100K Pathogen Genome Project Selects PacBio SMRT® DNA Sequencing to Generate High-Quality, Finished Genomes
Note: The following news announcement was produced in cooperation with Pacific Biosciences of California. Dr. Bart Weimer, director of the project is a professor in the School of Veterinary Medicine, where the project is based.
MENLO PARK, Calif., — January 8, 2013 — Pacific Biosciences of California, Inc. (NASDAQ:PACB) provider of the PacBio® RS High Resolution Genetic Analyzer, and the University of California, Davis (UC Davis) today announced a partnership for the 100K Pathogen Genome Project. As part of the project, Pacific Biosciences' Single Molecule, Real-Time (SMRT®) technology will be used to sequence the genomes from at least 1,000 foodborne pathogen samples to completion, and to elucidate their epigenomes*. These bacteria represent major illness-causing pathogens, including Salmonella, Campylobacter, E. coli, Vibrio, and Listeria.
The 100K Genome Project was founded by the U.S. Food & Drug Administration, Agilent Technologies, and the laboratory of Dr. Bart Weimer at UC Davis School of Veterinary Medicine to create a consortium of partners from around the world that will sequence 100,000 foodborne pathogens using next-generation sequencing. This initiative addresses a significant shortage of bacterial pathogen information for use in designing molecular diagnostics, creates a resource to expand our understanding of infection mechanisms, and constructs a public repository for new insights into bacterial evolution by using large-scale genomics.
Pacific Biosciences' SMRT sequencing technology generates sequence reads an order of magnitude longer than other leading DNA sequencing technologies, thereby facilitating efficient de novo microbial genome assemblies. Long reads are critical for resolving genetic complexity in the assembly and finishing of genomes. The use of SMRT sequencing for the automated finishing of microbial genomes has been demonstrated in multiple recent publications, including for the genetic analysis of the Haitian cholera and German E. coli outbreaks.
The kinetic information acquired during SMRT sequencing can be used to elucidate the epigenome of bacteria. Epigenetic DNA base modifications, such as methylation, play an important role in the phenotypic variation, adaptability and pathogenicity of many bacteria, but they have been difficult to study due to the lack of a sequencing method to detect them. As part of the 100K Genome Project, the epigenomes of the pathogenic strains subjected to SMRT sequencing will be characterized, adding an important dataset to public database repositories.
“SMRT sequencing has been shown to be a powerful technology for the comprehensive determination of microbial genomes and epigenomes,” said Dr. Jonas Korlach, Chief Scientific Officer of Pacific Biosciences. “Through the combination of long reads, high consensus accuracy, and the lack of sequencing bias to GC content or sequence contexts, SMRT sequencing harbors the necessary requirements to construct finished genomes in an unbiased, hypothesis-free manner. The ability to detect methylation as part of the sequencing process is unique to SMRT sequencing, and will provide an invaluable resource to illuminate the epigenetic components controlling bacterial pathogenicity.”
“We are very pleased to utilize SMRT sequencing as part of the 100K Genome Project," said Bart Weimer, Professor and Director of the 100K Genome Project, "SMRT technology will enable production of complete genomes that will contribute great value toward databases for biological insight, new biomarker discovery, and reference genomes for food pathogen detection. A project of this scale is needed since microbial genome variations, including structural variations, the acquisition and loss of mobile elements, and phages or plasmids, are very difficult or impossible to detect without a de novo sequencing and genome assembly approach, yet they have a significant impact on food safety.”
The partnership will entail the sequencing of at least 1,000 samples by the 100K consortium member labs with access to the PacBio RS instrumentation, including pipeline constructions for high-throughput pathogen sequencing, de novo genome assemblies, epigenome determination, and data curation and deposition. Pacific Biosciences will provide technical guidance and training to support these activities, and interface closely with the involved laboratories to assist in the efficient construction of these pipelines.
For more information, please visit http://100kgenome.vetmed.ucdavis.edu/index.cfm and www.pacb.com.
About Pacific Biosciences
Pacific Biosciences of California, Inc. (NASDAQ: PACB) offers the PacBio® RS High Resolution Genetic Analyzer to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT®) technology, the company’s products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.
About The 100K Genome Project
Established in March 2012 by UC Davis, Agilent Technologies and the U.S. Food and Drug Administration, the 100K Genome Project is a landmark consortium that addresses the persistent food safety concerns by engaging world-wide partners to create a publicly available genetic database of the most common foodborne disease-causing microbes. By sequencing 100,000 pathogen genomes, the project will bring a new paradigm to public health to empower precise and robust molecular testing in the food chain – from the farm to the kitchen table. For more information, visit http:// http://100kgenome.vetmed.ucdavis.edu.
About UC Davis
For more than 100 years, UC Davis has engaged in teaching, research and public service that matter to California and transform the world. Located close to the state capital, UC Davis has more than 33,000 students, more than 2,500 faculty and more than 21,000 staff, an annual research budget of nearly $750 million, a comprehensive health system and 13 specialized research centers. The university offers interdisciplinary graduate study and more than 100 undergraduate majors in four colleges — Agricultural and Environmental Sciences, Biological Sciences, Engineering, and Letters and Science. It also houses six professional schools — Education, Law, Management, Medicine, Veterinary Medicine and the Betty Irene Moore School of Nursing.
*Epigenomes information comes from Wikipedia for informational purposes; it is not meant as a precise or comprehensive definition.
For Pacific Biosciences:
Maurissa Messier Trevin Rard
For Pacific Biosciences Pacific Biosciences
For UC Davis:
UC Davis News Service
(530) 752-9843 office
(530) 219-9640 cell
Dr. Bart Weimer
Professor, School of Veterinary Medicine
Director, 100K Genome Project