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Illumina Launches Assay for Analyzing Gene Expression in Paraffin-Embedded Samples

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Illumina last week announced that it has launched an assay for gene expression profiling of formalin-fixed paraffin-embedded samples and the first product for the assay, a cancer panel.

The DASL (cDNA-mediated Annealing, Selection, extension, and Ligation) assay can interrogate paraffin-embedded samples as well as other samples containing partially degraded RNAs. According to the firm, the assay enables researchers to measure RNA abundance of over 500 genes in parallel per sample. It probes three unique sequences per target gene, and PCR amplification is limited to genes of interest.

“The critical point of differentiation [from] a whole genome-array that we or Affymetrix or anybody else has put out [is that] you’ve got gene-specific content on the array itself,” explained Bill Craumer, Illumina’s director of corporate communications. With the whole-genome arrays, “you might have a 50mer or 60mer sequence …and that binds directly to the prepared sample. In our case, the lion’s share of the specificity and annealing and then binding to the target of interest all happens in solution.”

He added, “So the array itself is a universal array — there’s no sequence-specific information on the array. What there is is a bunch of little addresses, and those are complementary to an address in the assay that’s prepared in solution.”

The first product to be released for the assay is a standard DASL cancer panel. Illumina said that there are more than 400 million formalin-fixed paraffin-embedded cancer samples in North America alone, so “it was just a very logical place to start,” Craumer told BioArray News.

“The cancer panel is one content offering that can work with the assay. In this case, there are some 500 genes in the cancer panel, [but] you could develop another one for Alzheimer’s,” for example, he said.

Craumer noted that one of the difficulties of penetrating the market for analyzing these types of samples may be tracking them down. Despite the “huge” potential market size, “where they all are is still a big subject of debate,” he said. “We’d be real happy getting maybe 1 percent of those samples assayed,” at around $100 each, depending on the size of the study.

The standard method for analyzing the paraffin-embedded samples is through the use of qPCR, which is a low-multiplex approach and can be expensive. “QPCR does work, but it’s one target at a time and it’s very expensive,” he said. “You can’t look globally at a number of markers at once.”

Competition in the market will come from Affymetrix, which has an alliance with Arcturus, a Mountain View, Calif.-based firm that is commercializing laser capture microdissection instruments, to co-develop new tools for analyzing gene-expression data on paraffin-embedded clinical biopsy samples. Under that pact, Arcturus is providing Paradise reagents to extract and amplify RNA from paraffin-embedded tissues for study with an Affymetrix GeneChip.

Bob Schueren, COO of Arcturus, told BioArray News that the firm has been shipping kits to customers of both Affymetrix and Agilent for about a year. He didn’t provide a number for the market size of paraffin-embedded samples, but said, “There’s probably millions of samples out there in the archives, and there’s often data over time,” which would allow researchers to do retrospective studies.

Officials from Affymetrix and Agilent were unable to provide comment by the time this article was published.

The DASL assay was tested at nine different institutions over a two-year period, according to Illumina, and processed over 1,000 unique samples representing a range of biology and disease during that period.

The assay can run on either of Illumina’s BeadArray platforms — the 96-sample Sentrix Universal Array Matrix or the 16-sample Sentrix Universal BeadChip.

Illumina also said that it would soon launch its Human-6 and HumanRef-8 BeadChips, its highly anticipated microarrays for whole-genome analysis.

The Human-6 contains six whole-human genomes on a single BeadChip, and is actually two array strips, with each one interrogating 24,000 transcripts. “It’s all the known genes, a bunch of splice variants, and a bunch of genes that might be genes but nobody really knows,” Craumer said. The HumanRef-8 contains eight samples on a single chip, with 24,000 transcripts per sample.

Illumina has a target date for the launch of the chips, but Craumer would not disclose it, saying instead that introduction of the arrays would likely occur during the first half of this year. The firm still intends to offer the whole-human-genome arrays for roughly $100 per chip — much lower than the industry average of $500-$600 for other whole-genome arrays.

— EW

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