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BGI, OpGen Collaborate on Use of Optical Mapping to Improve Sequence Finishing

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By Julia Karow

This article has been updated from a previous version to include additional information from BGI and OpGen officials.

China's BGI and OpGen said last week that they are collaborating to use OpGen's optical mapping technology for de novo sequence finishing in human, plant, and animal genomes.

At the American Society of Human Genetics meeting last week, Bicheng Yang, director of marketing in the research and cooperation division at BGI in Shenzhen, said that optical mapping could provide a faster and more automated way to construct physical maps of genomes than conventional methods, such as radiation hybrid mapping. Combined with shotgun sequencing, such a map promises to improve the quality of a genome assembly by allowing researchers to anchor scaffolds and contigs to their correct positions on the chromosomes.

BGI and OpGen said in a statement that they have so far "successfully completed a study based on human genome data to close gaps in the existing sequence scaffolds."

According to Yang, that study used simulated human genome data assembled by BGI's SOAP de novo algorithm, and the optical map allowed the researchers to close 96 percent of gaps up to 100 kilobases in size. The groups have also been working with simulated mammalian genome data and are currently applying optical mapping to a new mammalian genome sequenced at BGI.

Xun Xu, vice president of research and development at BGI, said in a statement that the combination of optical mapping and next-gen sequencing will enable "more representative reference genomes at [a] much improved standard."

In addition, Xu said, the combined approach has "potential in human metagenomics research by developing improved microbe assemblies."

Optical Maps

OpGen's technology is able to construct whole-genome ordered restriction maps "independent of sequence information with reliable assembly accuracy," according to the company.

To date, optical mapping has primarily been used in microbiology, with applications in comparative genomics, strain typing, and whole-genome sequence assembly. The collaboration with BGI would expand the technology into human, plant, and animal genomics.

Michael Fitzpatrick, vice president of sales and commercial development at OpGen, told In Sequence at last week's ASHG meeting that the yield of the technology has "dramatically improved" over the last few years, allowing it to tackle larger genomes than before.

“We are very pleased to be working with BGI as we begin to expand the utility of Optical Mapping beyond microbial research," said Doug White, CEO of OpGen, in a statement. According to Yang, BGI expects to decide by the end of the year whether to bring the technology in house.

OpGen launched its Argus Optical Mapping System for microbial whole-genome analysis in June. The instrument has a list price of $300,000, and each optical mapping card — the microfluidic device used to stretch out, cut, and visualize the DNA — costs $400, including reagents. Multiple cards are required to analyze a mammalian-size genome, according to White.

He said that the instrument has been installed at eight sites so far, all of them government labs applying it to biodefense and public health research. The company expects to ship six more systems to customers before the end of the year, including one genome center.

In September, OpGen raised $17 million in Series B financing to market the system and to expand its use in new markets (IS 9/28/2010).

Xun Xu, vice president of research and development at BGI, said that the combination of optical mapping and next-gen sequencing will enable "more representative reference genomes at [a] much improved standard."

In addition, Xu said, the combined approach has "potential in human metagenomics research by developing improved microbe assemblies."


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