On the cutting edge

A roundup of instrumentation, software and other tools and technology news

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This month, go with the flow (cytometry) with Beckman Coulter in Asia, watch Advaxis and Memorial Sloan Kettering Cancer Center “MINE” the depths of oncology, follow the money with Quad Technologies and its cell separation kit and consider the evidence for QIAGEN’s new next-generation sequencing (NGS) system.

Beckman Coulter and IncellDx sign distribution partnership
MIAMI—Beckman Coulter Life Sciences and IncellDx Inc. announced in November that they have signed a distribution agreement which focuses exclusively on clinical researchers in China, Hong Kong and Taiwan working on the human papilloma virus (HPV) and cancer. The commercial partnership brings the power of multiparameter flow cytometry to molecular testing, improving workflow while delivering sensitive and highly reliable cell identification.
IncellDx’s next-generation investigational molecular assay used to quantify HPV E6, E7 mRNA in single cells has been specially optimized to run on Beckman Coulter’s innovative CytoFLEX flow cytometry system. The high-throughput system instrument has the precision to integrate E6, E7 mRNA overexpression with the measurement of cell cycle and cell proliferation.
“The CytoFLEX easily fits into today’s rapid workflow in research cytometry, combining ease of use with exceptional analytical performance and built-in automation,” said Mario Koksch, vice president and general manager of the Beckman Coulter Flow Cytometry Business Unit. “This innovative partnership with IncellDx enables us to expand our product offerings in clinical research applications, further strengthening the company’s growing infectious diseases portfolio.”
Dr. Bruce Patterson, CEO of IncellDx, commented: “We are excited about this opportunity to bring molecular testing to the flow cytometry field in a region of the world with a great appetite for innovation in the molecular space. The hallmark of cancer research is the quantification of oncogenes E6 and E7 in cells from the cervix, anus or head and neck. However, as cytology samples contain a heterogeneous mixture of normal and abnormal cells, it is critical that we are able to carry out quantification at the single-cell level.”

Advaxis launches MINE collaboration
PRINCETON, N.J.—Late October saw Advaxis Inc., a clinical-stage biotechnology company developing cancer immunotherapies, announce the launch of a research collaboration with Memorial Sloan Kettering Cancer Center (MSK) to evaluate the immunologic and antitumor activity of patient tumor-specific, neoepitope-based immunotherapy.
The goal of the collaboration, titled MINE (My Immunotherapy Neo-Epitopes), is to use Advaxis’ Lm Technology to develop neo-epitope immunotherapies based on an individual patient’s tumor (ADXS-NEO). MINE will first focus on a preclinical study of Advaxis’ new construct approach to evaluate the immunologic effects and antitumor activity of a personalized immunotherapy in a mouse tumor model. Advaxis will use lessons learned from the MINE collaboration to identify and target neoepitopes using Lm Technology and later develop patient-specific immunotherapy constructs that incorporate the neoepitope sequences identified in the patient’s tumor cells. Clinical studies using ADXS-NEO, to be conducted at MSK, are in development.
“Existing immunotherapies have been shown to very effectively augment tumor immunity in a subset of patients, leading to durable responses,” said Dr. Jedd D. Wolchok, chief of melanoma and immunotherapeutics service in the Department of Medicine and Ludwig Center at MSK. “However, recent advances in genome sequencing have made it possible to investigate the role of neoepitopes, or unique mutations, in an individual patient’s cancer, which may allow for the development of specific immunotherapies that generate and enhance an immune response directed against the neoepitopes contained in a patient’s tumor.”
Lm Technology reportedly has the bandwidth to potentially target all of a patient’s immunogenic cancer neoepitopes, eliminating the need to use predictive algorithms and enabling the development of truly individualized immunotherapies that can be manufactured in a cost-effective and timely manner.
“We welcome this collaboration with MSK, a top cancer institution, which will allow us to study our clinically validated Lm Technology in a new way to deliver precision medicine by personalizing neoepitopes specific to a patient’s tumor,” said Dr. David J. Mauro, executive vice president and chief medical officer of Advaxis.

