Celadon ProbeITy™

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Designing Allele Specific Primer Extension Assays with the VeraCode Assay Designer

Genotyping Complex Polymorphic Regions with the VeraCode® Assay Designer for Low Multiplex Panels

Celadon ProbeITy Supports
Industrial Genomics

Background
Anne is a masters-level technician in a genomics core facility. She supports a large Institute that has the mission of curing human disease.

Problem
Her customer demand is soaring for mega-base re-sequencing on the Roche 454 Sequencer, Illumina Genome Analyzer, and ABI SOLiD platforms. Her bottleneck is designing the hundreds of primer sets she needs to cover each mega-base region. She is diverting 25% of her over-committed time – one week a month – to make assay designs.

Solution
Celadon is aware of Anne's problem. It spends several days configuring ProbeITy, its primer and probe design software, so as to automate primer design for re-sequencing. It also spends a few days integrating ProbeITy into her data management system.

Outcome
On her next project, Anne tries ProbeITy. With a few clicks of her mouse, she selects her customer's 176 Kb target region. She selects ProbeITy's re-sequencing method and submits her request. Two and a half minutes later she has forty overlapping primer sets, each of which amplifies precisely 5,000 bases (±100).

With another few clicks of her mouse, Anne accepts these sets and sends an order for the primers to her favorite vendor. Her vendor electronically receives the order, adds it to its sales system, and schedules it for manufacturing. When Anne tests the primer sets in the lab, the acceptance rate equals her historic rate, which is 95%. And, signal is more consistent, thereby reducing laboratory optimization efforts.

ProbeITy is web-based software for multi-method, oligonucleotide design for assay and other molecular biology techniques. It is an expert system whose purpose is to identify, as quickly and with as little user decision making as possible, optimal combinations of oligonucleotides for the selected genomic me6thod and inputted gene sequences. The software employs the most advanced science, computational algorithms, and software engineering available. Its methods have been validated at leading core facilities worldwide, including the U.S. National Cancer Institute.

Applications: Genetic Variation/SNPs, Gene Expression and Pathogen Detection

Current Methods: MGB Eclipse/QuantiTect (Qiagen), VeraCode Allele-Specific Primer Extension (Illumina), Taqman (Life Technologies –Generic), Amplifluor (Serologicals), PCR - Single Base Extension, Asymmetric PCR, PCR Resequencing, MassExtend (Sequenom – Generic), Restriction-Enzyme PCR, High Resolution Melt, Scorpions (Quiagen – Generic)

Future Methods: Next-Generation Resequencing, Isothermal Amplification (Point of care), Copy Number Variation, DNA Nanotechnology

The use of ProbeITy results in faster, more accurate, and less-costly design for a variety of oligonucleotide methods. These methods apply to fundamental and widely-used genomic applications including: amplification, sequencing, gene expression, SNP genotyping, gene expression analysis, and quantitative PCR. These methods help scientists to identify genes that are involved in disease, to identify new drugs, and to describe the effects of drug candidates. In addition to the methods listed above, a number of other methods are available, including: TaqMan qPCR; Amplifluor SNPs; Amplifluor Gene Expression; and siRNA for RNA Interference.

ProbeITy is the underlying core technology for numerous vendors' branded products, making it almost ubiquitous and indispensable in the essential task of automated scientific probe and primer design for research and biomedicine. Such diverse branded products as Illumina's VeraCode Assay Designer™, Qiagen's Quanti-Tect Probe Design™, ELITech's MGB Eclipse Design™, Biosearch's RealTimeDesign™, Millipore's AssayArchitect™, Capital Genomix' GeneSystem320™, Sigma-Aldrich's siRNA Designer™, and Thermo-Fisher's RE-PCR™ rely on Celadon ProbeITy.

Increasing Sales for Custom Nucleic Acid Product Vendor: Biosearch Technologies, Inc.
In 2004, Celadon's future customer Biosearch Technologies, Inc., was a vendor of customized nucleic acid products, primarily used as primers and probes. Its management decided that the existing industry standard their design – either relying on the customer's design, or using its own highly-skilled employees internally for manual design – was not the most productive or profitable approach to the problem. Biosearch contracted with Celadon to customize Celadon's recently-commercialized web-based ProbeITy software platform to design DNA primers and probes for Amplifluor, a genomic analysis method that Biosearch had recently licensed.

