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Omicia to Put Annotation Tools To Work Analyzing Sequence Data for Genomic Cancer Care Alliance


By Uduak Grace Thomas

After several years of silence, bioinformatics firm Omicia is moving into the limelight.

Earlier this month, Omicia was named as a partner in the Cancer Genomic Care Alliance, a cancer genome sequencing project spearheaded by Life Technologies. The partners in the alliance, who include the Fox Chase Cancer Center, Scripps Genomic Medicine, the Translational Genomics Research Institute, and US Oncology, plan to assess the usefulness of whole-genome sequencing data in making individualized cancer treatment decisions (In Sequence 06/08/2010 and PGx Reporter 6/10/2010).

Founded in 2002, Omicia has stayed relatively quiet as it built an IT infrastructure targeted specifically at personalized medicine. Now, as Edward Kiruluta, chief technology officer, told BioInform, the company feels that it's finally able to "even have the kind of conversation that we are having with the consortium.”

Omicia specializes in the analysis of genetic variants. Kiruluta said that the company has developed several of its own algorithms to classify variants, as well as "a couple of algorithms that take existing pathogenic information in databases like OMIM and map them precisely onto the genome.”

The company has also developed tools that allow it predict to some extent new variants that aren’t in published literature and a gene viewer that lets it visualize the genetic information.

The company currently has 10 employees and is funded by several grants from the National Institutes of Health. An NIH database lists two grants for the firm in 2009 totaling $868,126.

In 2006, Omicia hosted an “annotation jamboree” with several partners to map 2,000 disease genes to the human genome reference with the aim of building a knowledgebase of correlated genotypes and phenotypes (BioInform 10/20/2006).

Omicia founder Martin Reese told BioInform at the time that while the firm had not yet settled on a business model, it viewed its database of correlations as an “internal powerful engine to drive personalized medicine.”

Now, with whole-genome sequencing within the reach of the clinic and demand for efficient annotation tools on the rise, it appears that the company may find an eager market for its tools.

Working with the Alliance

Kiruluta said that Omicia will work closely with the sequencing companies in the Cancer Genomic Care Alliance to process, annotate, and interpret raw cancer genome data and convert it into a format that physicians can actually use.

"We have been working on developing a set of platforms that take into consideration the quality of the sequence and perform an annotation of the sequence,” he said. “We have also developed systems that take all the public disease annotations out there and we process them and we put an ontology on top of them and then map them back onto the genome.”

The company then interprets the combination of those two datasets, Kiruluta said.

When the system receives new data, the information is processed and stored in a GFF3-based file format called GVF. Next, annotation pipelines integrate all the relevant genetic information stored in the system’s internal database and map it back onto the genome. As a final step, the system interprets the data and converts it into a usable format for clinicians.

Kiruluta did not say where the data stored in the system originated from. He did say, however, that published cancer data and knowledge will be integrated and used to interpret patient genomes. As different types of tumors are sequenced, the new information will be added to the system’s database to automate future analysis.

Kiruluta noted that Omicia’s infrastructure can handle genomic data in various formats; from raw genome sequence reads to pre-processed variant files, and is capable of processing data from all current sequencing platforms.

According to Kiruluta, the company’s main focus now is increasing the system’s usability and scalability.

“We are trying to reduce the amount of effort that goes into running the system,” he said. “So [we] are increasing the level of automation so that you don’t have to spend a lot of time connecting various tools that are currently running separately as well as increasing scalability so we can handle the growing number of genomes out there.”

Kiruluta said that although clinicians are the primary target group for the cancer alliance project; the company is looking to work with clinicians and researchers alike.

To reach its target market, Omicia plans to focus on building collaborative partnerships with groups within and outside the alliance that would give the company a platform to showcase its whole-genome analysis capabilities. These partnerships, he added, will drive the company’s marketing strategy.

“In the next two years, there will be more and more types of projects that are being run like this and we will be looking to get involved in more of those kinds of projects,” he said. “We know that the amount of sequence [data] available is going to grow very fast and we want to make sure that the system we are building is going to be able to handle that kind of throughput.”

According to Kiruluta, the company’s main competitors would be companies like Knome, which uses proprietary bioinformatics tools to analyze whole-genome sequence data with an eye toward disease risk associations, but he suspects that as the space matures, many companies will end up forming collaborative partnerships much like the Cancer Genomic Care Alliance in order to compete.