NUREMBERG, Germany — Oxford Gene Technology will soon add another cancer-focused array to its menu of CytoSure chips for cytogenetic research. Separately, the company is planning extensions to its Genefficiency sequencing services.
Spencer Howell, OGT's director of cytogenetics, said that the array, called Cancer+SNP, will soon be available to the British firm's customers via an early-access program. OGT developed the array with researchers at the University of Lausanne in Switzerland, and the chip is targeted for wide use in cancer cytogenetics. It contains copy number variants and SNPs covering 1,500 cancer-related genes, with enhanced coverage of 17 select genes.
Howell spoke with BioArray News following an OGT workshop at the European Society of Human Genetics annual meeting, held here this week.
He said the new array is available in Agilent Technologies' 4x180K format, meaning that four 180,000-marker arrays are available on each microarray slide. Agilent manufactures OGT's arrays, and OGT is an Agilent certified service provider.
OGT is keen to expand its menu for cancer cytogenetics research. Earlier this year, it rolled out its CytoSure Hematological Cancer +SNP array, a tool it designed to study a number of hematological malignancies, including chronic lymphocytic leukemia and multiple myeloma (BAN 3/6/2012). That chip is available in an 8x60K format, meaning that each slide contains eight distinct arrays of 60,000 markers.
The company also offers a number of arrays for constitutional cytogenetics, such as its CytoSure ISCA+SNP array, which it launched in March (BAN 3/6/2012).
Howell said that the firm anticipates that cancer-focused cytogenetics chips could be even more successful than those that have been launched for constitutional research, though questions about gaining reimbursement for such tests have slowed their adoption.
"Until recently, we focused more on the constitutional area, but there has been interest in the cancer space," said Howell. "At the moment, depending where you go, it is not as reimbursed as it is for the constitutional market," he said. "As the reimbursement comes in, and people use it a lot more, and it has been shown that it is informative … the uptake, if anything, will be higher than constitutional."
According to Howell, the new Cancer+SNP chip covers more regions than the Hematological Cancer +SNP array in "greater detail," and can be used to detect copy number changes in hematology and solid cancers. While OGT's collaborators at the University of Lausanne assembled the gene list for the new array, OGT took the lead in selecting its SNP content.
"We have spent hundreds of man hours identifying the most informative SNPs, as a lot of SNPs are not informative," said Howell. "We picked out the SNPs that have allele frequency between 0.4 and 0.6 in the population," he said. "So, if you look at our array, although it has fewer SNPs than other platforms, our SNPs are more informative."
OGT has no shortage of competitors. Affymetrix, for instance, offers CytoScan HD, which contains 2.6 million copy number and SNP markers, to cancer cytogenetics researchers. And Agilent Technologies has its own CGH+SNP design for the cancer cytogenetics market, as does OGT rival BlueGnome.
As it does for OGT, Agilent also manufactures BlueGnome's CGH+SNP arrays. However, OGT's CGH+SNP arrays rely on internally developed chemistry that makes its assay protocol different from Agilent and BlueGnome's. As James Clough, vice president of clinical and genomic solutions, told BioArray News earlier this year, in OGT's protocol, an intensity-based comparison is made between the SNP probes, there are no changes to the standard CGH protocol, no restriction digest is required, and any reference sample can be used (BAN 3/6/2012).
When asked about OGT's claims, a BlueGnome spokesperson this week said that the Cambridge, UK-based company continues to see "strong demand" for its cancer-focused array offerings. She did not elaborate.
Looking forward, OGT anticipates adding more cancer-focused arrays to its menu. Howell said that OGT has been developing an array based on the Cancer Cytogenomic Array Consortium's gene list. He did not provide a date by when that array could become available.
RNA-seq
While OGT prepares its Cancer+SNP array for launch, it is also expanding its menu of Genefficiency genomic services. Daniel Swan, senior NGS computational biologist at OGT, told BioArray News here this week that the company will soon offer RNA-seq as a service to its customers.
OGT added whole-exome sequencing, as well as custom targeted sequencing of any genomic region of interest, to its menu of genomic services last year (BAN 5/31/2011).
Swan said that RNA-seq was the "next logical offering" for OGT in terms of sequencing services. He said that OGT has been offering RNA-seq to early-access customers for the past few months with a wider launch anticipated for later this year.
According to Swan, RNA-seq enables customers to investigate differential promoter usage, and identify differentially expressed splice variants between experimental conditions, "allowing analysis of different transcript start sites and different coding sequence usage within transcripts."
He noted that researchers could technically do some of the same work on Illumina or Affymetrix's exome arrays, "but obviously you can get into greater detail" with RNA-seq "because you partner that with being able to do de novo discovery of transcripts, then you find the things that are not captured by the array technologies."
Both Swan and Howell said that many OGT customers have shown interest in using the firm's next-gen sequencing services, especially because the rate at which the technology is evolving has made researchers hesitant to invest in their own systems.
"People are worried to buy sequencing equipment at the moment, not just because of the capital costs, but because they don't know if it is going to be out of date in three years," said Swan.
"I think the set-up costs [are high] and the technology is changing so rapidly that it is hard for people to dip their toes in the water," said Howell of OGT's sequencing customers. "There are a lot of people running arrays, some are doing next-gen sequencing, a lot of them are looking to do it," he said, "so they will send us the samples and they build up from that."