NEW YORK (GenomeWeb) – Japanese researchers will now have access to a new microarray designed specifically for studying the Asian country's population.
Toshiba and Affymetrix earlier this month announced the availability of the chip, called the Japonica Array, as a service. Specifically, Toshiba has the exclusive right to provide genotyping services on the array to Japanese universities, hospitals, pharmaceutical companies, and other research organizations.
"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," Takuzo Takayama, senior manager of Toshiba's Life Science Business Department, told GenomeWeb.
"The need for a supercomputer to carry out the mapping and specialist researchers" pushes the cost to more than ¥500,000 ($4,190) per individual, Takayama said. "To overcome this prohibitive expense and long mapping time, Toshiba decided to create this genotyping service."
In comparison, Toshiba has said that with the Japonica Array, mapping takes a week and costs ¥19,800, before tax, to genotype a single sample.
Toshiba's Life Science Business Department falls under its Healthcare Medical Business Promotion Division, and healthcare is one of the Tokyo-based company's business pillars, Takayama noted.
The content on the Japonica Array was based on a whole-genome reference panel developed at Tohoku University's Tohoku Medical Megabank Organization in Sendai. The organization hosts a biobank established to combine genomic and medical information as part of a larger effort to rebuild community medical systems in the area following the Great East Japan Earthquake of 2011.
The Japonica Array contains 675,000 SNPs common among Japanese, making it possible to genotype Japanese individuals within a short time, and is designed to streamline imputation of unobserved genotypes in order to reconstruct the whole-genome sequence of over three billion base pairs from low-coverage sequencing reads, according to Takayama.
Satoshi Tsunakawa, president of Toshiba Healthcare, said in a statement that the Japanese firm decided to work with Affymetrix "after reviewing various microarray technology providers." He said that Toshiba selected the Axiom platform for the project because of its "high-throughput capability, cost effectiveness, [and] superior performance," and the vendor's "highly reproducible manufacturing process."
Going forward, Toshiba will offer the array as a service through its analysis center. Takayama said that the company hopes its 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," he added.
According to Matthew Levy, Affymetrix's vice president of commercial operations for the Asia Pacific region, the new Japonica Array is the "first widely available Japanese-focused genotyping array targeted for biobank research" offered by the Santa Clara, Calif.-based company.
Affymetrix maintains an office in Japan and has worked with at least one other local customer to design a population-optimized array. Earlier this year, Genesis Healthcare, a Tokyo-based consumer genomics company, announced that it was using custom Axiom arrays in its direct-to-consumer offering.
Affymetrix does offer a number of arrays optimized for Asian populations, including its CHB 1 and CHB 2 Axiom Genome-Wide Array Plates, which are focused on the Han Chinese population but include coverage of a wide range of other Asian populations, as well as its ASI 1 and EAS 1 Axiom Genome-Wide Array Plates, both of which "cover a broad range of Asian populations," Levy said.
Much of the interest in these arrays comes from customers in the region who desire arrays tailored to their populations of interest, rather than more generic whole-genome genotyping arrays, many of which are modeled on European populations.
"A large part of our human genotyping business is providing custom population and disease-focused arrays," said Levy. "Our customers tell us they do not want to use common catalog arrays that contain large numbers of markers where many of the variants are irrelevant to their population," he said. Levy noted that Affymetrix has therefore "developed many different population-specific custom array designs for private and public studies in all the major Asian countries as well as other populations around the globe."
Affymetrix has disclosed a number of deals to develop custom arrays for biobanks in recent years. Last year, it announced an agreement with the UK Biobank to genotype its 500,000-sample repository, as well as another to provide the chips to genotype several hundred thousand samples as part of the US Department of Veterans Affairs' Million Veteran Program.