The development project was completed on time and on budget, and launched on Biosearch's website soon thereafter as RealTimeDesignTM. It was a quick success – sales increased markedly and Biosearch's customers were happy with well-performing probes. In the subsequent six years, Celadon has developed several new ProbeITy modules for new Biosearch products, including molecular diagnostic assays, that require increasingly sophisticated design and ordering tools. Biosearch has also used ProbeITy's fast, high-capacity platform internally, to create large volumes of custom assays for major customers.

Extending Reach at Retail: Epoch BioSciences and Qiagen
By 2001, Epoch BioSciences (now ELITech) had developed and out-licensed molecular assay chemistry to Applied BioSystems (ABI), which incorporated it into its TaqMan qPCR and SNP genotyping systems. Marketed these methods as TaqMan MGB (Minor Groove Binder), it quickly became the industry standard, motivatingEpoch to develop its own, unique MGB assay system, MGB Eclipse™. Epoch contracted with Celadon to adapt Celadon's web-based assay design software, ProbeITy, to MGB Eclipse, advancing the platform as well as Epoch's ability to reach retail customers.
In 2004, Epoch management decided to focus on development of molecular diagnostic kits, and out-licensed Eclipse to Qiagen for retail customers. Qiagen re-branded the technology and the software as Quanti-Tect, using it to generate designs for catalog assays as well as an on-line ordering tool for scientists.

Supporting Industrial Genomics and Next-Gen Sequencing: the National Cancer Institute (NCI)
The Core Genotyping Facility (CGF) of the U.S. National Cancer Institute contracted with Celadon to advance ProbeITy to support its re-sequencing and genotyping effort to identify genetic influences on cancer. Under this contract, Celadon made substantial improvements and additions to the original platform, bringing ProbeITy to the forefront of genomic design-and-order software platforms..

In 2010, the CGF asked Celadon to explore various improvements to the software for new applications; discussions with the agency are proceeding.

Additional Future Applications of ProbeIty in Depth

• Manufacturers of custom oligonucleotides can use ProbeITy to:
  • Add modules for existing products, high-profit specialty chemicals, and up-and-coming methods, such as isothermal amplification.
  • Reduce administrative costs by integrating ProbeITy Online into sales and manufacturing systems.
  • Improve customer experience by increasing assay design success rates.
  • Develop catalog assays.
  • Increase distributor sales volume.
• Manufacturers of genetic analysis instruments can:
  • Broaden the utility and appeal of their products by supporting more methods.
  • Develop catalog assays.
• Vendors of genomic reagents can:
  • Broaden the utility and appeal of their products by supporting more methods.
  • Develop catalog assays.
  • Enhance and complement reagents.
• Proprietary genomic method developers can:
  • Customize and brand ProbeITy for their propriety method.
  • Provide customers with method-specific design, which is essential for customer adoption of proprietary method.
  • Develop diagnostic tests faster, with less optimization and cost.
  • Develop catalog assays.
• Point-of-care and other diagnostic device or assay developers can:
  • Customize ProbeITy for their novel or preferred method and conditions.
  • Develop diagnostic tests faster, with less optimization and cost.
  • Speed time to market.
• Developers of pre-designed research assays can:
  • Automate the design process, and integrate it into laboratory management system, so as to reduce development costs and increase productivity.
• Large pharmaceutical, biotechnology, and other life science institutions can:
  • Lower the cost of research and development by providing consistent, enterprise-wide design process and standards.
  • Integrate assay design with laboratory data management systems and purchasing systems so as to increase productivity and reduce errors.
• Academic and industry researchers can:
  • Speed research; increase productivity; generate more consistent results; lower assay development costs; and better utilize student efforts.
• Genomic services and CRO organizations can:
  • Provide value-add service.
  • Serve customers needs better.
  • Lower costs and barriers, eliminate mistakes, and simplify processes by providing or enhancing online communication with customers.
  • Provide consistent, enterprise-wide design process and standards.
• Life science software vendors can:
  • Establish long-term revenue source with royalties on oligonucleotide sales.
  • Enter new markets.
  • Integrate with and complement existing products.