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Ambry Debuts New Cytogenomic Cancer Dx Chips; OGT, Signature Ready Theirs


By Justin Petrone

Growing demand for arrays designed to detect tumor copy-number changes is enticing more chip manufacturers to offer tools tailor-made for cancer research.

Ambry Genetics is the latest company to debut a cancer-screening service based on array comparative genomic hybridization. But competitive offerings loom on the horizon, with new products expected from Signature Genomics and Oxford Gene Technology, among others.

Aliso Viejo, Calif.-based Ambry announced the availability of its CancerArray last week. Manufactured by Agilent Technologies and offered as a service through Ambry's clinical lab, the 180,000-probe array offers genome-wide probe coverage at an average resolution of 20 kilobases with higher-density coverage in more than 400 known cancer-associated genes.

The array partially comprises content from the Wellcome Trust Sanger Institute's Cancer Gene Census, a catalogue of genes for which mutations have been causally implicated in cancer.

Ambry has to date offered themed arrays designed to identify the causes of genetic disorders, and for stem cell research. Though it has run catalog CGH arrays for cancer researchers, it never offered an oncology-themed product.

Until now. Ambry's decided to expand into oncology research because of "increasing demand" for CGH-based cancer studies brought on by CGH platforms "becoming more perfected," along with cheaper arrays, said Ardy Arianpour, Ambry's vice president of business development.

"Since we run a lot of cancer [array CGH] for genomic services, we knew there was a need and interest from researchers to run these arrays," Arianpour told BioArray News this week. "Many of our clients were looking for aberrations in small subsets of cancer genes, but were running standard catalog arrays since there were no other options.

"With a focused array we can now detect single exon variants in select cancer genes as well as larger abnormalities throughout the genome," he added.

Ambry's cancer debut coincides with a proliferation of new tools for the same market, and most of the firms involved have followed the same route: from offering arrays for constitutional genetics to providing chips for oncology research.

'A Natural Progression'

Ambry's entrée follows a number of companies and precedes others focused on CGH-based cancer testing. In the past year alone, companies like Signature Genomics, BlueGnome, and iKaryos Diagnostics have introduced oncology-themed arrays in hopes of grabbing a slice of the demand.

Meantime Oxford Gene Technology has pledged to launch its own cancer-focused chips by the end of the year.

Spokane, Wash.-based Signature Genomics rolled out its oncology testing service from its clinical lab in January. On its website, the vendor says it offers high-resolution microarray analysis designed to detect chromosome abnormalities associated with hematological malignancies including gains, losses, and balanced translocations.

A business segment of PerkinElmer since 2010, Signature relies on the OncoChip, a Roche NimbleGen-manufactured array comprising 135,000 probes targeting 1,800 genes with known or potential relevance to cancer.

Signature said its chip can detect copy-number abnormalities down to 10 kilobases in targeted regions, and 140 kilobases in the genomic backbone.

In addition to the OncoChip, Signature has launched nine copy number-evaluation panels, each focused on a specific hematologic malignancy. It also assesses a group of balanced translocations — chromosomal abnormalities caused by the rearrangement of parts between nonhomologous chromosomes — that are seen in a specific cancer type.

To date, Signature has launched panels for acute myeloid leukemia, B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, T-cell acute lymphoblastic leukemia, and multiple myeloma.

Signature cofounder Lisa Shaffer, who is now chief scientific officer of PerkinElmer's molecular diagnostics business, told BioArray News this week that Signature's cancer array-testing menu is "much different than anyone else's" and that it has been "very well received by the oncology community." She did not elaborate.

Though its menu previously comprised tests for hematological malignancies, Signature recently launched a panel for multiple myeloma, which has "generated a lot of excitement," said Shaffer. She added that the disease is "especially difficult to diagnose with conventional [cytogenetic] methods because of the need to examine the plasma cells."

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"Our work has demonstrated that arrays are superior to conventional methods for all hematologic disorders, but especially" for multiple myeloma, said Shaffer, adding that Signature would offer additional information about the test next month at the American Society of Human Genetics annual conference in Montreal.

