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Halo Genomics to Launch Targeted Sequencing Product that Combines Single-Tube Amplification, Library Prep


By Julia Karow

Halo Genomics of Uppsala, Sweden, is working on a new product for targeted resequencing that is based on its Selector technology and combines single-tube target amplification and library preparation.

The company is currently looking for a handful of early-access customers to test the product, which it plans to launch in the second quarter, initially for use with the Illumina sequencing platform.

According to CEO Olle Ericsson, the technology offers the advantages of PCR – high specificity and coverage – over hybridization-based target enrichment methods, but at lower cost and higher throughput than competing platforms, such as RainDance or Fluidigm, which require dedicated microfluidics. "The most striking difference [to competing technologies] is the fact that we’re replacing all instruments and robotics with a plastic tube," he said.

Known as Olink Genomics until last year, the firm changed its name to Halo Genomics in January to distinguish itself from its parent, Olink Bioscience, which founded the subsidiary in 2008 in collaboration with a group of scientists from Uppsala University (IS 9/9/2008).

Also in January, Halo Genomics moved into new digs in the Uppsala Science Park that more than doubled its space to accommodate future growth.

Last month, the company signed distribution partnerships with Cambio, which will sell its products in the UK, and Integrated Sciences, which will sell them in Australia and New Zealand.

The company's goal is to commercialize the Selector technology, a single-tube multiplex amplification method developed at Uppsala University (IS 5/22/2007), for next-generation sequencing. The technology, which can amplify several thousand genomic targets in a single tube, relies on oligonucleotide selector probes. These bind to the ends of restriction fragments that encompass the target and circularize them. The circular DNA is then amplified and sequenced.

Last November, Olink Genomics and its Uppsala University collaborators published a description and demonstration of an improved version of the method in Nucleic Acids Research. For the study, the researchers amplified 501 exons of 28 cancer genes in cell lines, frozen tumor biopsies, and formalin-fixed tumor biopsies using multiple displacement amplification instead of PCR, and sequenced them on the SOLiD platform. They found the specificity to be 94 percent, and 98 percent of the intended targets were covered.

Last summer, the company released its first product, the SelectorKit, to early-access customers, enabling them to amplify up to 100 genes per reaction from a microgram of DNA (IS 6/8/2010). That kit, which is compatible with several sequencing platforms, is now generally available. Pricing depends on the number of reactions and the size of the target region, but for 100 reactions and a 200- to 400-kilobase target, it is $265 per reaction.

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Later last year, the firm launched six gene panel kits, for targeted sequencing of genes involved in cell signaling pathways and for sequencing the BRCA1 and BRCA2 genes. The BRCA gene panel kit costs $300 per reaction for 10 reactions, and $200 per reaction for 50 reactions.

Halo Genomics developed the BRCA kit — one of the first examples of a clinical application for the method — in collaboration with Edwin Cuppen and Wigard Kloosterman at the University Medical Center in Utrecht, the Netherlands. According to Ericsson, the Dutch center, which uses the SOLiD platform, is currently validating the assay.

In addition, the company has been offering a target selection service for targets on the order of 100 genes.

The upcoming product that combines amplification and library prep will incorporate Illumina sequencing primers and sample barcodes in a PCR reaction that follows the enrichment.

Halo decided to develop the product for Illumina sequencing initially because of that platform's large market share, but it already has "good preliminary data" for other sequencing systems and plans to make it compatible with the 454, SOLiD, Pacific Biosciences, and Ion Torrent platforms in the future, according to Ericsson.

Currently, users can target up to 400 kilobases of sequence, but the method is scalable and a whole-exome product is currently in development.

According to Ericsson, initial applications include targeted sequencing of up to several hundred candidate genes in up to 96 samples, with plans to increase the number of sample barcodes to 384 later on.

No list prices are yet available, but Ericsson said the product's pricing will be "highly competitive" since the "time-consuming and expensive library preparation" will be eliminated, and prices will decrease with volume.

This, along with the product's high specificity and coverage, will make it attractive for clinical sequencing applications, he said.

Current beta users include Jay Shendure at Washington University, a member of the firm's scientific advisory board (see Paired Ends, this issue), as well as researchers at Uppsala University.

Shendure told In Sequence that his lab only recently started working with Halo Genomics but he believes the technology could be "particularly helpful for projects requiring a fixed set of targets and a large number of samples, and where sample quantities are also limited."

Have topics you'd like to see covered in In Sequence? E-mail the editor at jkarow [at] genomeweb [.] com.