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OGT Releases New CytoSure™ Microarray for Cancer Research

Oxford Gene Technology (OGT), provider of innovative genetics research and biomarker solutions to advance molecular medicine, has released a new microarray to improve the accuracy and efficiency of cancer research. The CytoSure™ Cancer +SNP array (4x180k) combines long oligo array comparative genomic hybridisation (aCGH) probes with fully validated single nucleotide polymorphism (SNP) content, providing the superior detection of both copy number variations (CNVs) and loss of heterozygosity (LOH) on a single chip. The array has been optimised in collaboration with Professor Jacqueline Schoumans from the Lausanne University Hospital in Switzerland, an expert in both aCGH and cancer genomics. Unique to the proprietary CytoSure™ Cancer +SNP array, any reference sample can be used for analysis without changes to the standard aCGH protocol and, thanks to novel SNP probe chemistry, no restriction digest is required. The capacity to use matched samples is a particular advantage for research into genetic aberrations in cancer, enabling any constitutional abnormalities to be filtered out.

Professor Schoumans commented: “The development of a new microarray with the capacity to detect both CNVs and LOH simultaneously was vital for improving the efficiency and quality of our research. By working very closely with the technical experts at OGT, we have constructed a new array that allows users to simultaneously screen a wide genomic background for CNVs and LOH, while also enabling in-depth CNV analysis on 1500 known cancer-associated genes. This approach produces accurate and insightful data, with all aberrations clearly highlighted and filtered using OGT’s excellent CytoSure Interpret Software.”

The 60-mer oligonucleotide probes utilised in the array provide a high signal-to-noise ratio and highly sensitive detection; this makes them ideal for research into complex malignant tissues. Thanks to OGT’s CytoSure Interpret Software, data analysis is rapid, reliable and simple to carry out, including updated features, such as the B-allele frequency plot, that have been optimised for the identification of biologically relevant genomic variants in tumour samples.

James Clough, Executive Vice President Commercial at OGT, said: “The new CytoSure™ Cancer +SNP array forms part of OGT’s ongoing strategy to design specialised microarrays to help increase our understanding of cancer formation and development. We plan to further add to this portfolio in the coming months, with the introduction of our Cancer Cytogenomics Microarray Consortium (CCMC) array design. By offering both genome-wide CNV and SNP detection, these arrays will prove a valuable tool for efficiently and accurately defining the genetic nature of a given tumour, facilitating research into more efficacious, targeted treatments.”

For more information on the full range of OGT’s solutions for cytogenetic research, please visit www.ogt.com/cancer.

Source: Oxford Gene Technology

Recon 2 Modeling May Help Tailor Treatments for Patients with Metabolic Diseases, Cancer

An international team of researchers, including an investigator with the Virginia Bioinformatics Institute at Virginia Tech, has produced what may be the most comprehensive computer model of human metabolism yet developed.

The discovery, detailed Sunday (March 3, 2013) in the journal Nature Biotechnology, advances understanding of human metabolism in health and disease. Called Recon 2, the model builds and improves upon earlier-generation metabolic reconstruction systems and may be useful for finding biomarkers of metabolic diseases, such as glycogen storage disorder, as well as identifying cancer drug targets and predicting unwanted drug side effects.

A variety of models and approaches have co-existed with the common goal of reconstructing human metabolism, but this one connects the dots, adding metabolic information from a variety of databases including content from the DrugBank database, which details the reactions caused by experimental and FDA-approved drugs to individual enzymes and reactions typical of the metabolic system.

“This is important because we are finally mapping the links between the human genome and metabolism,” said Pedro Mendes, a computational systems biologist and leader of the Biochemical Networks Modeling Group at the Virginia Bioinformatics Institute. “The results provide a framework that will lead to a better understanding of how an individual’s lifestyle, such as diet, or a particular drug they may require, is likely to affect them according to their specific genetic characteristics. The model takes us an important step closer to personalized medicine, where treatments will be tailored according to the patient’s genetic and metabolic information.”

Scientists from Blacksburg, Va.; Manchester, Cambridge, Edinburgh, Reykjavik, San Diego, Berlin and others mapped 65 human cell types and more than 1,000 enzymes that are known drug targets.

