NEW YORK, April 11 – Microbead maker Lynx Therapeutics seems to have finally succeeded in getting its message out to the market.
Wednesday, the company announced the latest in a recent string of deals for its Megaclone bead technology, used in gene expression studies. This agreement, in which Lynx will genotype RNA from different varieties of the Tilapia fish for Norwegian marine genomics company GenoMar, is the fifth commercial collaboration Lynx has announced since the end of February.
“What you see happening now is the result of months and months, even up to a year’s worth of discussions about our technology and its commercial applications,” said Ed Albini, the company’s chief financial officer.
In addition to the deal with GenoMar, the company has begun two separate collaborations with AstraZeneca, one for disease gene expression analysis and another for asthma SNP detection. The company has also agreed to provide Celera with gene expression data generated using its technology and it has signed a deal to identify cancer genes for prostate cancer biotech company UroGene. Additionally, Lynx of Hayward, Calif., has recently initiated five technology development partnerships with different academic researchers.
“If you look at the diversity and number of agreements that they have signed up recently, the message is that the fundamentals are accelerating and the technology is broadly enabling and broadly applicable,” said Todd Nelson, an analyst who covers Lynx for Dain Rauscher Wessels
Lynx, which was founded in 1992 by Sam Eletr, a co-founder of Applied Biosystems, has struggled for years to produce a commercially viable product. As recently as this winter, the company had no marketing department and was just starting to think about how to get the word out. The company was further crippled by the difficulties in explaining how its microbeads work.
“Our technology is quite a bit different than the way that others apply things. It takes a while for people to understand it," said Albini.
Lynx's foundation technology, Megaclone, uses microbeads to sort millions of DNA molecules according to sequence. Each different molecule binds to a microbead, with each bead able to hold up to 100,000 identical molecules. Fluorescent tags on each bead indicate how much of a particular DNA molecule is on the bead.
Megasort uses Megaclone to extract genes from two samples and compares their expression levels in a single assay. One probe from each sample is hybridized with a population of megaclone microbeads that have copies of DNA fragments or genes from each sample. The relative fluorescence of different beads indicates differences in expression.
Other applications of MegaClone include the company’s Massively Parallel Signature Sequencing technology, which simultaneously generates sequence information from millions of DNA fragments using MegaClone, and its MegaType SNP detection technology.
The MPSS system identifies each molecule by a 16 to 20 base signature sequence and can detect the levels of gene expression in cells, even when a gene is rare, Lynx said.
In MegaType, which is still in development, the beads with two different groups’ DNA fragments are pooled, then sorted to reveal the specific nucleotide differences between them. The advantage of MegaType over other SNP detection methods, according to Lynx, is that the detection of multiple SNPs can be completed in a single experiment rather than thousands or millions of assays.
Additionally, Lynx is developing microbead-based protein profiling technology for proteomics experiments.
One advantage of all these applications, said Albini, is that experimenters can do SNP detection and genotyping without first having a complete genome in hand.
With microarrays, on the other hand, researchers would have to have a pre-selected set of known genes to place on the array, and to hybridize to the test sample, in order to use the arrays to detect genetic variations. But with Lynx’s megaclone technology, researchers quickly determine the sequences of millions of fragments of DNA, then detect only the differences in gene sequence through noting the differences in microbead hybridizations.
In the case of the GenoMar collaboration, this feature proved particularly advantageous, Albini said. Tilapia fish may be known as the chicken of the sea, but the sequence of its genome remains a mystery. To resolve this issue, Lynx can build a MegaClone library of DNA using this genome and can perform a massive amount of sequencing in order to fish out sequences that may be of use to breeders. Financial terms of the deal were not disclosed.
Lynx’s success with its collaborations and technology has so far evaded Wall Street’s favorable gaze. Wednesday afternoon, the company’s stock was trading on the Nasdaq at $7.96 per share, down over 90 percent from its March 2000 high of $99.50.
Nelson, however, attributed Lynx’s stock slide to the general genomics market slump. “These genomics companies trade together, so when the fundamentals turn around, this should benefit Lynx,” he said.