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Startup Diagnomics Joins Ingenuity and Knome as Genome Interpretation Partners for Illumina's IGN


By Uduak Grace Thomas

Diagnomics, a San Diego-based bioinformatics startup, is one of three firms recently tapped by Illumina to provide genomic analysis services for customers of its sequencing services business.

Diagnomics opened its doors about a year ago and offers a web-based platform called the Genome Annotation System, or GAS, which includes several annotation modules tailored for personal genomes, cancer genomes, transcriptomes, epigenomes, and metagenomes.

In addition to Diagnomics, Illumina has also selected Knome and Ingenuity to provide optional analysis tools and services to customers of the Illumina Genome Network, which links researchers conducting whole human genome sequencing projects with institutes that offer Illumina sequencing.

IGN sequencing partners include Canada’s Michael Smith Genome Sciences Centre, Korea's Macrogen/Genomic Medicine Institute, the Broad Institute, the University of Washington Department of Genome Sciences, and the National Center for Genome Resources. Illumina also provides IGN sequencing services through its in-house sequencing facility.

Tanya Boyaniwsky, market manager for Illumina's certified services provider program, told BioInform that researchers faced with large amounts of sequence data find it "a challenge to find actionable results," which is made worse in the absence of adequate bioinformatics support.

Partnering with the companies Illumina has selected will enable customers to, for example, apply different types of analysis filters or analyze multiple samples in larger studies and generate results that determine their next steps, she said.

Boyaniwsky said that Illumina plans to sign on further partners besides the three it has already disclosed and will "add them in as they fit a particular downstream analysis need."

Ingenuity and Knome

Ingenuity's IGN analysis services will draw on a number of its analysis tools, including its recently launched Ingenuity Variant Analysis application, which is designed to help researchers identify causal disease variants from human resequencing data. It is currently being used to identify cancer variants at the Translational Oncology arm of the University Medical Center Mainz (BI 1/13/2012).

Knome, meantime, said last week that as part of its arrangement with Illumina, customers who chose to use its offerings will receive "preferential" pricing for its genome interpretation tools and services — KnomeBase and KnomeDiscovery — although the company did not provide pricing details.

KnomeBase has a list price of a $3,750 and can be deployed on Amazon's cloud or locally. It is tailored for clients who require only genome interpretation services and includes tools to find candidate causal variants and to help users identify functional interactions between variants. The company’s KnomeDiscovery service provides whole-genome sequencing, curation, informatics, and interpretation for $4,998 (BI 12/22/2011).

Knome has also launched KnomeClinic, which offers interpretation systems to manage whole-genome sequence data; helps physicians interpret genomes to inform preventative, diagnostic, and treatment decisions; and helps medical researchers indentify causal variants associated with phenotypes of interest.

KnomeClinic includes the company's kGAP informatics engine, which standardizes, annotates, distills, and compares whole-genome sequence data from all major sequencing platforms with data from curated databases. It also includes clinical curation tools and server-side applications for storing and managing data.

The system generates physician reports containing genome interpretation results and desktop applications for researchers to visualize and identify genetic variants, genes, and gene sets.

Pricing details for KnomeClinic have not been disclosed.

Illumina's Boyaniwsky said that, so far, Illumina's arrangement with Knome has netted customers like Johns Hopkins University, which has contracted the informatics firm to provide informatics services and software for a 1,000-patient study focused on finding genetic variants linked to asthma (BI 1/13/2012).

Annotations for All

Like many biotech and informatics firms that dot the next-generation sequence data analysis space, Diagnomics' long-term vision is to develop products and solutions for the personalized medicine market, Min Seob Lee, the company's CEO, founder, and president told BioInform this week.

The seven-person company intends to focus its efforts on developing bioinformatics tools that help researchers as well as clinicians and lay individuals access and view genomic information, he said.

He explained that the web-based platform can be used to generate reports for physicians and lay customers with general information on things like ancestry and common diseases. On the other hand, more experienced informatics researchers who want to dig deeply into the data and look for genetic markers, SNPs, and so on can purchase access to a customized version of the platform that allows them to adjust multiple filters and parameters, and create and run custom queries to extract information they need from genomic data.

The company isn't disclosing pricing for its system, though the company offers a range of licensing models.

Under a term license, customers can upload an unlimited amount of sequence data. This option would best fit the needs of research customers with high data volume that require in-depth analysis, Lee said. Under this option, the company can also develop custom modules for licensed users.

Low-volume users, meantime, can access the company's system on a case-by-case basis, but this model is more costly than the term license model on a per-genome basis, Lee said.

Finally, Illumina IGN customers can use the company's service for a "specially negotiated price," and "without paying [the] licensing fee," he said, though he declined to elaborate.

Lee added that the company will work with interested customers to ensure that its pricing is "reasonable" and that the cost of bioinformatics analysis does not become a "bottleneck" for genome sequencing.

"This genome annotation market is very new to everyone," he said. "Our vision is to make personal genomics useful and affordable to every level of customers," he said.

Currently Diagnomics' platform isn't meant for diagnosing and treating patients in clinical use cases but the company is preparing its annotation system to be employed in clinics in the near future, Lee said.

Vying for the same space Diagnomics hopes to inhabit are companies like Knome and Omicia, who currently offer tools and services for functional interpretation of genomic data; and GenomeQuest, which is already venturing aggressively into the clinical diagnostics arena (BI 12/22/2011).

Lee believes that the "strength" of his firm's platform is its user friendliness and its ability to addresses the needs of both researchers and end users.

The current GAS platform uses several open source packages like the Burrows-Wheeler Aligner and the Broad's Genome Analysis Toolkit; and it incorporates information from both public and private databases as well as peer-reviewed literature to generate its annotations.

However, Diagnomics has combined these tools and resources in such a way that "each individual part works in harmony ... like an orchestra" to process the data.
The company offers several flavors of GAS targeted at different analysis needs. Its Personal Genome Annotation System, for example, provides an automated pipeline system for personal genome annotation that is available for targeted, exon, and whole-genome sequencing. It includes a customized genome variation mining tool, a genetic body map, common and rare disease analysis, genetic ancestry, as well as drug response and personal trait annotation.

The company's Cancer Genome Annotation System, or CAS, provides a suite of web-based bioinformatics tools for processing sequencing data from both normal and cancer patient samples.

Lee told BioInform that the company's personal genome and cancer genome annotation systems are the focus of its development efforts right now as these two application areas have the largest share of the sequencing market.

Meanwhile, the company is developing the Transcriptome Annotation System, or TAS, which will provide solutions for exploring results derived from transcriptome analysis pipelines; Diagnomics' Epigenomics Annotation System, or EPAS, which will provide resources and data-mining capabilities tailored for epigenomics studies; and its Metagenome Annotation System, or MAS.

Diagnomics has netted a number of customers, Lee said, although he could not disclose who these groups are.
The company is also working to secure a round of financing, which it will use to hire additional scientists and engineers as well as to purchase additional servers to handle its data analysis activities.

The company is located at the American Internet Services data center in San Diego, which gives it access to ample servers.

As such, the scalability needed to handle large quantities of genomic data is not an issue for Diagnomics, Lee said.

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