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Anagnostics, Austrian Blood Bank Developing New Target Enrichment Method


By Justin Petrone

Anagnostics and the Central Blood Bank of Linz in Austria are developing a new way to enrich targets of defined DNA sequences for use in next-generation sequencing applications.

The blood bank will use the new approach, developed on Anagnostics' three-dimensional Hybcell array platform, for applications such as human leukocyte antigen subtyping.

Markus Jaquemar, managing director of sales, marketing, and business development at Anagnostics, said that Linz is using Anagnostics' so-called "compact sequencing" application to design the enrichment assays.

"We basically do an enrichment step where there are targeted sequences which are amplified with PCR and we perform a primer extension for these specific sequences" on the Hybcell platform, Jaquemar told BioArray News this week. "With specific primers we can enrich very specific target sequences, and then [the Central Blood Bank Linz] can sequence them using next-generation sequencing for confirmation purposes."

The partnership is Anagnostics' first publicly discussed deal concerning its compact-sequencing approach, which it debuted last year as an assay for KRAS mutations.

Such mutations are found at a high rate in leukemias and colon, pancreatic, and lung cancers. Anagnostics' compact sequencing method relies on an internally developed, three-stage primer-extension method to detect variants in codons 12 and 13 in the KRAS gene (BAN 10/26/2010).

Anagnostics claims the approach is more sensitive and faster than competing methods. Using the company's Hybcell arrays, scientists can "get down to less than 1 percent detection of mutation versus wild-type DNA," Jaquemar said in October. "Others are around between 5 and 10 percentage detection sensitivity."

The total processing time for the assay is three hours from sample preparation to result. The compact sequencing assay can also detect mutated DNA in formalin-fixed, paraffin-embedded samples, according to the firm.

Anagnostics' KRAS assay pits the company against rivals such as Qiagen and Roche, which sell PCR-based assays for mutation detection. And its move into target enrichment sets it up against the likes of Agilent Technologies, Roche NimbleGen, Illumina, RainDance Technologies, Fluidigm, CustomArray, and a host of other firms, all looking to dominate the enrichment-technologies market.

According to Jaquemar, Anagnostics sees compact sequencing as a "companion" to next-generation sequencing because "we are searching for very specific sequences compared to when you are sequencing unknowns."

Anagnostics' approach is a "good adjunct to sequencing efforts where we can help in a very easy and pretty rapid [way] to enrich or identify specific sequences," he said. "This is what the blood bank is doing with our technology."

The target enrichment-development project is partially funded by the state-supported Austrian Research Promotion Agency. The partners expect the first results of the proof-of-principle study to be available in the middle of the year.

An e-mail to researchers at the Central Blood Bank Linz seeking comment was not returned in time for this publication.

Branching Out

Separately, Anagnostics recently inked a distribution pact with Invicon Diagnostics, which has been distributing the firm's drugs-of-abuse screening products to customers in Germany since January.

Munich-based Invicon also produces clinical chemistry reagents, calibrators, and control materials — "areas in which Anagnostics and Invicon have collaborated for quite some time," said Jaquemar.

He added that Anagnostics "is looking forward" to selling through Invicon more diverse products as they become available. He did not elaborate.

Anagnostics markets its own products in Austria; the company, founded in 2005, is based in St. Valentin, southeast of Linz. The firm is engaged in "several discussions about distribution in countries such as Italy, Turkey, Australia, [and] Switzerland," he said.

Anagnostics' Hybcell DNA or protein arrays differ from competing slide-based platforms because they comprise detector molecules that are immobilized on the surface of a cylinder, which is enclosed within a cylindrical container. Users can fill this external cylinder with sample, and up to 96 Hybcell arrays can be processed at a time in the company's Hyborg system, which integrates a thermal cycler, a hybridization station, and a scanner (BAN 2/9/2010).

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The company sells two Hyborg systems: a DX and SX model.

The former is a "black box system" intended for routine analysis and processes prefabricated Hybcells only with "locked-down application protocols," Jaquemar said.

The latter, meantime, is aimed at the research market to enable scientists to write, edit, and modify protocols and interact with Anagnostics' staff to design their own Hybcell applications. The researchers at the Central Blood Bank Linz are currently using the Hyborg SX.

In February, Anagnostics introduced a second generation of the Hyborg instruments. Jaquemar said that the new systems are "faster" and "more precise" than the previous generation, but that the bulk of alterations were made on the manufacturing side. "We have moved from a prototype to a routine, standardized technology platform," said Jaquemar.

Last summer, Anagnostics launched two panels to screen samples for the presence of drugs of abuse in urine. The first, Hybcell DoA Urine Basic, screens for six major drugs of abuse: amphetamine; cocaine; methadone, buprenorphine, and other opiates; and THC.

The second, Hybcell DoA Urine Screening, includes an extended panel for 19 drugs and drug classes: amphetamine; cocaine; methadone, buprenorphine, oxycodone, fentanyl, tramadol, and other opiates; THC; MDMA; benzodiazepines; barbiturates; phencyclidine; tricyclic antidepressants; methamphetamine; ethylglucuronide; zolpidem; and zopiclone.

In addition to selling drugs-of-abuse screening tests, Anagnostics is developing arrays to screen for the presence of sexually transmitted and infectious diseases.

Jaquemar said that Anagnostics is in the "final preparation of the external validation" for obtaining a CE mark for its drugs-of-abuse product. He estimated that the STD assay will become available in the second half of this year.

Looking ahead, Jaquemar said that Anagnostics will likely seek funding to expand its menu of assays and commercialization activities.

"We don't want to cover 25 different applications, but in the areas we want to cover — infectious disease, oncology — we want to expand the menu," said Jaquemar. "For those two areas we are looking for an additional investment. We need resources for developing those new assays."

Anagnostics is also in the midst of negotiating some original equipment manufacturing deals with "significant" companies, Jaquemar added, another expansion of the firm's business strategy.

"We are discussing with significant companies how our technology could be used for their purposes, on an OEM basis, on a co-development basis," said Jaquemar. "This is a significant difference in terms of what we are doing and what we are following up on."

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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