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Sequencing an alliance
January 2010
by David Hutton  |  Email the author


 STATE COLLEGE, Pa.Ambry Genetics and SoftGenetics have entered into an agreement to provide extended bioinformatics genomics services using SoftGenetics' NextGENe software for next-generation sequencing projects performed at Ambry, the companies announced in December. 


Ambry Genetics is both a clinical, CAP-accredited and CLIA-certified commercial laboratory as well as a genomics services laboratory headquartered in Aliso Viejo, Calif. Ambry has been providing next-generation sequencing services to pharmaceutical, biotech and academic clients for a wide range of applications including targeted resequencing through custom or exome sequence capture, transcriptome, ChIP and de novo sequencing.


According to Anja Kammesheidt, Ambry's CSO, the team at Ambry has been providing genomics solutions on Illumina's Genome Analyzer platform for two years.


"In light of diversifying applications, increasing project sizes, and new genomes to be explored, having a proven and innovative partner for bioinformatics is key," says Kammesheidt. "While some of our clients are interested in performing their own analyses, others are asking for extended support. We have been impressed with SoftGenetics' software tools, as well as their approach to take care of the clients' needs, which is very much in line with Ambry's philosophy. We are looking forward to working together to provide tailored services to our clients."


SoftGenetics LLC, located in State College, Pa., specializes in the development of genetic analysis tools for both research and diagnostic applications.


Kammesheidt says Ambry chose SoftGenetics for many reasons: "We think their software tools are exceptional, and their focus on client services is in line with Ambry's high standards. 


"We have combined expertise, speed and the ability to respond best to our client needs, and thereby can provide a one-stop service solution for our clients," Kammesheidt adds. "We feel it is a great fit for our two organizations to align, and this partnership demonstrates our commitment to offering the best complete services solutions."


Ambry Genetics already has in-house bioinformatics capabilities, but with the new alliance with SoftGenetics, Kammesheidt says the company will now have a broader base to draw from.


"We have really been impressed with their software and the way they respond to the client needs in the same way we respond to requests for custom workflows and applications," Kammesheidt points out. "SoftGenetics recently added comparative genomic tools, fast, whole large genome analysis, metagenomic tools, structural variant tools, forensic human identity tools, splice junction detection, as well as mapping, SNP and large indel detection. In addition, they are interested in adding new functionalities going forward. Ambry also has had a recent surge in project requests, and one challenging aspect is ensuring that we can fit all the project requests within given deadlines. But now with this alliance there is no doubt that we can increase our level of service for more groups, while attaining the high quality of data delivery more efficiently for their next-generation sequencing projects."


Jonathan Liu, vice president of research and development at SoftGenetics, echoed Kammesheidt's thoughts and added that "the SoftGenetics/Ambry partnership provides a new strategic alliance that will not only provide a single streamlined source for next-generation sequencing researchers, but will also provide SoftGenetics with a deepened vision of future researcher requirements, allowing NextGENe to remain at the forefront of next-generation sequencing software."


According to John Fosnacht, vice president of sales and marketing at SoftGenetics, there are several areas of "attractiveness" between Ambry and SoftGenetis that influenced his company's decision.  


"The corporate culture both firms are nimble and fast-moving with our large corporate structures that sometimes hinder strong response to customers," she says. "We believe this is a key strength that will allow a very high level of communication between our two firms as well as provide the ability to very quickly meet customer requirements."


Fosnacht points out that the alliance also provides researchers wishing to utilize the power of next-generation sequencing a distinctive value proposition by combining the technical quality of Ambry Genetics sequencing with the unique analysis capabilities of NextGENe without the heavy investment typically required in next-generation sequencing instrumentation and bioinformatics. Fosnacht also points out that Ambry has quickly grown into a market leadership position in genetics.


"They are one of very few Illumina-certified service providers for next-generation sequencing, meaning that the quality of their work is quite superior," he notes. "In addition, Ambry is the world's first certified provider for Agilent Sure Select for exome and custom targeted sequencing."


In genetic analysis, Fosnacht points out that it is imperative to receive quality data as the downstream analysis is quite dependent upon on the data received. 


"Ambry's quality will eliminate a host of problematic analysis areas, allowing SoftGenetics to provide the highest results in the shortest timeframe."


Fosnacht says SoftGenetics' role in the partnership is twofold: "For more or less routine analysis, SoftGenetics will process the data supplied for Ambry with our NextGENe software, perform data review and editing and supply results back to Ambry in a manner consistent with customer requirements, which includes custom report formats that are meet the customer's pipeline requirements," he says. "Another critical aspect of SoftGenetics role is as a bioinformatics consultant to both Ambry and their customer.  We, either through Ambry or in direct contact with customers, will advise as well as create custom analysis for the customer's data."


An example of SoftGenetics' capabilities is Indel and structural variant analysis, he says.

"Our Condensation Tool technology, which not only removes sequencing errors, but elongates short reads from the Illumina GA allows us to detect Indels up to 33 percent of elongated reads," Fosnacht says. "For one leading clinical development group this has provided accurate detection of a 50 bp Indel in 45 bp reads following 4 cycles of condensation."


In the collaboration, Ambry will remain the point of contact for the clients, arrange the workflow and be responsible for sample prep, Illumina Genome Analyzer runs as well as final data delivery.


"SoftGenetics will be involved with select larger or custom projects, when our clients request more extensive bioinformatics support than the standard deliverables of raw sequence and alignment files or simple analysis," Kammesheidt says. "Data will be delivered to the client from Ambry Genetics. In addition, SoftGenetics, being at the forefront of next-gen sequencing tool development, will be involved when clients need custom tailored solutions."


As Ardy Arianpour, director of business development and genomic services at Ambry Genetics, points out, next-generation sequencing services are more valuable to any scientific researcher if you can offer a full menu for bioinformatics support.


"Ambry Genetics has now become the genomics community's one-stop service shop for next-generation sequencing services," Arianpour notes. "We can handle large projects and we can offer the most robust data analysis through the exclusive alliance with SoftGenetics."


While there are confidential financial goals, Fosnacht says there also are other crucial gauges to measure success of the alliance.


"We believe both firms truly wish to provide cutting-edge genomics," he says. "One of our critical goals is the continual enhancement of NextGENe, which can only be accomplished through user interaction both from enrichment of the user interface as well as the addition of novel functionalities. We strongly believe the alliance will provide these opportunities."


"At the end of the day, we have happy clients and a growing customer base," adds Kammesheidt. We talk to our clients all the time and know when people are happy with the results or not. All of our feedback so far has been very positive. Ambry has had a surge of scientists requesting to run projects with us due to our complete menu for next-generation sequencing."

Code: E011012



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