Quad Technologies launches cell separation solution following successful investment round
WOBURN, Mass.— The most promising areas of translational medical research, including CAR-T cancer therapies and stem cell-based regenerative medicine, require the isolation and purification of large numbers of viable, functional cells. There is growing demand from researchers and clinicians for technologies that provide high viability, enhanced efficiency and scalability to optimize conventional cell separation techniques.
Quad Technologies Inc., developer of a novel cell separation technology, has secured a substantial amount of capital from its Series A round to accelerate development of disruptive cell processing technologies for translational medicine applications. The investment has enabled Quad to launch its MagCloudz Streptavidin Cell Separation Kit, which is the first commercially available product incorporating its proprietary QuickGel technology. The MagCloudz kits are said to enable straightforward, scalable and fast cell separation with unique magnetic particle dissociation, resulting in complete label-free cells for applications including T cell purification, stem cell isolation, circulating tumor cell separation and immunotherapy.
QuickGel is a unique dissolvable hydrogel technology that enables high-efficiency purification and release of cells of interest. Delivering what Quad calls “drastically improved cell viability, purity and recovery,” QuickGel overcomes the limitations of other commercially available cell capture chemistries and enables researchers to simplify their cell separation and cell therapy workflows.
Ian Ratcliffe from Keswick Ventures, one of the investors in the financing round, explained: “Immunotherapy, cell therapy and cell separation are significant growth areas within regenerative medicine and all face challenges around scalability. The availability of the MagCloudz kits will revolutionize the cell separation market and provide researchers with the speed, quality and adaptability they need. We are excited to be part of this next phase of growth and looking forward to working with the team at Quad to deliver this game-changing solution to market.”
“Utilizing our groundbreaking QuickGel technology, our MagCloudz kits will truly disrupt existing cell separation and cell therapy research workflows to develop breakthrough therapies for the clinic, and we are delighted to be the first to bring these benefits to market,” explained Quad CEO Sean Kevlahan. “We will continue to strengthen and build on our existing collaborations to solve the current challenges associated with cell separation and evolve our solutions to meet customer needs in high-value applications.”

Evaluation confirms QIAGEN’s NGS system delivers valuable clinical insights
HILDEN, Germany—In early November, QIAGEN N.V. announced that an evaluation has affirmed the performance of the company’s GeneReader NGS System in detecting gene variants known to be clinically relevant in colorectal cancer. Results of the analysis, performed by the Broad Institute of MIT and Harvard, were presented at the Association for Molecular Pathology 2015 Annual Meeting on Nov. 4, 2015, in Austin, Texas.
This inquiry is the first assessment of the GeneReader NGS System’s performance in delivering insights on relevant cancer mutations in a laboratory setting. Data from the GeneReader NGS System compared favorably with QIAGEN’s therascreen RAS mutation tests based on real-time qualitative polymerase chain reaction (PCR) and pyrosequencing, as well as with a next-generation sequencing (NGS) workflow using a competitor’s sequencer. All of the methods were used to test the same 43 tumor samples of confirmed metastatic colorectal cancer from FFPE as sample material.
“Next-generation sequencing can deliver valuable insights for clinical research and diagnostic labs, but users urgently need a simpler, more efficient and cost-effective workflow for NGS technology to enter the mainstream. QIAGEN created the GeneReader NGS System as the first complete Sample to Insight NGS solution designed for any lab to deliver actionable results—and this analysis supports that capability,” said Peer M. Schatz, CEO of QIAGEN. “Integrated with the most comprehensive, up-to-date knowledge base through our QIAGEN Clinical Insight software, the GeneReader NGS System is a turnkey solution that is affordable, easy to run and delivers clinically relevant insights.”
In the analysis, data from the GeneReader NGS System were found to be 100-percent concordant with results of QIAGEN’s FDA-approved therascreen KRAS RGQ PCR assay and the company’s CE-labeled therascreen RAS Extension Pyro Assay. In comparison to these technologies, the GeneReader workflow identified additional aberrations, enabling a more comprehensive investigation of clinically actionable variants (e.g. in the BRAF-gene). Compared to data of the other NGS workflow, which involved an Illumina MiSeq Sequencer, the GeneReader showed 100-percent positive agreement. Because the data generated by the QIAGEN GeneReader NGS System had fewer FFPE artifacts, it reportedly rendered a more accurate reflection of genuine somatic mutations in the samples.
For the analysis, the Broad Institute used the Actionable Insights Tumor Panel, the first member of the family of GeneRead QIAact panels powered by QCI, which was designed with the QIAGEN Knowledge Base to focus only on genes and variants with direct clinical relevance. The panel will be commercially available in the coming weeks.
The QIAGEN Clinical Insight Interpret tool builds on the QIAGEN Knowledge Base and streamlines the creation of a customizable report for each sample based on the test results, with direct links to source information on therapeutic agents, practice guidelines or clinical trials. The comprehensive test report with all the relevant information delivers actionable insights with the highest confidence and efficiency. QIAGEN’s complete NGS solution also includes a software package linking the workflow to a lab’s laboratory information system, enabling tracking of samples and tests, triangulation of NGS data with other results and a holistic view of each individual case.
“We were pleased with results of the analysis, and optimistic about the system’s potential to deliver accurate and actionable data with high efficiency and low adoption hurdle,” said Dr. Scott Steelman, associate director of technology labs for the Broad Institute, who led the institute’s analysis of the new NGS workflow.

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