By Julia Karow
This article was originally published Oct. 5.
Genetic testing company Correlagen Diagnostics plans to launch a comprehensive assay for genetic cardiovascular disease this month that will run on a Helicos BioSciences' sequencing platform in its CLIA lab, In Sequence has learned.
The assay, Correlagen's first to run on a next-generation sequencer, will cover approximately 300 genes associated with hereditary cardiovascular disease. Going forward, the company plans to use the Helicos system for other assays in the areas of endocrinology, neuropsychiatry, and immunology.
Helicos and Correlagen said last week that the Waltham, Mass.-based genetic disease diagnostics company was acquiring a Helicos Genetic Analysis system (see In Sequence 9/29/2009). In addition, the two have started a scientific collaboration to optimize sample-preparation methods for targeted resequencing on the HeliScope as well as to integrate Correlagen's processing, variant annotation, and interpretation applications into Helicos' bioinformatics pipeline.
Correlagen Chairman and CEO David Margulies told In Sequence that the company has been collaborating with Helicos for about six months, and expects to receive its own Helicos Genetic Analysis system this week. He could not disclose the terms of the deal, but said that "it's a real sale."
Correlagen, which is privately held and has a CLIA-certified laboratory, has developed "hundreds of gene tests," both for its own testing service and for third parties, Margulies said. Over the last few years, it has built a workflow for automated Sanger sequencing, based on Applied Biosystems 3730 sequencers.
But the need to reduce the cost of increasingly complex genetic tests recently prompted Correlagen to look into next-generation sequencing. "The critical driver of a clinical diagnostic business is to have assays of utility at affordable costs," Margulies said. Over the last few years, advances in science meant Correlagen's assays had to become more comprehensive, covering larger numbers of genes. "The size of our assays has been climbing for a number of years," he said.
As a result, the company started to consider new sequencing technologies to reduce the cost of its assays. "We spent a lot of time working with all the different suppliers, and we concluded that the technical advantages of the HeliScope are formidable," Margulies said, adding that the firm plans to publish comparative data from different sequencing platforms.
In particular, Correlagen found that Helicos' amplification-free single-molecule sequencing process introduces less bias than other platforms, and has "a much easier workflow, leaving less room for error," according to Margulies.
He said the error rate of Helicos' chemistry is "widely misunderstood," adding that Correlagen has "carefully evaluated the composite error rates of several platforms and has been able to use coverage to assure high fidelity reads on the HeliScope."
Margulies also believes that Helicos' technology will allow Correlagen to interrogate somatic and germline mutations, copy number variations, and gene expression "all in a single assay," which he said other platforms cannot do right now.
In the near term, he said he expects the Helicos platform to improve further, with better chemistries, longer reads, flexible flow-cell geometries, and improved image analytics.
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In addition, to be on the safe side, Correlagen has been validating its assays on more than one sequencing platform. The company uses a proprietary DNA target enrichment method that is compatible with any of the three other currently available next-gen sequencing platforms, according to Margulies. "We are not going to be platform-dependent," he said.
Correlagen plans to launch its first assay on the Helicos platform this month, making it initially available to a limited number of customers, followed by a more general release in early December. The company will present the assay — aimed at cardiovascular disease — at a conference on hypertrophic cardiomyopathy in Minneapolis next week.
The assay covers "all genes known to have a monogenic effect on cardiovascular disease," Margulies said, including 125 causative genes and 175 genes "of research interest." The company sequences these genes on the Helicos platform first, and confirms all mutations it finds by automated Sanger sequencing.
Because the assay is so comprehensive, doctors can order it for patients with various types of cardiovascular disease — including aortic disease, early-onset coronary artery disease, cardiomyopathy, and arrhythmia — who also have a family history of that disease.
The assay is "greater than an order of magnitude" cheaper on the Helicos platform than it would be on a Sanger instrument, Margulies said, including not just reagent costs but also instrument depreciation. The list price for the Helicos Genetic Analysis system, which includes computing equipment, is just under $1 million — about twice as much as competing next-gen sequencers — but Margulies said that compared with Illumina's Genome Analyzer, "it's really not that different when you add in the IT."
Correlagen will update its clinical reports over time as more genetic variants are linked to the diseases that it tests. The company regards its variant scoring and automated reporting as its "core ability," according to Margulies.
Under their collaboration, Correlagen and Helicos will optimize sample prep methods for targeted resequencing and integrate Correlagen's processing, variant annotation, and result interpretations applications with Helicos' bioinformatics pipeline. "It's our expectation that over time, other CLIA laboratories will be able to benefit from this collaboration," Margulies said.