With this new map, researchers will be able to deepen their understanding of the role human metabolism plays in health and disease.

Study: A community-driven global reconstruction of human metabolism

Source: EurekAlert!

Definiens and Advanced Cell Diagnostics Introduce RNAscope SpotStudio – Early Access Program Started

Definiens and Advanced Cell Diagnostics (ACD) recently unveiled the details of the RNAscope SpotStudio image analysis software to attendees at the Molecular Medicine Tri-Conference meeting in San Francisco, USA. The software has already been sold to a top pharmaceutical company and a leading academic medical center under an early access program. This advanced image analysis solution brings objective and accurate quantification to RNA in situ hybridization and enables a new generation of diagnostic applications based on single cell analysis. For the first time, gene expression can be measured quantitatively at single-cell resolution and interpreted by pathologists within histopathological context.

Empowering Pathologists with an Easy-to-Use Tool for Quantitative Biomarker Analysis

Quantitative RNA in situ hybridization analysis has recently been made possible by the single molecule sensitivity and digital nature of RNAscope® assay technology. However, manual scoring is time consuming and prone to subjectivity and poor reproducibility. RNAscope SpotStudio software is designed for pathologists with no prior training in image analysis. It is an intuitive automated solution that generates standardized and objective results in minutes. Testing has shown that results obtained with RNAscope SpotStudio are comparable to careful manual annotations by pathologists. The software is compatible with image data from whole slide scanners and microscopes.

“In situ biomarker analysis tools such as immunohistochemistry (IHC) have been limited to subjective semi-quantitative scoring. RNAscope and the SpotStudio image analysis software take in situ biomarker analysis to a whole new level, where quantitative data at the single cell level can be obtained and interpreted within the histopathological context of the clinical specimen”, said Yuling Luo, Founder, President and CEO of ACD. “RNAscope combines the advantages of IHC and PCR, making it a superior tool for tissue-based diagnostics and companion diagnostics”, Dr. Luo added. “Definiens’ invaluable expertise with tissue image analysis made it an ideal partner for the joint development of RNAscope SpotStudio.”

“Coming from a leading position in providing image analysis solutions to the life sciences market, Definiens is rapidly expanding its footprint in tissue diagnostics. We are very excited about this partnership with ACD representing a great example of advanced diagnostic solutions based on Definiens image and data analysis capabilities that will drive next generation diagnostics to truly enable personalized medicine”, said Thomas Heydler, CEO of Definiens.

Definiens and ACD will showcase RNAscope SpotStudio at the Molecular-Med Tri-Con in San Francisco (booth 210). The solution will be marketed and distributed by ACD and is currently being distributed to selected customers in an early access program. General availability is planned for the second quarter of 2013.

While RNAscope Spot Studio supports the analysis of brightfield images, RNA FISH assays can be quantified with Definiens Tissue Studio. With over 450 deployed licenses, Definiens Tissue Studio is the leading image analysis solution for digital pathology. Beyond the detection of spot-like stains, Definiens Tissue Studio provides morphological and molecular expression profiles from any solid tissue (IHC and IF) on a cell-by-cell basis.

Source: Definiens

Tumors Evolve Rapidly in a Childhood Cancer, Leaving Fewer Obvious Treatment Targets

An extensive genomic study of the childhood cancer neuroblastoma reinforces the challenges in treating the most aggressive forms of this disease. Contrary to expectations, the scientists found relatively few recurrent gene mutations—mutations that would suggest new targets for neuroblastoma treatment. Instead, say the researchers, they have now refocused on how neuroblastoma tumors evolve in response to medicine and other factors.

Veridex and LabCorp Agreement Brings CellSearch CTC Test to China

Veridex, LLC recently announced an agreement with LabCorp Clinical Trials that makes the CELLSEARCH® circulating tumor cell (CTC) test available for researchers conducting clinical trials in China. This marks the first clinical reference laboratory in China that offers CTC testing and comes on the heels of China’s State Food & Drug Administration approval of CELLSEARCH® as an in vitro diagnostic to manage patients with metastatic breast cancer.