Illumina and Oxford Gene Technology independently last week introduced new arrays into a cytogenetics market that the vendors have described as “significant,” “rapidly growing,” and “huge.”
Illumina is new to the cytogenetics tools market and OGT formally launched arrays for the space last year. The firms’ new additions will play in a field crowded with offerings from rivals such as Affymetrix, BlueGnome, and Empire Genomics.
Illumina’s debut into the market is the Infinium High-Density HumanCytoSNP-12 DNA Analysis BeadChip. The 12-sample array contains nearly 300,000 genetic markers per sample and targets cytogenetic abnormalities found in genes and disease pathways linked to mental retardation, autism, and other common chromosomal anomalies. Illumina has also launched an accompanying software package called KaryoStudio, designed specifically for use by cytogeneticists.
Meantime, OGT’s new products include upgraded content for its CytoSure Chromosome X array, called the Chromosome X High Density array, and a second version of its CytoSure Syndrome Plus array, both manufactured by Agilent Technologies. All of the new products are intended for research use only.
Unlike most rival offerings, which rely on comparative genomic hybridization to identify constitutional abnormalities in patients, Illumina is offering a genotyping array that can screen SNPs associated with diseases, analyze structural variation, and identify copy-neutral loss-of-heterozygosity events such as uniparental disomy, which is connected to Prader-Willi and Angelman syndromes, the firm said.
During Illumina’s annual Analyst Day meeting, which was webcast on Nov. 6, CEO Jay Flatley said the array addresses a “largely untapped market” for the company and represents an “enormously large opportunity” for Illumina in the future.
“The market for cytogenetics is huge,” Flatley said. He said that the market is currently worth about $2 billion, and Illumina expects it to double by 2012. While the bulk of cytogenetics testing still employs fluorescent in situ hybridization and molecular karyotyping, Flatley estimated that array-based cytogenetic tests make up $200 million of the overall cyto-testing market and are growing 20 percent per year.
“The market is dominated today by FISH, and though we don’t expect to replace that any time soon, we think there is a great opportunity to phase traditional cytogenetic screening technologies over to array-based technologies, because of the automation, because of the ease of use, and because of the human intervention that is required using traditional approaches,” said Flatley.
He added that he expects Illumina’s arrays to eventually be used in neonatal screening, amniocentesis, and in vitro fertilization applications.
Syndrome Plus and Chromosome X
Oxford, UK-based OGT stands to be an Illumina competitor in the cytogenetic-testing space. The company last week announced it has expanded its CytoSure menu of CGH arrays for use by cytogeneticists.
OGT first began offering catalog arrays for cytogenetic testing in July 2007 with the launch of its CytoSure Chromosome X array and its CytoSure Syndrome Plus array, both intended for research use only. However, the company said that diagnostics — including CE Marking in Europe and a 510(k) route to clinical use in the US — could be in their long-term future (see BAN 6/26/2007).
The Chromosome X array was an exon-specific array, a high-density array with 44,000 features all focused on the X chromosome, which OGT originally targeted because of its association with disabilities such as Duchenne muscular dystrophy and hemophilia. OGT’s initial Syndrome Plus array covered 85 distinct genetic syndromes — including Cri du Chat, diGeorge, Downs, and Prader-Willi — in two 105,000-feature arrays printed on one slide.
“Arrays are now widely used and are set to replace traditional metaphase cytogenetic techniques.”
Last week, OGT upgraded the content on both arrays by introducing the Chromosome X High Density array and the second version of Syndrome Plus. According to OGT, the Chromosome X HD chips come in formats of two 105,000-spot arrays printed per slide; higher resolution, with one probe present for every 1.6 kilobases of the chromosome; a new, gene-centric design, with one probe present for every 500 basepairs for all known gene loci; and increased targeting of genes, exons, microRNAs, rRNAs and snRNAs on the X chromosome
OGT’s new Syndrome Plus v2 chip now contains markers for over 200 syndromes with one probe every 3 kilobases and 33 probes for each gene. The new array also includes 410 genes associated with autism, mental retardation, and heart and eye diseases. The array is also available in the 105K, two-plex format. Both the Chromosome X HD and the Syndrome Plus v2 are manufactured by Agilent Technologies.
According to OGT marketing director James Clough, the new arrays are the result of a redesign of the original arrays to meet customer demands.
“When we first started, we were focusing primarily on syndromes, and it was more of a targeted array. We put a lot of probes into the syndromic regions,” he told BioArray News last week. “Now, we have realized that we have more than enough probes in the syndromic regions, and we have reduced the number of probes on the syndromic regions, added a comprehensive list of syndromes to the array, and used the new space to give better backbone coverage.”
Doug Hurd, project manager of the CytoSure line, told BioArray News that the company’s customers are “more interested in genomic backbone coverage, so that is why we expanded that at [the] expense of syndromic regions.”
He said that the customers also want extra coverage of mental retardation, autism, and heart disease as well.
While Clough declined to provide market size estimates, he said that the cyto market potential for arrays is “significant” even though it is still in an “early adopter” phase. “I have been going to cyto meetings for years,” he said. “There has been a sea change. Arrays used to be only mentioned here and there. Now they are the core part of the discussion.”
“What is really exciting is that when we started with oligonucleotide-based array CGH people were saying that sometime in the future oligo array-CGH may be useful [in cytogenetics], but karyotyping is number one,” Clough said. “Now, a lot of labs are running an oligo array instead of karyotyping. It has been such an expansive area.
“It has been fascinating to see how groups that have been traditionally microscopy-based have rapidly adopted the technology and it has moved faster than many people did and would have predicted,” he added.
’Healthy and Good’
Clough admitted that the array-based cyto-testing market has been growing more crowded, but said that OGT will seek to differentiate itself based on its oligo-array design expertise as well as its CytoSure software-analysis tool. “Competition is healthy and good, and it is more manageable from a commercial point of view when the market is growing,” he said.
Another firm that recently entered the cytogenetics testing market is Affymetrix, which in March launched its Cytogenetic Solution, a product that pairs its high-density SNP Array 6.0 with new software to detect chromosomal abnormalities associated with congenital diseases such as autism and mental retardation (see BAN 3/25/2008).
According to Affy, the Cytogenetic Solution has been adopted by 40 customers, including Laboratory Corporation of America, which moved to the Affy platform from the Spectral Genomics’ CGH platform in January.
During Affy’s third-quarter earnings call last month, Chairman and outgoing CEO Steve Fodor called cytogenetics “one of the probably very exciting areas that ultimately will build recurring revenue streams from products that are closer” to the clinical and consumer markets. “Cytogenetics is growing very rapidly,” he added.
Another rival is Cambridge, UK-based BlueGnome. Graham Snudden, vice president of engineering at the firm, told BioArray News that the company’s “sales have doubled in each of the last five years, and we expect them to do so again next year.”
“Arrays are now widely used and are set to replace traditional metaphase cytogenetic techniques,” Snudden said. “The key barriers to acceptance remain the obvious ones, [including] capital-equipment budgets, reimbursement, and integrating the new approaches within existing laboratory and reporting procedures.”
According to Snudden, the company is looking to distinguish its place in the market via its data-analysis and management tools, plus its catalog of confirmatory FISH probes, which allow users to validate the results they obtain using the company’s arrays.
“Arrays are increasingly a commodity,” Snudden said. “The real value is shifting to the tools provided for the management and confirmation of results.”