NuGEN and Caliper partner to eliminate NGS sample prep bottlenecks

Methods are being developed to enable high-throughput, automated extraction, amplification and preparation of difficult and compromised samples for next-generation sequencing

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HOPKINTON, Mass.—NuGEN Technologies Inc. and Caliper LifeSciences Inc. have announced a co-marketing agreement for the development ofautomated methods for next-generation sequencing (NGS) sample preparation onCaliper's Sciclone NGS Workstation.
The collaboration aims to enable researchers to leverageNuGEN's Ovation and Encore reagent solutions on Caliper's liquid handlingplatforms to automate the processing of a wide range of sample types such asnucleic acids extracted from sorted cells, fine needle aspirates,formalin-fixed paraffin-embedded (FFPE) tissue and other limited andcompromised clinical samples.
The collaboration is the first between the two companies butwas "a natural fit," says Kevin Hrusovsky, president and CEO of Caliper,because it provides both companies with the ability to extend market reach andcreate revenue opportunities beyond their direct product offerings.
Caliper had already developed a complete suite of solutionsfor NGS applications "aimed to reduce manual manipulations, increase throughputand improve sample-to-sample consistency. The collaboration provided Caliperwith access to NuGEN's innovative and versatile sample preparation reagents toenable Caliper to address an even broader range of NGS applications," Hrusovskyadds.
The agreement calls for Caliper and NuGEN to firstco-develop automation scripts for NuGEN's Ovation RNA-Seq System and Encore NGSMultiplex System I on Caliper's Sciclone NGS Workstation to provide end-to-end,high-throughput library construction from as little as 500 pg of total RNA. Theautomation scripts will be jointly developed and some equipment modificationswill be required.
"The methods will be developed on the Sciclone NGSplatform," Hrusovsky notes, which do not require any modification for methoddevelopment. 
Caliper will distribute the jointly developed methods to itsSciclone NGS customer base.
The automation solution is scheduled to be available beforethe end of March after having been introduced at the 2011 Advances in GenomeBiology and Technology (AGBT) conference in February. The Sciclone NGSWorkstation can be integrated with Caliper's LabChip GX, which is an analyticalQC platform, and the LabChip XT, a preparative nucleic acid fractionation platform,for extended hands-off automation. Additional applications will follow, thepartners say.
Caliper's liquid handling platforms can be integrated withthe company's LabChip GX, which is an analytical QC platform, and the LabChipXT, a preparative nucleic acid fractionation platform, to acceleratehigh-throughput amplification, fragmentation and library preparation, whichremoves key bottlenecks in sequencing workflows and enables researchers toproduce high-quality libraries for a wide range of sequencing applications,including RNA-Seq, digital gene expression, whole genome and exome sequencing.
"NuGEN's Ovation RNA-Seq System is the first RNA-Seqpreparation kit without any requirement for poly(A) selection or ribosomal RNAdepletion," says Elizabeth Hutt, CEO of NuGEN Technologies. "Working from totalRNA reduces the bias inherent in the selection steps, and results in a morecomplete data set and a more comprehensive understanding of the transcriptome,including non-coding RNAs. Our sample preparation capabilities nicelycomplement Caliper's Sciclone NGS Workstation to provide our customers with astreamlined workflow and easy access to the most advanced sample preparationtechnologies."
The collaboration is primarily centered on RNA applications,particularly with respect to NuGEN's amplification technologies, Hrusovskysays. Future development will also include DNA sequencing library preparation,he notes.

Caliper teams up with U of Miami to automate next-gen sequencingworkflows

HOPKINTON, Mass.—Caliper Life Sciences Inc. also announcedlast month a collaboration with the John P. Hussman Institute for HumanGenomics (HIHG) at the University of Miami in which the parties will developautomated protocols for exome capture and library preparation workflows.
Founded in 2007, HIHG is engaged in research on geneticinfluences on humans and is translating the Human Genome Project intoinformation that can benefit patients directly. HIHG has also been an earlyaccess partner for the recently released, high-sensitivity assay for Caliper'sLabChip GX platform.
"At HIHG, we conduct genetic studies that contribute to thebetter understanding of inherited genetic diseases and disorders," says Dr.John Gilbert, professor and director of the Center for Genome Technology atHIHG. "With our recent implementation of higher capacity sequencingtechnologies, and our focus on exome sequencing projects, sample preparationhas become a bottleneck. We are actively working with Caliper to automatemultiple steps of this process and increase our overall sequencing throughput."
Further details were not disclosed by press time.

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