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Firefly Bioworks Releases Expanded Multiplexed MicroRNA Assay

Recently, Firefly BioWorks announced the expansion of its microRNA assay, FirePlex® miRSelect, from a maximum of 23 multiplexed microRNAs to 68.

“The expanded capability of miRSelect will resonate with researchers looking to validate early discovery studies on statistically significant numbers of samples. This latest version of miRSelect is an important step toward our mission of enabling all scientists to engage those ambitious explorations that are considered too expensive, labor intensive or time consuming with existing technology,” says Dr. Davide Marini, co-founder and Chief Executive Officer of Firefly BioWorks. The expanded Firefly platform allows for rapid and cost-effective testing of large numbers of samples across more microRNA targets than ever before. In addition to validation studies, miRSelect is applicable to a broad array of research areas, including biomarker discovery, translational research, developmental biology and model organism research.

FirePlex® miRSelect is a rapid, robust, and sensitive method for multiplexed detection of microRNAs across a wide range of sample types. The product does not require purchase of dedicated equipment or lengthy sample preparation protocols. Instead of using predefined microRNA panels, researchers can build a panel customized to their needs, by choosing 10 to 68 targets from miRBase or by specifying novel sequences. For scientists approaching the field of microRNA for the first time, Firefly BioWorks offers a special-purpose search engine (PubmiR) to provide objective ranking of the most important microRNAs associated with specific diseases or biological pathways, according to published literature.

“The goal of this release is to provide researchers with the maximum flexibility, both in terms of number and nature of microRNA targets to be profiled in each sample,” says Dr. Daniel Pregibon, co-founder and Chief Technology Officer of Firefly BioWorks.

Firefly BioWorks was founded to commercialize an innovative, open approach to multiplexed detection of biomolecules. The company’s flagship product, FirePlex® miRSelect, enables high-throughput and targeted microRNA profiling by flow cytometry. The product is also available as a service.

Source: Firefly BioWorks

Tenfold Boost in Ability to Pinpoint Proteins in Cancer Cells

Better diagnosis and treatment of cancer could hinge on the ability to better understand a single cell at its molecular level. New research offers a more comprehensive way of analyzing one cell’s unique behavior, using an array of colors to show patterns that could indicate why a cell will or won’t become cancerous.

A University of Washington team has developed a new method for color-coding cells that allows them to illuminate 100 biomarkers, a ten-time increase from the current research standard, to help analyze individual cells from cultures or tissue biopsies. The work is published in the March 19 issue of Nature Communications.

“Discovering this process is an unprecedented breakthrough for the field,” said corresponding author Xiaohu Gao, a UW associate professor of bioengineering. “This technology opens up exciting opportunities for single-cell analysis and clinical diagnosis.”

The research builds on current methods that use a smaller array of colors to point out a cell’s biomarkers – characteristics that indicate a special, and potentially abnormal or diseased, cell. Ideally, scientists would be able to test for a large number of biomarkers, then rely on the patterns that emerge from those tests to understand a cell’s properties.

The UW research team has created a cycle process that allows scientists to test for up to 100 biomarkers in a single cell. Before, researchers could only test for 10 at a time.

The analysis uses quantum dots, which are fluorescent balls of semiconductor material. Quantum dots are the smaller version of the material found in many electronics, including smartphones and radios. These quantum dots are between 2 and 6 nanometers in diameter, and they vary on the color they emit depending on their size.

Cyclical testing hasn’t been done before, though many quantum dot papers have tried to expand the number of biomarkers tested for in a single cell. This method essentially reuses the same tissue sample, testing for biomarkers in groups of 10 in each round.

“Proteins are the building blocks for cell function and cell behavior, but their makeup in a cell is highly complex,” Gao said. “You need to look at a number of indicators (biomarkers) to know what’s going on.”

The new process works like this: Gao and his team purchase antibodies that are known to bind with the specific biomarkers they want to test for in a cell. They pair quantum dots with the antibodies in a fluid solution, injecting it onto a tissue sample. Then, they use a microscope to look for the presence of fluorescent colors in the cell. If they see particular quantum dot colors in the tissue sample, they know the corresponding biomarker is present in the cell.

After completing one cycle, Gao and co-author Pavel Zrazhevskiy, a UW postdoctoral associate in bioengineering, inject a low-pH fluid into the cell tissue that neutralizes the color fluorescence, essentially wiping the sample clean for the next round. Remarkably, the tissue sample doesn’t degrade at all even after 10 such cycles, Gao said.

