The National Institute of Advanced Industrial Science and Technology (AIST) (President: Hiroyuki Yoshikawa) launched "The Research and Development about Advanced Biotechnology Research Facility with Gigasequencers" as the FY2008 advanced biotechnology research facility improvement project of Okinawa Prefecture (Governor: Hirokazu Nakaima), in collaboration with the Okinawa Science and Technology Promotion Center (President: Shigemitu Shokita) and Tropical Technology Center Ltd. (Representative Director: Hozumi Nakou).  In this project, we conduct research on genomes from various microorganisms to the human, using the latest next-generation DNA sequencers that were introduced in Okinawa Prefecture in the fiscal year 2007.  We promote research and development in the following subjects that makes the best use of the characteristics in the Okinawa region: (1) development of the preprocessing and data-processing techniques (2) identification of the genetic diseases specific to the Okinawa region and the development of treatment methods (3) the identification of target molecules for cancer therapy and development of treatment methods (4) the analysis of industrially useful microorganisms and gene resources (5) the development of microorganisms serving as pharmaceuticals and health-food resources, and useful gene resources.

The creation of new industries, including pharmaceutical and health-food industries, and the development of the fermentation industry in Okinawa Prefecture would be accelerated.  Furthermore, it would also enhance the research and development on domestic biotechnology and industrial promotion, e.g. the analysis of a Japanese standard genome that can function as the basis of genome drug discovery in our country.

Figure 1 Next Generation GIGA  Sequencer, Okinawa Health Biotechnology Research&Development Center, Uruma-City, Okinawa Prefecture,

The Human Genome Project, which was conducted by the International Human Genome Sequencing Consortium, ended in 2001, and all base sequences of the human genome were made public.  The availability of this data led to "post-genome researches" in areas such as those concerning the diagnosis or the medical treatment based on the genomic sequences, interaction of proteins, expression analyses.  And the research on the analysis of the genomic sequence seemed to have stagnated.  However, the base-sequence-analysis technique advanced drastically, and a next-generation sequencer (Giga-sequencer), which has an ability to decipher DNA of 1 billion (giga) bases at once with more than 100 times the analytical speed and 1 hundredth of the cost of conventional sequencers, was put to practical use in 2007.  In foreign countries, institutes including the Sanger Institute (U.K.), Broad Institute (U.S.A.), and the Beijing Genomics Institute (China) introduced next-generation sequencers.  These institutes are promoting research and development with increasing speed in areas such as of the re-analysis of the human genome, the acquisition of individual genome information and the genome analysis of industrially useful organisms utilizing the increased analytical speed of the latest sequencers.  In Japan, Okinawa Prefecture promptly introduced three next-generation sequencers in March 2008 and, thus, formed a hub for the research using the next-generation sequencers.

Okinawa Prefecture is furthering research and development of biotechnology based on the Okinawa Promotion Plan (Prime Minister's decision; July 10, 2002).  It has promoted the collection and the use of regional resources such as microorganisms peculiar to the subtropical area and the research and development on diseases peculiar to this region at Okinawa Science and Technology Promotion Center, Tropical Technology Center Ltd., University of the Ryukyus, Okinawa National College of Technology, and research organizations of Okinawa Prefecture (Industrial Technology Center and Agricultural Research Center, etc.).  It aims at the advancement in areas such as medical treatment, health industry, and fermentation industry in the prefecture in the light of the new genomic studies that use the next generation sequencers.

AIST has completed analysis of the genome of Aspergillus(yellow Aspergillus) by a joint research with the National Institute of Technology and Evaluation, and is performing the genome analysis of black Aspergillusthat can be used as a standard.  We also have established the bacterial artificial chromosome (BAC) library (330,000 clones) from a single Japanese genome.  This library is the only one in the world that is constructed purely from genomic sequence of an individual of Japanese origin, which differentiates it from of genome data where the race and individual are uncertain decoded by Human Genome Project, and includes enough scale and volume of information equivalent to about 15 times of the human genome.  Though careful consideration to ethics issue is necessary, the accumulation of individual genomic data is required for the development of curative measures that are appropriate for the individual.  For this, the Japanese standard genome sequence functioning as a basis for research is indispensable.  The introduction of the latest next-generation sequencers has opened new avenues in this direction.  

Chiefly, the following 3 research items are to be executed in this project.  

First, we establish technology system for the analysis of genomes using next-generation sequencers and analyze genomes of the microorganisms and the gene resources, and perform a comparison analysis based on the data.  Those would lead to the promotion of the traditional fermentation industry such as Awamori and the pharmaceutical and health-food industries in Okinawa Prefecture.  In addition, we will acquire and analyze the Japanese standard genome sequence.  It will be a basis for the development of diagnostic and medical technologies using individual genome information.  It would be useful, as we facing the coming society with many elderly individuals and reduced birthrate, and medical care for individuals.

Figure 2. Implementation system

We will establish technical systems using next-generation sequencers, and cooperate with domestic and foreign universities, research institutions and companies as a research base of genome-research in our country.  It is thought to be important to make such a research base for next-generation sequencers in our country, because it is not a system that can be managed by individual researchers or a single institution.

The use of next-generation sequencers is expected to be useful in the safety evaluation of advanced medical treatment of diseases such as chromosomal abnormalities by assessing the stability of genome, in the pursuit of effects such as genomic modification in gene therapy of hereditary disorders, and in the regenerative medicine that uses the embryonic stem cell or the induced pluripotent stem cell.  We are planning to join in regenerative medicine research programs in the future.