Skip to main content
Premium Trial:

Request an Annual Quote

Signature Genomic Labs to Solely Offer Array CGH Services on Roche NimbleGen Platform

Premium

By Justin Petrone

Roche NimbleGen will manufacture, market, and sell worldwide comparative genomic hybridization arrays designed by Signature Genomic Laboratories for cytogenetics research, while Signature will provide and support software analysis tools for Roche array customers, the companies said last week.

Spokane, Wash.-based Signature previously had offered its services on an internally produced bacterial artificial chromosome array platform and an oligonucleotide platform manufactured by Agilent Technologies.

As part of the new deal, the company will solely offer its services on a Roche NimbleGen-manufactured array platform and will discontinue use of its BAC array platform by the end of this year.

Bassem Bejjani, Signature's chief medical officer, said the deal "has unique depth in the life-sciences field" and "goes beyond just adopting a new platform." Signature recently switched to Roche NimbleGen from Agilent due to the "quality of their products and by the strategic opportunities that such a partnership would offer both our companies," Bejjani told BioArray News last week.

Founded in 2003, Signature initially offered its service on a homemade BAC array platform before introducing an Agilent-made oligo design in 2007 (see BAN 10/23/2007). The oligo array, called the SignatureChip OS, offered coverage of more than 150 chromosomal syndromes, and contained 105,000 features per array with an average of 50 oligos per clinical target. The array also had a backbone of one oligo for every 35kb.

Bejjani said that Signature's new Roche-manufactured array has a similar design to the arrays that were manufactured by Agilent. "We target genes that are known or suspected to play important roles in organogenesis, patterning, development, and other important function, in addition to designing a 'backbone' across the genome," he said.

Bejjani said that Signature is "focused on technology" and is "always evaluating the best technology that fulfills our needs." He said the firm recently made the decision to discontinue its BAC array manufacturing by the end of 2009. "For the foreseeable future, we will be using exclusively the Roche NimbleGen arrays."

In explaining the technology switch, Bejjani mentioned Roche's array-manufacturing technology, which he said "allows for virtual unlimited increase in the density of the oligonucleotides on the array" as well as "multiplexing not afforded by other arrays."

Specific differences between the two platforms include a density divide. For instance, Roche NimbleGen's HD2 array platform provides 2.1 million oligo probes on an array. Agilent's SurePrint G3 arrays, meantime, offer users access to a million oligos per array.

The combination of the ability to use higher-density arrays and to process more samples per array has "many implications" for Signature's workflow as its number of samples increases, Bejjani said. For instance, Bejjani told BioArray News in March that Signature had run more than 35,000 arrays since its inception (see BAN 3/24/2009). Last week, he said that the firm now has more than 40,000 samples in its database.

'Mutually Beneficial'

For its part, Roche NimbleGen last week announced its new Signature-designed NimbleGen CGX arrays for genome-wide analysis of chromosomal abnormalities.

The arrays, which will become available later this month, are available in formats of 3 samples per slide and 12 samples per slide. A 6-sample-per-slide format will become available early in 2010, according to the firm.

According to Roche NimbleGen, the whole-genome oligonucleotide arrays enable users to survey more than 200 cytogenetically relevant regions, over 675 functionally significant genes, 5 megabases of telomeric and pericentregions covered with one oligo every 10 kilobases, pseudoautosomal regions covered with one oligo every 10 kb, and whole-genome backbone coverage of one oligo every 35 kb.

NimbleGen CGX arrays are supported by the Madison, Wis.-based company's reagents and instrumentation, in addition to Signature's Genoglyphix data-analysis software, which Signature will provide to CGX customers and support.

Vanessa Ott, Roche NimbleGen's CGH and CNV array product manager, told BioArray News last week that the chips are for research use only. While the US Food and Drug Administration weighs increasing its oversight over the use of arrays in cytogenetic testing, Ott said that Roche's goal is to "maintain compliance with current regulations and support research labs that are using the arrays for that purpose" (see BAN 10/13/2009).

[ pagebreak ]

Roche is supporting the roll-out of its CGX arrays with a series of workshops in Europe and Asia. Last week, Signature CEO Lisa Shaffer presented at four workshops in Leuven, Belgium; London; Munich, Germany; and Geneva. Roche over the coming week will also host CGX workshops in Beijing, Hong Kong, Taipei, Bangkok, Singapore, Seoul, and Mumbai, India.

Ott said that the firm sees cytogenetics research as a "large growth market" and "one of the biggest growth areas for CGH" as labs that used older technologies like karyotyping and fluorescent in situ hybridization transition to array CGH.

Roche NimbleGen's main rivals in the array market have also sought to tap into the space. Agilent has retained a role as a self-described "array foundry," making chips for companies and labs like Oxford Gene Technology, BlueGnome, Baylor College of Medicine's Medical Genetics Laboratories, and Emory Genetics Laboratory in Atlanta. Affymetrix and Illumina, meantime, have developed specific products geared toward cytogenetic research on their respective platforms.

By partnering with Signature, Roche NimbleGen is offering an externally designed array to the market on its internally developed platform. Ott noted that the CGX arrays are Roche's "first set of products that are specifically designed by cytogeneticists."

The firm's partnership rests on Signature's chip design, Roche's manufacture and support of the arrays and related reagents and instrumentation, and customer access to Genoglyphix. The web-based interface allows users to compare their results to more than 40,000 Signature samples.

Genoglyphix "was developed by cytogeneticists for other cytogeneticists," said Ott. "It has a lot of rich annotation to help with data analysis and the software is linked to a database of samples that Signature has analyzed over the years." Signature will provide technical support for the software, according to the companies.

Ott said that Roche has "had relations" with Signature for several years and that Signature had been a "standard customer" though it had used Agilent-made arrays in its service. She said the "business-to-business relationship" evolved from Signature's desire to make its design available to other customers.

"It's a mutually beneficial agreement," she said, noting that while Roche gets access to a growing array market, Signature stands to benefit from Roche's global reach, as evidenced by the recent string of European and Asian workshops.

Signature's Bejjani said that since its founding, Signature has been "convinced that array CGH is a very valuable technology for cytogenetics" and is "committed to disseminate the use of array CGH to all cytogenetic laboratories that are interested in adopting this technology because it is extremely useful."

Shaffer, for instance, told BioArray News in 2005 that the firm was mulling ways to export its success to other labs, but was wary of providing technical support for Signature's arrays. "I don't want to have to troubleshoot 300 labs in the country," she said of Signature's stance at the time (see BAN 11/2/2005).

Bejjani said that "there are many laboratories that do not have the expertise to design arrays that fit their needs" and that, by partnering with Roche, the firm is finally able to "move the field of cytogenetics forward" by "sharing our array."

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.