Medicinal Genomics Sequences the Cannabis Genome Using Roche's GS FLX+ System
"Despite compelling evidence of the therapeutic benefits of Cannabis, very little genomics research has been performed in this area," said Kevin McKernan, founder and head of scientific operations of Medicinal Genomics. "With the goal to sequence multiple Cannabis varieties, we initially took the approach of using short-read next generation sequencing technology on the C. sativa strain. We very quickly realized that this method was not going to provide a clear picture of the genome required to tease out the important biological pathways. This realization caused somewhat of a paradigm shift in the way we approached this project. At this point we moved to triple backcrossed cultivars and longer read technology."
Surprised in part by the finding that genomic variation between Cannabis strains is over 1%, a figure that is 10 times the variation of human genomes, the team at Medicinal Genomics turned to Roche's 454 Sequencing Center in Branford, Connecticut to sequence the Cannabis indica strain on Roche's new GS FLX+ System, the latest advance in long read next generation technology. The researchers obtained roughly 18x genome coverage with the 700-800 base pair long reads, enabling a high-quality draft assembly of this complex plant genome.
"I was stunned by the data quality and more impressively the read lengths of the data coming off the GS FLX+ Instruments," said McKernan. "With the long reads we can sort out the variation in the strain and phase alleles so that we can make biological sense of the sequencing data. We can assemble some key synthase genes into much longer phased blocks, allowing us to focus more on the biology and less on the computational concerns over collapsed polymorphic assemblies we were seeing with the shorter read systems."
"We are pleased to see an industry-renowned expert in the field of next generation sequencing recognize the value of the long reads offered with our new GS FLX+ System," said Todd Arnold, Vice President of Development at 454 Life Sciences, a Roche Company. "This project, along with other work on a variety of large plant and animal genomes, confirms the power of long reads for high-quality assembly and, most importantly, for correlating sequence content with biological significance."
Later this fall Medicinal Genomics plans to release the raw sequence data of the Cannabis indica genome as well as a full genome annotation. With the genomes in hand, researchers can begin to identify non-psychoactive compounds or enzyme pathways to better elucidate the therapeutic benefits of Cannabis, including the plant's anti-cancer properties. These pathways can be optimized in the plant or cloned into other hosts for more efficient biologic production. In addition, it may be possible through genome directed breeding to attenuate the psychoactive effects of Cannabis while enhancing the medicinal aspects.
For more information on the 454 Sequencing Systems, visit www.454.com.
About Medicinal Genomics
Medicinal Genomics is the first known organization to sequence the complete genomes of Cannabis sativa and Cannabis indica. Aside from being a useful tool to discover small molecule therapeutic drug candidates, there are many other commercial applications of these sequences, including the design of genomic assays that measure genes predictive of Cannabinoid levels in the plants at seedling stages. Use of these genomic assays will help regulate the medicinal Cannabis market through better oversight and labeling and will inform selective breeding in both Cannabis and hemp production. Medicinal Genomics maintains its corporate headquarters in Marblehead, Mass. All scientific operations are conducted at the company's research facility in Amsterdam, Netherlands in collaboration with DNA Genetics. For further information, please visit www.medicinalgenomics.com.
About Roche Diagnostics Deutschland GmbH
Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world's largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in diabetes management. Roche's personalised healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2010, Roche had over 80'000 employees worldwide and invested over 9 billion Swiss francs in R&D. The Group posted sales of 47.5 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.