Tartu, Estonia, home to SNP array maker Asper Biotech, is a long, long way from Silicon Valley. But Asper has not given up on its California style high-tech dream of success with its array-based SNP genotyping system.
“We are looking at a low cost, high-throughput platform,” said Asper co-founder and chief scientific officer Andres Metspalu. “Our glass slides and 50,000 SNPs would be the ideal mix. In this we can beat anybody.”
Do they even think they can beat companies such as Sequenom and Illumina with more in the bank and veterans of the genomics industry at the helm?
“We can put everything on one slide, and it takes five minutes to scan the slide,” Metspalu said.
Asper has just backed up its boasts by publishing a paper in PNAS describing its chip-based resequencing of the p53 gene, (Proc. Natl. Acad. Sci, 99 (8) 5503), and presenting several posters on different applications of its technology at the European Society for Human Genetics meeting in Strasbourg. A second peer-reviewed paper, in which researchers from Asper collaborated with the Sanger Center to resequence chromosome 22 in the Estonian population using APEX technology, is coming out this month in Nature.
“These papers show that the technology is robust and high fidelity,” said Kalev Kask, the company’s Palo Alto, Calif.-based director of business development. “What people should check out is how easy [APEX] is to use.”
The company’s APEX technology consists of 25-mer oligos that are immobilized at their 5’ end on the coated glass surface of a chip. Complementary fragments amplified by PCR then anneal to the oligos. The complementary fragments are slightly longer than the 25-mers, extending upward by several base pairs. They are designed so the first base extending above the hybridized region is the one where the SNP occurs.
To detect this SNP, a mixture containing four separate nucleotide bases, each of which is labeled with one of four fluorescent dyes, is added to these hybridized pairs. These bases attach to the first base of the complementary strand that is extending out above the 25-mer, making it a 26-mer with one of four labels on the top base. The complementary strand is then washed off, and the signal on the top of each oligo is read. The identity of the signal determines the specific polymorphism.
Alternatively, the complementary strands can be designed so each has one base difference on each end, and this labeling technique can be used to resequence a gene, as with the company’s p53 resequencing assays or the resequencing of chromosome 22 in the upcoming Nature article.
This latter article, however, was not just intended as a demonstration that the technology works for linkage disequilibrium mapping of a chromosome. “The chromosome 22 study was meant to demonstrate that Estonians are not genetically different than anyone else in Europe,” said Metspalu. “A British linkage disequilibrium map was compared to an Estonian one, and was identical.”
The reason for this interest is more than national pride of a reemergent Baltic republic intent on showing its Western European brothers a thing or two. Just as Iceland became a giant island laboratory for population genetics once DeCode Genetics got its hands on the country’s health records, startup EGeen International would like to do a similar thing for Estonia. EGeen just raised $2 million in April, and has exclusive commercial rights to information from the Estonian Gene Bank, a government-sponsored effort to gather DNA samples from a large portion of the Estonian population. Just as DeCode garnered initial revenues from a huge collaboration with Roche, EGeen is looking to collaborate with established pharma and biotech companies in using its database to find genetic drug targets and profiles useful in pharmacogenetics.
Asper is not yet doing official business with EGeen, but the two share management: Kask is EGeen’s CEO. As to future collaborations, the timing depends on the progress of the Estonian Genome Project. Currently, the project has just finished setting up its DNA processing facility in Tartu. “The entire thing is not there yet,“ admitted Kask. “But things may happen very fast.”
Without this project, Asper does not have enough SNPs to play with on the high-density chip. “We are trying to use as much as possible the SNPs in the public database,” said Metspalu. “The biggest problem is, almost half of the [ostensible] SNPs in the public database are not usable. The vast majority are not polymorphisms.”
But while Asper waits for the science to catch up with its technology, its 35 employees are concentrating on conserving the remainder of its $2 million nest egg, and producing short-term revenue in the form of coated slides and instruments. The company sells a four-color detector, the Genorama, and consumables so customers can spot their own slides and use the APEX system to do on-chip genotyping. The detector and software sell for $79,000.
Currently, Asper has 12 customers for the Genorama system, including one at Columbia University. But the company knows it has to expand its customer base if it is going to get off the ground. “We are still trying to get a foothold in marketing,” said Kask. “We really need to get a kick start.”