Toshiba Corporation launches genotyping service using Japonica Array™, a Japanese population genotyping array

Toshiba Corporation (Tokyo: 6502) today launched a genotyping service for universities, hospitals, pharmaceutical companies and other research organizations. The service employs Japonica Array™, a genotyping array optimized for ethnic Japanese.

Japonica Array™, the focal point of the service, facilitates genome sequencing and genotyping of blood, saliva or DNA samples, which Toshiba performs at its analysis center. The genotyping service will accelerate efforts by Japanese researchers to identify genetic markers associated with diseases and specific traits, and help to advance health maintenance, disease prevention and therapies tailored to unique individual genetic characteristics. The new service will also improve Japan’s international competitiveness in this field.

The human genome is estimated to have about 3 billion base pairs, and it takes even the most advanced genome sequencer over a month to map it. The need for a supercomputer to carry out the mapping and specialist researcher pushes the cost to more than 500,000 yen. To overcome this prohibitive expense and long mapping time, Toshiba’s genotyping service uses the Japonica Array™ to focus on genetic information unique to the Japanese population. As a result, mapping takes only a week or so and it costs 19,800 yen (before tax)*1 to genotype a single sample.

Japonica Array™ was developed as a Center of Innovation Program (COI) STREAM project at COI sites*2, and is based on the whole-genome reference panel developed by the Tohoku University Tohoku Medical Megabank Organization (ToMMo)*3. It contains approximately 675,000 single-nucleotide polymorphisms*4 (SNPs) with a base sequence*5 common among Japanese, making it possible to genotype a Japanese person in a short time. It is designed to be able to infer (“impute”*6) unobserved genotypes in order to reconstruct the whole-genome sequence of over three billion base pairs from low-coverage sequencing reads.

The high-quality and cost-effective Axiom® Genotyping Solution platform from U.S.-based Affymetrix, Inc. is used as a platform for the custom-design Japonica ArrayTM and its unique genetic content.

Tohoku University, Hirosaki University and Niigata University currently plan to use Toshiba’s newly launched genotyping service. The company will also promote it to research institutes and pharmaceutical companies.

Toshiba will continue to collaborate with COI STREAM to identify base sequences unique to different ethnic groups and to develop ethnic genotyping arrays.

“It is a privilege to collaborate with Toshiba Corporation Healthcare Company and Tohoku University on the development of this important custom genotyping array design that will be offered by Toshiba’s Japonica Array™ Service. We are further honored that Affymetrix and our Axiom® Genotyping Solution was selected as the platform of choice for this program that we believe the research using this technology will lead to new insights into the association of genes and diseases that are unique to the Japanese population can ultimately lead to improved health and wellbeing for all Japanese people.”

Notes:
1: Additional cost is required when extraction of DNA from blood or saliva samples are needed.
2: COI sites = Main locations where COI teams’ activities take place
   Reference: Center of Innovation Science and Technology based Radical Innovation and Entrepreneurship Program (COI STREAM)
   URL: http://www.mext.go.jp/a_menu/kagaku/coi/ (Japanese only)
   Reference: Center of Innovation (COI) program
   URL: http://www.jst.go.jp/coi/outline/outline.html
3: Tohoku Medical Megabank Organization (ToMMo)
   URL: http://www.megabank.tohoku.ac.jp/english/index.php
4: A Single-Nucleotide Polymorphism (SNP, pronounced snip) is a genomic base sequence variation occurring in over 1% of a population in which a single nucleotide differs between members of a biological species or paired chromosomes.
5: The genetic code is encoded in a sequence of four constituent bases of nucleic acids: adenine (A), guanine (G), thymine (T) and cytosine (C).
6: A process for statistically inferring unmeasured genotypes based on an imputation genome reference panel.

* Japonica Array is a trademark of Tohoku University.
* Affymetrix and Axiom are registered trademarks of Affymetrix, Inc.