Sequencing an alliance

Ambry Genetics, SoftGenetics form partnership for extended bioinformatics support for next-generation sequencing projects

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 STATE COLLEGE, Pa.—Ambry Genetics and SoftGenetics haveentered into an agreement to provide extended bioinformatics genomics servicesusing SoftGenetics' NextGENe software for next-generation sequencing projectsperformed at Ambry, the companies announced in December. 


Ambry Genetics is both a clinical, CAP-accredited andCLIA-certified commercial laboratory as well as a genomics services laboratoryheadquartered in Aliso Viejo, Calif. Ambry has been providing next-generationsequencing services to pharmaceutical, biotech and academic clients for a widerange of applications including targeted resequencing through custom or exomesequence capture, transcriptome, ChIP and de novo sequencing.


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


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


SoftGenetics LLC, located in State College, Pa., specializesin the development of genetic analysis tools for both research and diagnosticapplications.


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


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


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


"We have really been impressed with their software and theway they respond to the client needs in the same way we respond to requests forcustom workflows and applications," Kammesheidt points out. "SoftGeneticsrecently 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 challengingaspect is ensuring that we can fit all the project requests within givendeadlines. But now with this alliance there is no doubt that we can increaseour level of service for more groups, while attaining the high quality of datadelivery more efficiently for their next-generation sequencing projects."


Jonathan Liu, vice president of research and development atSoftGenetics, echoed Kammesheidt's thoughts and added that "theSoftGenetics/Ambry partnership provides a new strategic alliance that will notonly provide a single streamlined source for next-generation sequencingresearchers, but will also provide SoftGenetics with a deepened vision offuture researcher requirements, allowing NextGENe to remain at the forefront ofnext-generation sequencing software."


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


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


Fosnacht points out that the alliance also providesresearchers wishing to utilize the power of next-generation sequencing adistinctive value proposition by combining the technical quality of AmbryGenetics sequencing with the unique analysis capabilities of NextGENe withoutthe heavy investment typically required in next-generation sequencinginstrumentation and bioinformatics. Fosnacht also points out that Ambry hasquickly grown into a market leadership position in genetics.


"They are one of very few Illumina-certified serviceproviders for next-generation sequencing, meaning that the quality of theirwork is quite superior," he notes. "In addition, Ambry is the world's firstcertified provider for Agilent Sure Select for exome and custom targetedsequencing."


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


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


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


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

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


In the collaboration, Ambry will remain the point of contactfor 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 customprojects, when our clients request more extensive bioinformatics support thanthe standard deliverables of raw sequence and alignment files or simpleanalysis," Kammesheidt says. "Data will be delivered to the client from AmbryGenetics. In addition, SoftGenetics, being at the forefront of next-gen sequencingtool development, will be involved when clients need custom tailoredsolutions."


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


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


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


"We believe both firms truly wish to provide cutting-edgegenomics," he says. "One of our critical goals is the continual enhancement ofNextGENe, which can only be accomplished through user interaction both fromenrichment 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 growingcustomer base," adds Kammesheidt. We talk to our clients all the time and knowwhen people are happy with the results or not. All of our feedback so far hasbeen very positive. Ambry has had a surge of scientists requesting to runprojects with us due to our complete menu for next-generation sequencing."


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