Genetic Engineering & Biotechnology News

OCT1 2012

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D; community with critical information on the tools, technologies, and trends that drive the biotech industry.

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OMICS Sample Prep Continued from page 1 these approaches for use in academic labs and as ready-for-market devices. Traditionally, nucleic acid preps are de- signed to gather long stretches of RNA and/ or DNA, with those less than 50 nucleotides considered merely uninteresting fragments. Although that view has drastically changed in the past decade or so, most protocols for extracting RNA still purposefully get rid of diminutive species like the ~22 nucleotide miRNA. Those protocols that do specifically in- clude small nucleic acids typically include centrifugation and/or filtration steps, notes Bee-Na Lee, Ph.D., senior applications scien- tist at Beckman Coulter Life Sciences (www. beckmancoulter.com). "These methods usually do not produce consistent yield of miRNA for downstream applications, and they are not very amenable to high throughput." To rectify this and allow miRNA to be isolated from FFPE and cell culture samples in an automated fashion, Dr. Lee modified the binding and rebinding buffer conditions used with Beckman Coulter's Agencourt FormaPure and RNAdvance Cell v2 kits, respectively. These kits utilize the company's solid- phase reversible immobilization (SPRI) tech- nology. SPRI's negatively charged carboxyl- coated magnetic beads would normally repel the negatively charged nucleic acids. However an aqueous pocket is created by using a "crowding reagent" which allows the nucleic acids to move to the polar phase and reversibly bind to the beads in the pres- ence of binding buffer. After exposure to a magnetic field, the beads that bind nucleic acids will pull to form a ring at the bottom of a well. "You can remove all the contamination. Aspirate everything out, touching the tip to the bottom," explains Dr. Lee. The DNA or RNA is then eluted with buffer that is "mainly just water," preventing inhibition of downstream applications that can occur with other protocols. For small RNA expression applications, "we normally will put the total RNA in … our yield is so high we don't require enrich- ment," she continues. For this she credits the SPRI technology, which in addition to proprietary reagents utilizes homogenous-sized beads that are slow to aggregate or sediment, alleviating the need to frequently re-suspend. A large surface area:mass ratio allows for a high binding capacity, thus allowing the beads to rapidly respond to the magnetic field. Taking on Sepsis When looking for a needle in a haystack— or a single bacterium in a milliliter of blood— "the main problem becomes sample prep," explains Sergey Dryga, Ph.D., vp of immu- nology at nanoMR (www.nanomr.com). Because the concentration of microor- ganisms responsible for sepsis is low—on the order of one colony forming unit (CFU) per mL of infected blood in bacteremia, for example—rapid tests using small volumes of NEWS Genomics & Proteomics > Test Predicts Differential Treatment Benefit between Chemotherapy and Targeted Therapy for Lung Cancer Patients Results from a VeriStrat analysis of se- rum or plasma samples taken from a Phase II study evaluating erlotinib, gemcitabine, and erlotinib plus gemcitabine in elderly advanced non-small cell lung cancer pa- tients showed that the VeriStrat test was able to identify patients more likely to have a slower progression of disease and longer overall survival when treated with either single agent chemotherapy, gemcitabine, or targeted therapy, erlotinib. Biodesix developed VeriStrat as a blood-based test for patients with cancer to provide results on the patient's pro- teomic profile. > Thermo Fisher Licenses Protein Metrics' ByomicTM Database Search Software Thermo Fisher Scientific inked a nonex- clusive agreement with Protein Metrics to license the company's Byonic™ software, a next-generation proteomics search en- gine. The database search software sys- tem will add next-generation capability to streamline analysis of glycopeptides and other post-translational modification data, according to a Thermo official. In addition, Thermo introduced its Proteome Discoverer software version 2.0 for analyzing qualitative and quanti- tative proteomics data. > CLC Bio Wins $2M for Pathogen Sequencing Bioinformatics software firm CLC bio has been awarded $2 million in EU funding as part of the $10 million Pathseek project, a clinical microbiology initiative that aims to demonstrate the use of next-generation sequencing for detecting pathogens and drug resistance directly in clinical samples. CLC's involvement will focus on develop- ing a user-friendly software package that will allow clinical laboratories to carry out pathogen identification, host biomarker identification, pathogen-variant character- ization, and molecular epidemiology. "Current platforms in diagnostic labo- ratories are limited by the amount of time required for generating a result and by the limited sequence information available for pathogens, " comments Roald Forsberg, vp of R&D; at CLC. "To overcome these limita- tions we're going to develop a disrup- tive diagnostic technological pathogen sequencing platform which utilizes our world-leading bioinformatics expertise to enable scientists to go from a patient sample to a result, in less than 48 hours. " > Collaboration Focuses on Blood Biopsy Tumor Profiling Transgenomic and NYU Langone Medi- cal Center inked a collaboration focused on application of the firm's Ice Cold-PCR mutation detection technology to identify treatment-related mutations in the circulat- ing tumor cells (CTCs) of patients with surgi- cally operable early-stage lung cancer as a means to help tailor therapy. The partner- ship follows on from Transgenomic's recent collaboration with researchers at the MD Anderson Cancer Center, which is focused on exploiting the Ice Cold-PCR to character- ize tumor-derived DNA in blood and CTCs from patients with a variety of cancers. 26 | October 1, 2012 | genengnews.com | Genetic Engineering & Biotechnology News The partnership will involve isolating CTCs from the blood of about 200 patients using ScreenCell's ScreenCell® CTC capture system both before and after surgery to determine if CTC numbers change, or are linked with disease recurrence or progres- sion. DNA from these cells and also cell- free DNA (cfDNA) will then be analyzed using the Ice Cold-PCR technology to iden- tify mutations known to be linked with a response to targeted drugs. > ShanghaiBio Partners with In- genuity on Genomic Data Analysis ShanghaiBio and Ingenuity Systems signed a collaboration agreement en- abling ShanghaiBio to extend its current lab service offering to include Ingenuity solutions for downstream analysis and interpretation of genomics data. ShanghaiBio officials say they will com- plement their sequencing, genotyping, and gene expression lab services by cre- ating a bundled solution with Ingenuity's applications, which combine analytics and biomedical content to help get actionable insights from experiments. Q The main goal of sample preparation is to confirm that the sample in question is in the best possible condition with the required standard of purity for subsequent analysis. Radu-Ion Huculeci/Fotolia blood do not have the sensitivity to deliver a statistically significant result. Currently only those starting from a posi- tive blood culture can do so. However, the cultures must be grown for 12–48 hours before a pathogen might even be detected, and another 12–24 hours to identify the of- fending organism, with the delay impacting the ability and cost to successfully treat the infection, Dr. Dryga points out. nanoMR's pathogen capture system (nanoMR PCS) uses antibody-coated mag- netic nanoparticles to pull out pathogens from blood and deliver purified DNA in less than an hour, without the need to lyse the blood or purify the bacteria, Dr. Dryga continues. "The method is old but nobody knows how to do it in blood, because blood is a very complicated matrix. Our innovation is that we basically developed bead chemistry, anti- bodies, and conditions that work in blood." To use the nanoMR PCS a 10 mL vacu- tainer of blood is delivered to a VCR tape- See Sample Prep on page 29

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