BGI Unveils Significant New Global Research Collaborations at The 6th International Conference on Genomics
Collaborative Initiatives to include Three Million Genomes, 10,000 Rice Genomes and 1% Danes’ Genome Project
Updates Also Provided on Ongoing Projects
November 16, 2011, Shenzhen, China – At the 6th International Conference on Genomics (ICG-6), one of the most influential global genomics conferences, multiple new global collaborative projects were announced, including three Million Genomes Projects, 10,000 Rice Genome and 1% Danes’ Genome Project. Updates were also provided on different areas of ongoing research, including human disease, biomedicine, agriculture, ecology and synthetic biology. The three-day conference, co-organized by BGI, GigaScience, Johns Hopkins Medicine, and Genetic Engineering & Biotechnology News (GEN),was attended by more than 500 participants, including leading scientists and experts from universities, research institutes, academic organizations, and enterprises in the biotechnology and pharmaceutical fields.
Among the major announcements and updates provided in the areas of human disease, agriculture and micro-ecosystems were:
“Three Million Genomes Projects”- M & M & M Projects
The Three Million Genomes Projects, or “M & M & M Projects,” introduced by Dr Jun Wang, Executive Director of BGI, will consist of the “Million Plant and Animal Genomes Project,” “Million Human Genomes Project” and “Million Micro-Ecosystem Project.” They will provide a clear classification on the studied species, and advance the understanding of the species genome and the application of genome-based research for different objectives.
With the objective to understand and use the digital version of “Tree of Life,” the Million Plant and Animal Genomes Project aims to sequence a million economically and scientifically important plants, animals and model organisms. This includes species that play a key industrial role or are considered valuable food sources, as well as endangered species that have evolutionary or scientific importance.
The first part of the project is to build up all reference genomes; the second part is the variation genomes, which select variations as targets for artificial selection; the third part is the breeding genomes, such as using the whole genome based molecular assisted selection for breeding. BGI has finished sequencing 540 plant and animal reference genomes and 25,239 variation genomes in this project, according to Dr. Wang’s report.
To understand the baseline and build a reference standard of the population, to discover the relationships between phenotype and genotype, and to develop personal genome and personalized medicine, the Million Human Genomes Project focuses on large-scale population and association studies that use whole-genome or whole-exome sequencing strategies. The studies include ancient human genome from an evolutionary perspective, population genomes based on the population or individual specific variation, medical genomes that focus on genetic diseases, cell genomes that target different cell types in human body, and personal genomes with an objective to develop the “4P model” - Predication, Prevention, Precaution, and Personalized Healthcare. BGI has already sequenced 38,123 human samples, according to Dr. Wang’s report.
Given the important role of microbes in their host environment (e.g. human body) and the ecosystem, as well as the wide applications of micro-organisms in food processing, agriculture, biotechnology, biomedicine, biogas production, waste management, among others, the Million Micro-ecosystem Genomes Project plans to sequence the metagenome and cultured microbiome of several different environments, including micro-environments within the human body. Dr. Wang noted that BGI has already finished sequencing the genome of more than 600 microbial species, including over 3,500 strains and 1,800 metagenomes.
The Human Variome Project (HVP)
Genomic approaches to understand genetic disorders and mechanisms of diseases were keynoted in the concurrent sessions. The Human Variome Project (HVP) introduced by Dr. Richard Cotton from the University of Melbourne highlighted the importance of genomics study in human disease. The project was initiated in 2006 to collect and share all genetic variations effecting human disease at a global level. Dr. Cotton shared that the primary goal of this project was to promote the collection of all mutations and genes from all countries in the world. While he described this as “mission impossible,” he emphasized the importance of achieving this goal because those data are needed for genetic healthcare around the world. In addition to the HVP Australia Database introduced by Dr. Cotton, the HVP China Database was introduced by Dr. Qiming from BGI in his talk while he also talked about genomic medicine in China and clinical practice of medical genetics in North America.
The Rice 10,000 Genome Project
Genomics-assisted plant breeding has been an important strategy in agriculture to increase yield and improve quality of crops. The urgent need for these goals was highlighted in the collaborative Rice 3,000 Genomes Project conducted by International Rice Research Institute (IRRI), The Chinese Academy of Agricultural Science (CAAS) and BGI. This project, introduced by Dr. Kenneth McNally from IRRI, aims to sequence 3,000 rice genomes to represent its global diversity. An extension of this project to sequence 10,000 rice genomes, the 10K Rice Genome Resequencing Project, was formally launched by Dr. Wang on Nov. 15.
Dr. McNally highlighted the importance of the Rice 3,000 Genome Project relative to the birth of the seven billionth human on Oct. 31, 2011, and expected population growth in the next 25 years. He emphasized the fact that the production of rice needs to follow the trend of population growth.
1% Danes’ Genome Project
Population genomics study not only provides us numerous opportunities to understand the distinctive features of the population groups, more importantly, it provides an innovative strategy in health care. This has been one of the main objective in the 1% Danes’ Genome Project, which is proposed to be launched in February 2012, and will initially plan to sequence the genome of 50,000 people with the aims to build up a Danish database, to provide cohort data of Danish for future disease researches, and to develop new mathematics models and bioinformatics analytic tools to promote the development of analytic methodology for population data. This project will work together by University of Copenhagen, Aarhus University, Aalborg University, Herlev Hospital, Technical University of Denmark, BGI, and other participant groups. The Danish database in this project will consist of regional branches established in different regions in Denmark, such as the Digital Healthy Danish Databases in Copenhagen. By building up database for local population, it will help better finding and locating mutations in personal genomes and aid in clinical genetic testing at the local hospitals.
