project that [email protected] will participate in is the 100K Genomes Project, which is a collaboration led by UC Davis, the US Food and Drug Administration, and Agilent to sequence 100,000 pathogens. The project recently released 20 completed genomes (IS 7/30/2013).
The UC Davis partnership complements BGI's partnership with the Children's Hospital of Philadelphia, [email protected] That facility focuses on pediatric genetic disorders, while UC Davis' primary expertise is in agriculture, said Lewin. UC Davis' "status in agriculture and environmental science" was the "hook" for the BGI partnership, Lewin said, but the two organizations will pursue other opportunities as well, he said. "The big projects we have in the pipeline are related to plants and animals," he said, but down the road the center will move into clinical projects in connection with UC Davis' Comprehensive Cancer Center and Institute for Regenerative Medicine, Lewin said.
[email protected]' sequencing center is currently not CLIA certified, but Lewin said that "if there becomes a need, we'll do it."