SelectScience
Join Free
Accelerating Science
NewsLife Sciences

Affymetrix and BioDiscovery Announce Software to Accelerate Cancer Translational Research

Affymetrix, Inc.
7 Jul 2013

Product news

Affymetrix, Inc. and BioDiscovery announce the availability of the Nexus for OncoScan® Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan® FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscovery's flagship Nexus Copy Number™, is available to customers who are analyzing data generated using this service.

Obtaining high-quality copy number data using limited amounts of DNA from degraded FFPE samples is extremely challenging for cancer researchers. Utilizing Affymetrix' unique Molecular Inversion Probe (MIP) technology, the OncoScan FFPE assay is capable of analyzing highly degraded DNA in FFPE tumor samples, even from less than 100 ng of starting DNA material, and is currently available as a service through Affymetrix Research Service Laboratory (ARSL) based in Santa Clara, California.

OncoScan FFPE Express 2.0 Service has been successfully used by more than 30 leading cancer research institutes, including M. D. Anderson Cancer Center, University of California San Francisco, and the Huntsman Cancer Institute at theUniversity of Utah.

"Cancer translational researchers have been able to quickly and easily analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data," said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. "Nexus for OncoScan Software is especially optimized for solid tumor copy number analysis and can generate whole genome copy number calls from raw data in minutes. We are very excited to continue to partner with BioDiscovery to bring this powerful and easy-to-use software to the cancer research community."

"The OncoScan FFPE assay is an amazing technology for cancer researchers allowing them to unlock DNA information from masses of archived FFPE samples to obtain high quality data," said Soheil Shams, President of BioDiscovery. "Combining the powerful OncoScan FFPE technology with the proven power of Nexus Copy Number gives scientists a unique solution that is sure to accelerate cancer research, impact diagnosis, and ultimately lead to better patient care and treatment. We are very pleased to partner with Affymetrix in offering this powerful solution."

A next generation OncoScan FFPE product will be available in late 2013 enabling researchers to perform the assay and analysis in their own lab. Delivering results in about 48 hours, this new product will provide whole genome copy number coverage with high resolution in known cancer genes, loss of heterozygozity (LOH) as well as clinically relevant somatic mutation data - all from a single assay. An updated version of Nexus for OncoScan Software will be released in conjunction with the launch.

Links

Affymetrix, Inc.Company website

Tags

PCR and Thermal CyclingPolymerase chain reaction (PCR) kits and thermal cyclers are used for the in vitro amplification of DNA permitting subsequent analysis and experimental procedures. Explore a range of high-quality polymerase, primers and nucleotides or simplify your workflow with a PCR mastermix. Find reverse transcription PCR (RT-PCR) and cDNA synthesis kits for RNA products and libraries. Quantitatively measure the amplification of DNA with real-time PCR (qPCR) and droplet digital PCR (ddPCR) kits and systems, and discover automated PCR setup solutions to increase throughput. Alternative DNA amplification methods also include recombinase polymerase amplification (RPA) kits. Find the best PCR kits and thermal cyclers and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.DNA / RNA Extraction and PurificationPurified DNA and RNA are required for numerous downstream molecular biology applications. Consequently, the importance of high-quality DNA/RNA extraction and purification equipment cannot be underestimated. Many purification kits are available and are typically optimized for nucleic acid type and source, including plasmid DNA, genomic DNA, mRNA, RNA and viral nucleic acid purification kits. Automated extraction and purification of nucleic acids can be implemented with magnetic bead separator instruments or high-throughput purification workstations. Find the best DNA/RNA extraction and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.DNA SequencingDNA sequencing, such as sanger sequencing, is a biological technique that determines the precise order of nucleotide bases in a fragment or template of DNA. DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Gene Expression and Molecular CloningMolecular cloning is a set of techniques that utilizes vectors to transfer recombinant DNA into host cells and is an essential tool for investigating the expression of genes and proteins in bacterial or mammalian cells. A variety of vectors optimized for gene cloning and expression in a range of host organisms are available, alongside competent cells for genetic replication. Here, you can explore a range of molecular tools, high-quality genomic and cDNA libraries, premade clones, transformation and transfection reagents and mutagenesis or gene expression detection assays and expression arrays. Find the best gene expression and molecular cloning products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.BiomarkersBiomarkers are biological markers which can be measured and evaluated to indicate a biological state. The use of biomarkers in research and diagnosis can indicate a normal or disease state or drug response of cells / tissues. Biomarkers include genetic markers, cell surface markers such as antigens, antibodies or receptors and secreted molecules such as cytokines. An assay system is required for identification of biomarkers. :Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Light MicroscopyLight microscopes or optical microscopes are used to visualize microscale objects under magnification, including cells, clinical specimens and materials. Lab equipment for light microscopy includes confocal microscopes, fluorescence microscopes, zoom and stereo microscopes. Microscope slides and imaging reagents are available for visualizing samples, as well as various microscope stages and incubators for large or temperature-sensitive samples. Find the best light microscopes in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Software PlatformsSoftware platforms are useful for various stages of laboratory experiments from data collection to data storage and processing. For instance lab software is available for system control, data management, data analysis and qualification / validation.FFPEFormalin-fixed paraffin-embedded (FFPE) tissues are commonly used in medical research, particularly in histology and cancer studies. The preservation process allows long-term storage of tissue samples for later analysis. Explore FFPE research products in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.Cancer ResearchAlthough cancer is often referred to as a single condition, it actually consists of more than 100 different diseases. Microscopy, mass spectrometry, high throughput sequencing and flow cytometry are some of the most common techniques employed in cancer research labs.Genome SequencingGenome sequencing involves determining the complete DNA sequence of an organism's genome. It provides crucial information about genetic variations, mutations, and diseases. Advances in sequencing technologies, such as next-generation sequencing (NGS), have accelerated research in genomics, diagnostics, and personalized medicine. Explore genome sequencing tools in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.Translational Research

Related articles

Affymetrix and BioDiscovery Announce Software to Accelerate Cancer Translational Research