BGI Retools Complete Genomics Technology for Its New High-Throughput Benchtop Sequencer

By Bio-IT World Staff

October 28, 2015 | At the International Conference on Genomics held over the weekend in Shenzhen, China’s public-private genomics agency BGI revealed a new sequencer to be made available exclusively to Chinese customers beginning in 2016. The BGISEQ-500 is the third sequencer to be introduced by BGI ― the China FDA cleared two of the company’s instruments for use in hospitals last year ― but the first to have been substantially designed inside China. Previously, BGI had released the BGISEQ-100, a retooled Ion Torrent device, and the BGISEQ-1000, largely similar to the machines built by Complete Genomics of Mountain View, Calif. (now BGI’s American subsidiary) for its sequencing-as-a-service business.

The BGISEQ-500 also uses a variation on the “DNA nanoballs” sequencing method invented by Complete Genomics, but it has been hugely reengineered. While Complete Genomics’ instruments are restricted to sequencing whole human genomes and exomes, the new instrument is much more flexible and will launch with capabilities in RNA sequencing (including in single cells), panels for non-invasive prenatal sequencing, and genotyping panels, among other applications. It also has a greatly reduced footprint, fitting neatly on a benchtop.

No user data is available, but based on the BGISEQ-500’s specifications, BGI clearly intends for the sequencer to compete with Illumina’s line of NextSeq instruments, as a benchtop machine with high-throughput capabilities. It is priced to undercut the NextSeq 500, at a 30-40% discount, and its reported throughput on the larger of its two flow cell options is 200 gigabases per run, roughly double NextSeq’s most powerful mode. The BGISEQ-500 will also be capable of rapid runs producing as little as 8 gigabases of data, an advantage for clinical assays; BGI plans to submit the instrument to the China FDA for clearance.

If these figures pan out in practice, Illumina could find itself in the unfamiliar position of competing on features like read length rather than on scale and price ― especially if the BGISEQ-500 is eventually released to global markets.

The instrument is the culmination of a long process that began with the purchase of Complete Genomics in 2013. At the time, Complete Genomics sequencing was available only as a service; BGI, already a much larger service provider in its own right, pivoted its new subsidiary entirely to making commercial instruments.

Complete Genomics was not, however, stripped for intellectual property; instead it has focused on its own sequencing system, Revolocity, unveiled this summer and also scheduled for its first installations in early 2016. Revolocity hews much closer to the original vision of Complete Genomics, to produce whole human genomes at an industrial scale. Under BGI’s influence, it has been redesigned for extreme ease of use in a clinical setting, with automation and software built in to go all the way from a blood sample to a variant call file. (For more, see “With Revolocity, Complete Genomics Eyes New Markets for DNA Sequencing.”)