This article has been updated from a version posted Feb. 1 to include comments from Almac officials.
Almac Diagnostics this week said that it has begun offering data analysis services for next-generation sequence data.
The company, which has its headquarters in Craigavon, Northern Ireland, said that its analysis portfolio will include a range of NGS solutions for things like study design, sample processing, and analysis for DNA and RNA samples.
Customers can use the service on a standalone basis or they can combine it with other bioinformatics offerings from Almac, which will also work with users to create customized pipelines for their analysis needs.
Almac expects its solutions to be used for biological analysis projects, biomarker and drug discovery, and diagnostic product development.
The new service adds to Almac's bioinformatics consultancy unit launched last February, which is aimed at providing expertise and support for pharmaceutical, biotechnology, and diagnostics companies looking to outsource their informatics needs (BI 2/25/2011).
Michael Sloan, Almac's vice president of business development, said that the firm is expanding its bioinformatics business in order to provide customers with "cutting-edge technologies" as well as to open "new avenues" in their research efforts that could lead to improvements in human health.
Almac has been keeping a "close eye" on next-generation sequencing with the intent to incorporate the technology into its biomarker discovery and development business, Austin Tanney, Almac's scientific liaison manager, told BioInform this week.
Now that NGS has become more "clinically relevant ... we can see this as being a valuable diagnostics technology and ... we are focusing on [it] as ... an expansion to our current biomarker services," which are primarily targeted toward pharmaceutical and biotechnology companies, he said.
Furthermore, "it's an expansion of our bioinformatics consultancy business where we aim to support technologies and research in areas even beyond simple biomarker discovery and development," he said.
Gavin Oliver, Almac's bioinformatics team leader for sequence analysis, told BioInform this week that the company opted to launch a standalone bioinformatics services business in response to customer demand for its internal informatics capabilities and expertise.
The consultancy has seen a lot of demand since it launched, Oliver said, although he could not mention specific customers.
In terms of DNA analysis, Almac's service relies on tools for identifying SNPs, insertions and deletions, and larger structural variations, Oliver said. The company also has software for analyzing array-specific expression and transcript discovery in RNA-seq data.
The company's pipelines are comprised of a combination of open source software and internally developed algorithms, which provides the necessary flexibility to create customized solutions for customers, OIiver said. He added that third-party commercial solutions are by nature "too locked down," making it difficult to tailor analysis.
He said that the company is considering a number of aligners, including the Burrows-Wheeler aligner, the Blat-like Fast Accurate Search Tool, and the Short Oligonucleotide Analysis Package, and is currently comparing their efficiency for diagnostic purposes. Additionally, it opted to use the Broad Institute's Genome Analysis Toolkit over SAMtools for calling SNPs and indels; and BreakDancer to find larger variations.
Finally, Almac uses Bowtie and Cufflinks as well as a number of R-based packages for analyzing RNA-seq data, he said.
Nevertheless, the company is still monitoring commercial solutions in order to identify those that are "good enough for the kinds of analysis we offer," he said.
In addition to analyzing the data, the company's bioinformatics team of 20 helps customers design their studies, including selecting the right sequencing technology and analysis tools that would be best suited for their experiment, Oliver said.
Almac outsources the actual sequencing to a third party whose identity isn't being disclosed.
Pricing for the service isn't being disclosed either, although Tanney said it is a fee-for-service model and depends on the scope of the project.
Tanney also said that the companies that compete against Almac's offerings would vary depending on the study "niche."
"In some cases, we are developing companion diagnostics for large pharma companies and in other cases, we are doing relatively small-scale analysis studies for an academic," he said. "Depending on the nature and scale of the project, the competitor would be very different."
When it has to contend with competitors, Almac expects that the expertise it has built up over the years from projects within pharma and biotech as well as its own internal research and development activities will be a "key differentiator," Tanney said.
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