Human Genome Project at large scale – 1,000 Genome Project and 10,000 UK Genome Project
Large-scale genome sequencing projects were launched with the rapid development of sequencing technology. Two projects were introduced by Dr. Durbin from the Welcome Trust Sanger Institute. The 1,000 Genome Project launched in January 2008, was the first human genome project targeted to sequence the genome of a large number of people, and it aims to build up detailed map of human genetic variation. 2,500 individuals from 27 populations worldwide were planned to be sequenced in this project and BGI has participated in this project for sequencing the genome of 400 individuals. According to Dr. Durbin, about 1,700 samples will be sequenced by late 2011 and the 2500 samples will be completed in 2012. A more recent larger scale project was launched by Welcome Trust Sanger Institute in June 2010 -- the 10,000 UK Genome Project (UK 10K). This project included sequencing of 4,000 cohort samples from TwinsUK and ALSPAC studies in a collaboration between Sanger Institute and BGI, and 6,000 exome from samples with extreme phenotypes, such as obesity, or neurodevelopmental disease. The project will help researchers to discover rare genetic variants that play a key role in many human diseases.
The 1000 Genomes Project, an international public-private consortium to build the most detailed map of human genetic variation to date, announces the completion of three pilot projects and the deposition of the final resulting data in freely available public databases for use by the research community. In addition, work has begun on the full-scale effort to build a public database containing information from the genomes of 2,500 people from 27 populations around the world.
Launched in 2008, the 1000 Genomes Project first conducted three pilot studies to test multiple strategies to produce a catalogue of genetic variants that are present in one percent or greater frequency in the different populations chosen for study (European, African and East Asian). Disease researchers will use the catalogue, which is being developed over the next two years, to study the contribution of genetic variation to illness. In addition to distributing the results on the Project’s own web sites, the pilot data set is available via the Amazon Web services (AWS) computing cloud to enable anyone to access this unprecedentedly large data set, even if they do not have capacity to download it locally.
The Earth Microbiome Project
The Earth Microbiome Project (EMP) is a massively multidisciplinary effort to determine the functional and evolutionary diversity of microbial communities across the globe for the benefits of the planet and mankind. Dr Jack Gilbert from the Argonne National Laboratory, University of Chicago has introduced new predictive models including Microbial Assembly Prediction (MAP) and predictive relative metabolite turnover (PRMT), have been applied in the EMP Project and helped to explore new knowledge of microbes. He also reported the latest progress of EMP. There are approximately 10,000 environmental samples being processed in the project utilizing 16S/18S rRNA survey and shotgun metagenomics sequencing. Over 60,000 samples were collected from over 100 sites around the world, and more than 120 researchers are currently associated with the project around the world. BGI participated in the EMP project to identify sample collection in Asia and to provide sequencing for metagenomics projects, and to support this project with development of a bioinformatics pipeline.
The most important goals for current scientific researchers are the development of new approaches to improve human health, produce sustainable crops, promote bio-energy, and protect the environment. Rapid progress in genome science and a glimpse into its potential applications have spurred observers to predict that biology will be the foremost science of the 21st century. Technology and resources generated by genomics research are already having profound effects on agriculture, human disease, micro-ecosystem research.
The development of sequencing technology, starting from the early 1970s, has provided the rapidly growing knowledge of DNA sequences that is indispensable for basic biological research and discovery. Genomics have the ability to widen the breadth of knowledge with which scientists are able to unveil the secrets of all living organisms in the biological world. “We have a dream to sequence everything on earth and to sequence everybody in the world.” said Professor Huanming Yang, Chairman of BGI, at the welcome ceremony held on the first day of the conference. “In the near future, genome sequencing technology will provide even greater opportunities for us.”
The future looks promising when comparing the sequencing output from the present to the past. The human genome project, which formally began in 1990, took almost 13 years by about 3,000 participants in 6 countries at a cost of $3 billion U.S. to sequence a single human genome. At present, the sequencing speed has increased dramatically along with reduced costs driving accelerated genomics research. As Dr. Yang noted, “We are experiencing a rapid sequencing revolution; now BGI alone is able to sequence 100 human genomes per day.”
Today, genomics research is being conducted across a wide range of study areas and is involved in numerous applied fields, including biotechnology, biomedicine, diagnostics, among others. The plenary program was focused on the latest genomic technology, cross-omics platforms, bioinformatics and bio-cloud computing.
In addition to expert presentations, panel discussions were conducted on improving information flow from China, ELSI (ethical, legal and social issues), and developing academic-industry collaborations to promote idea exchange and collaboration among international researchers.
In this conference, BGI announced the collaboration with Johns Hopkins University on synthetic yeast project to accelerate the development of synthetic biology. (http://en.genomics.cn/navigation/show_news.action?newsContent.id=8950). In addition, BGI and Professor Lennart Hammarström from Karolinska Institute Huddinge Hospital also signed MOU for collaboration and joint education program in immunogenetics, aiming to facilitate researches and develop new strategies in the fields of immunogenetics.
ICG-6 provides a platform for researchers to exchange their knowledge and insights on cancer research, one of the most important topics in biology. It also strengthens the international cooperation in cancer study between the two countries. As a world-class research institution, BGI has established its own technology platforms based on large-scale genome sequencing, efficient bioinformatics analysis, and innovative genetic health-care initiatives. In the future, BGI will continue to increase the domestic and international scientific cooperation and bring more advancement to the research of human healthcare.