Integromics said this week that it is partnering with the Galician Foundation of Genomic Medicine to develop inexpensive informatics solutions for analyzing next-generation sequence data in clinical laboratories.
With a three-year, €1 million ($1.3 million) grant from the European Regional Development Fund and the Spanish government, Integromics and FPGMX will work on a project called Advanced Analysis and Interpretation of Low-Cost Next Generation Sequencing Data for Clinical Applications, which aims to provide improved procedures and optimized tools to help clinical labs use NGS data in routine healthcare.
Eduardo González Couto, Integromics' chief strategy officer, told BioInform that by the end of the current quarter, the company plans to provide a beta version of a software suite, dubbed OmicsOffice for Clinics, that will include analysis and interpretation tools for finding genomic mutations associated with diseases as well as improved procedures for sequence analysis.
Specifically, the new software will be used to support the analysis and interpretation of exome data to identify causative mutations, he said.
The package will be an extension of the company’s existing OmicsOffice suite, which includes SeqSolve, an NGS data analysis package that Integromics brought to market in 2010 (BI 12/3/2010); RealTime StatMiner for analyzing real-time PCR data; and the Integromics Biomarker Discovery, or IBD, product for microarray data analysis.
It will also include an additional set of applications to compare results from different platforms, such as expression microarrays and RNA-sequencing, or RNA-seq and PCR, as well as functional analysis capabilities, he said.
The company is also working on an improved version of SeqSolve that will be able to handle resequencing data, he said.
In addition to some internally developed code to process and generate reports, the upcoming Integromics offering will incorporate some well-known packages such as SAMtools, Maq, the Integrative Genomics Viewer, and the Genome Analysis Toolkit for calling variants.
In terms of interpretation, Integromics is currently considering about five different software systems including some commercial offerings, Couto said.
Although he could not provide details about which commercial offerings the company is exploring, Couto did say that "if we find that a commercial module, package, or application is really what Integromics needs, we would apply a similar strategy to the one Tibco Spotfire applied with us."
Tibco sells Integromics' IBD software, which both companies worked together to develop (BI 9/19/2008).
Based on an agreement between the two companies, Integromics receives royalties from Tibco's IBD sales, Couto explained, adding that a similar type of agreement could be applied for any commercial code integrated into OmicsOffice for Clinics.
Some open source algorithms up for consideration include Annovar, which the company is using to functionally annotate identified variants and then, the company uses SIFT and PolyPhen to predict the effects of these mutations, he said.
The initial OmicsOffice for Clinics prototype will be used to analyze data from pediatric patients with genetic mutations linked to mental retardation as a proof of concept, Couto said. During beta testing, the company will work on extending the suite's capabilities to cover other pathologies such as cystic fibrosis and oncology, he added.
Integromics expects to launch OmicsOffice for Clinics in 2013, he said.
First Foray
This partnership marks Integromics' first foray into the clinical market and makes good on comments made by CEO Michael McManus in 2010, when he told BioInform that the company intended to integrate its software products into a single suite that would have "a lot of appeal for use in clinical settings" where users are looking to compare their NGS data with results from qPCR and microarray experiments (BI 10/8/210).
When it is launched, Integromics' newest offering will be tailored to work specifically for benchtop sequencers such as Life Technologies' Ion Torrent Personal Genome Machine and Illumina's MiSeq instrument. Such systems will "slowly but surely" carve a niche for themselves in hospitals, Couto said.
Integromics is working with a research team led by Angel Carracedo, director of FPGMX, which will provide data and patients that will be used to test the OmicsOffice for Clinics software. Carracedo was one of two winners of an Ion Torrent PGM grants program in which participants competed to receive a PGM machine to aid their research efforts (IS 2/22/2011).
Couto described that partnership as a complementary one, where FPGMX brings the medical expertise and necessary use cases, while Integromics offers software and technical knowhow.
Together the partners will work on building tools to analyze and interpret sequence data from instruments like the PGM and also plan to address sequencing bottlenecks associated with sample preparation, quality control, and other issues, Couto said.
The partners are looking to develop tools that keep analysis costs low and don’t require expensive hardware infrastructure in order to run, he said.
"We are not aiming at creating a new high-end and very expensive system," he said. Instead, "we are aiming [to build] systems and software that most hospitals will be able to use [and] acquire" as well as "solutions that are faster and will reduce the time spent in doing manual operations."
Other money-saving strategies the partners are hoping to adopt include automated analysis workflows — for example automating the ability to check sequencing results to ensure that coverage is homogenous enough to make specific conclusions — that should reduce the amount of manpower needed as well as save time and, by extension, reduce costs, he said.
Meanwhile, the partners are also looking at ways in which clinical labs can use information from reference databases, such as the Online Mendelian Inheritance in Man, ClinVar, and MutaDataBase to guide the data analysis and interpretation that's required for each disease type, Couto said.
For example, a clinical lab analyzing data from a cystic fibrosis patient could use the National Institute of Health's GeneTests database to find which genes are currently tested to find mutations responsible for the disease, he explained.
Although Integromics is trying to get its foot in the clinical genomics door, the company won't neglect the research market, Couto said.
The company will continue to market its microarray, PCR, proteomics, and NGS software as standalone products and it is also considering other possible combined offerings, he said
According to Couto, several pharmaceutical companies and other institutions have "expressed interest" in Integromics' software since it is one of only a few bioinformatics companies offering solutions for both genomics and proteomics.
These are groups that are "interested [in merging] these two areas ... better," he said, adding that Integromics is looking at ways of making a union possible.
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