For cancer research and treatment, in particular, it’s important to be able to look at a single cell at high resolution to examine its details. For example, if 99 percent of cancer cells in a person’s body respond to a treatment drug, but 1 percent doesn’t, it’s important to analyze and understand the molecular makeup of that 1 percent that responds differently.

“When you treat with promising drugs, there are still a few cells that usually don’t respond to treatment,” said Gao. “They look the same, but you don’t have a tool to look at their protein building blocks. This will really help us develop new drugs and treatment approaches.”

The process is relatively low-cost and simple, and Gao hopes the procedure can be automated. He envisions a chamber to hold the tissue sample, and wire-thin pumps to inject and vacuum out fluid between cycles. A microscope underneath the chamber would take photos during each stage. All of the images would be quantified on a computer, where scientists and physicians could look at the intensity and prevalence of colors.

Gao hopes to collaborate with companies and other researchers to move toward an automated process and clinical use.

“The technology is ready,” Gao said. “Now that it’s developed, we’re ready for clinical impacts, particularly in the fields of systems biology, oncology and pathology.”

The research was funded by the National Institutes of Health, the U.S. National Science Foundation, the U.S. Department of Defense, the Wallace H. Coulter Foundation and the UW’s Department of Bioengineering.

Study: Quantum dot imaging platform for single-cell molecular profiling

Source: University of Washington

Cancer Genetics, Inc. Receives Regulatory Approvals for MatBA®-DLBCL, a Proprietary Microarray Test for the Diagnosis, Prognosis, and Patient Risk Stratification of Non-Hodgkin Lymphoma

Cancer Genetics, Inc. (CGI), a leader in oncology-focused personalized medicine, today announced it has received CLIA and New York State approvals for clinical use of its proprietary mature B-cell neoplasm array or MatBA® (patent 13/475,034) for diffuse large B-cell lymphoma. MatBA®-DLBCL will assist clinicians in the diagnosis and prognosis of DLBCL.

DLBCL is the most common form of non-Hodgkin lymphoma (NHL), a diverse group of hematological malignancies. An estimated 190,000 people in the United State suffer from DLBCL, and up to 24,500 new U.S. cases diagnosed each year, which accounts for up to 40% of all NHL cases. Newly-diagnosed patients have a median age of 64 years, and disease progression and outcomes vary widely, due in part to the genomic characteristics of each individual patient’s cancer. This creates a strong clinical need for accurate and molecularly-informed prognostic testing both at the time of initial diagnosis and throughout ongoing disease monitoring efforts to ensure selection of the best treatment plan for an individual patient. However, current prognostic modalities rely primarily on clinical features.

CGI’s MatBA®-DLBCL microarray provides clinicians with information on genomic alterations in DLBCL, including regions of gain and loss that are associated with disease outcome.

A research collaboration between the Memorial Sloan-Kettering Cancer Center and CGI using 87 patient samples, as well as the analysis of two open datasets including 171 samples (GSE11318, Lenz et al.) and 51 high risk samples (E-MEXP-3463, Taskinen) and other published datasets showed that:

  • MatBA®-DLBCL has both diagnostic and prognostic value
  • MatBA®-DLBCL can assist in patient stratification for risk-adapted therapy when performed at diagnosis
  • MatBA®-DLBCL assesses the presence of single biomarkers as well as genome complexity as measures of overall survival following front-line immunochemotherapy

CGI believes that it is the only laboratory to have a CLIA and New York State approved microarray for the genomic assessment of DLBCL. The MatBA® -DLBCL Array CGH assay joins the DLBCL CompleteSM program offered by CGI, which includes a suite of esoteric tests used in the diagnosis, prognosis and clinical management of DLBCL patients. This newly-approved DLBCL test extends CGI’s ongoing commitment to developing new diagnostic and disease management tools for some of the most costly and critical unmet needs in oncology today. MatBA® -DLBCL joins MatBA® -CLL (chronic lymphocytic leukemia) and MatBA® -SLL (small lymphocytic leukemia) in CGI’s suite of CLIA- and New York State-approved proprietary microarrays for the clinical management of underserved hematological malignancies.

Source: Cancer Genetics

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

OGT Expands Commitment to Improved Cancer Profiling with CCMC Deal

Oxford Gene Technology (OGT), provider of innovative genetics research and biomarker solutions to advance molecular medicine, announced today that it has signed a licence agreement with the Cancer Cytogenomics Microarray Consortium (CCMC) to design a whole genome, cancer-specific microarray.