Another firm looking to carve out a niche in the CGH-based cancer-testing market is OGT. James Clough, vice president of clinical and genomic solutions at the Oxford, UK-based firm, told BioArray News this week that since microarrays have become widely adopted for constitutional genetics, "it is a natural progression to apply this powerful technique to … cancer."

He said that OGT has for "many years" served the oncology market via its custom array design service, working with cancer experts to develop cancer arrays to their specifications.

While these arrays have not been launched as catalog products, "the validated probes used are available to researchers wishing to design their own bespoke arrays," said Clough.

Now, the firm is preparing to offer catalog arrays for cancer. Clough said that OGT is collaborating with a number of cancer specialists and organizations to develop the chips, which will be made available "towards the end of 2011" through OGT's CytoSure Services facility.

While one of the hallmarks of Signature's offering is its ability to detect balanced translocations, Clough said that what sets OGT apart is that it can include SNP content on its CGH arrays, which enables users to detect regions of loss-of-heterozygosity.

"LOH is particularly common in cancers and its detection can allow further information about the mechanism of cancer progression to be elucidated;" said Clough. OGT's cancer arrays are currently being tested by early-access customers. He said that feedback from OGT's clients has also led to an enhancement in the firm's CytoSure Interpret software.

Consensus Designs

One organization that has made an impact on the market for such tools is the Cytogenomic Cancer Microarray Consortium, formed in 2009 by a group of clinical cytogeneticists, molecular pathologists, and molecular geneticists interested in applying microarray technologies to cancer diagnosis and cancer research.

CCMC has already developed standards for cancer-microarray designs, prompting at least two firms to create new products based on its current consensus design for cancer-themed arrays (BAN 11/30/2010).

The first is Cambridge, UK-based BlueGnome, which in December 2010 launched its CytoChip Cancer. To do this, the company paired CCMC's design with its own database and analysis software (BAN 12/21/2010).

BlueGnome had already had a presence in the market since 2008 when it launched its CytoChip Focus Hematology panel, which screens for more than 50 genomic regions associated with known hematological malignancies (BAN 9/2/2008). Both chips are manufactured by Agilent.

The second is CombiMatrix, which earlier this year introduced its DNAarray Oligo 180K Heme Profile array based on CCMC's design. Like Ambry, OGT, and BlueGnome's chips, CombiMatrix's arrays are made by Agilent.

And like BlueGnome, CombiMatrix was early to market with a catalog oncology offering. In 2007 the firm launched its HemeScan test. It also offers the HERScan test for HER2 analysis in breast cancer patients and an array-based, post-prostatectomy prostate cancer-stratification assay (BAN 4/12/2011).

Another firm that has had a cancer-testing service on the market for a number of years is Omaha, Neb.-based iKaryos Diagnostics. Launched in 2009, the service, called Virtual Karyotype, uses Affymetrix SNP-genotyping arrays to provide oncologists and pathologists with copy number and LOH information to help guide patient treatment (BAN 11/17/2009).

Comparing Ambry's offering with other arrays on the market, Arianpour said that the firm's CancerArray is "similar" to CombiMatrix's chip in that it is a targeted array manufactured on Agilent's 180K platform.

However, he pointed out differences between Ambry's offering and others currently available. For example, he said that CombiMatrix's HemeProfile array "appears to be more targeted to specific cancer types," while Signature's OncoChip is "on the NimbleGen 135K platform and only has a resolution of 10 kb in targeted regions, meaning it would have a hard time detecting single-exon events like the Ambry CancerArray."

Of SNP arrays, Arianpour argued that while such platforms are "beneficial for detecting LOH, your resolution is generally limited as you can only place probes where SNPs are located, and therefore these arrays are typically not targeted but tiled arrays."

While Ambry has said it expects demand to increase for its CancerArray, it is open to offering other oncology-themed arrays to stay competitive. "We are always working with new toys and have some plans to help the oncology market," said Arianpour. "Stay tuned."

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