Technology bridges strain typing and sequencing to correlate phenotype to genotype.

Beijing Genomics Institute (BGI) and OpGen have decided to work together to expand the use of the latter’s Optical Mapping technology for de novo sequence finishing in human, plant, and animal genomes. The companies report successfully completing a study based on human genome data to close gaps in the existing sequence scaffolds.

Optical Mapping bridges strain typing and sequencing to correlate phenotype to genotype. The Argus™ Optical Mapping System and MapIt™ Optical Mapping Services deliver ordered, whole-genome genetic maps from single DNA molecules. The platform provides automated, high-resolution, whole-genome analysis for strain typing, comparative genomics, and sequence assembly of microbial genomes.

This de novo technology is free from the limitations of gel, PCR, and sequencing-based methodologies and has broad molecular diagnostic applications that are currently in development, according to OpGen. The firm says that its customers include biodefense organizations, genomic research centers, academic institutions, clinical research organizations, and biotechnology companies.

Advances in DNA sequencing continue to drive down cost and increase the amount of sequence data available. These advances, though, leave much of the genome uncharacterized and unordered, BGI and OpGen point out. The Optical Mapping technology, when combined with current next-generation sequencing platforms, will enable the efficient and accurate finishing of assembled contigs into chromosomes, they add.

BGI brings sequencing capacity and computing power that enable the generation of thousands of sequences annually. OpGen has the capability to construct whole-genome ordered restriction maps independent of sequence information with reliable assembly accuracy. Optical Mapping has been used in genomics studies of microbiology, with applications in areas of comparative genomics, strain typing, and whole-genome sequence assembly, OpGen notes.

“We believe that Optical Mapping will play a significant and complimentary role with current and future sequencing systems as a tool to enable completion of large, complex genomes, and reduce the overall cost and time for these projects,” says Doug White, CEO of OpGen.

Xun Xu, vp of R&D at BGI, adds, “Applying the complementary technologies, we can develop more representative reference genomes at a much improved standard. Furthermore, the potential in human metagenomics research by developing improved microbe assemblies will facilitate the application in human disease studies.”

BGI was founded in September 1999 with the mission of supporting the development of science and technology, building strong research teams, and promoting the development of commercial scientific services. BGI reports that its projects include sequencing 1% of the human genome for the International Human Genome Project, contributing 10% to the International Human HapMap Project, completely sequencing the rice genome and the silkworm genome, and carrying out research to combat SARS and in the Sino-British Chicken Genome Project.

In 2007, BGI’s headquarters relocated from Beijing to Shenzhen. BGI-Shenzhen reportedly completed the first Asian diploid genome and the cucumber genome project. BGI-Shenzhen also established its own technical platforms based on large-scale genome sequencing, efficient bioinformatics analyses, and innovative genetic healthcare initiatives.

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