Tumor gene expression has proven effective in measuring immune response during cancer progression and therapeutic response. As emerging therapies reveal new biomarkers and expand the need for samples, the costs and labor required to complete this important work also rise. Cancer researchers now have a reliable, sensitive and cost-effective tool for identifying gene expression signatures from immune and cancer cells: the new Advanta™ Immuno-Oncology Gene Expression Assay, used with the Biomark™ HD system.

A powerful immuno-oncology focused assay

The Advanta Immuno-Oncology Gene Expression Assay was developed in collaboration with leading academic and biopharma researchers to provide the right balance of biomarker breadth, assay flexibility and workflow efficiency.

The panel consists of 170 genes, including 91 reported in Nature, where Roy Herbst et al. defined a gene set representing tumor and immune response. The panel includes markers for:

• Immune cell identification
• Immune and cancer cell function
• Immune regulation and cell fate
• Checkpoint therapy response

Optimized for FFPE and fresh frozen tumor samples, the Advanta Immuno-Oncology Gene Expression Assay uses TaqMan® chemistry to sensitively measure gene expression, with five reference genes serving as analysis controls. Combined with Fluidigm microfluidics technology, the assay uniquely offers significant workflow efficiencies over traditional gene expression profiling methods. Each reaction is miniaturized to nanoliter volume and controlled using precise automation to empower accurate and cost-effective qPCR analysis across a large dynamic range. Since assay introduction into the integrated fluidic circuit (IFC) is under user control, researchers also have the flexibility to add up to 17 new assays or exchange gene assays within the panel to achieve experimental goals—all without affecting the original panel content, protocol or workflow.

Immuno-Oncology Expression Assay

Table 1. The Advanta Immuno-Oncology Gene Expression Assay panels A and B. This two-panel set includes 91 target genes and 5 housekeeping genes on Panel A and 74 target genes and the same 5 housekeeping genes on Panel B. Panel B reserves 17 open assay inlets, so you have the added flexiblity to add new assays over time for customization. Each panel is available in packs of 2 or 10 (192 or 960 samples, respectively)

Sample case study

In a 2016 paper published by The Lancet for the POPLAR study, “Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer,” Louis Fehrenbacher et al. detailed how they “assessed efficacy and safety of atezolizumab versus docetaxel in previously treated NSCLC, analyzed by PD-L1 expression levels on tumor cells and tumor-infiltrating immune cells and in the intention-to-treat population.” The team showed that “patients with pre-existing immunity, defined by high T-effector–interferon-γ-associated gene expression, had improved overall survival with atezolizumab.”

Fehrenbacher’s group noted that atezolizumab “significantly improved survival compared with docetaxel in patients with previously treated NSCLC. Improvement correlated with PD-L1 immunohistochemistry expression on tumor ce/p>lls and tumor-infiltrating immune cells,” leading them to conclude: “PD-L1 expression is predictive for atezolizumab benefit. Atezolizumab was well tolerated, with a safety profile distinct from chemotherapy.”

The researchers performed the clinical trial using immunohistochemistry, and also ran a gene expression panel of 91 genes featured in the Herbst paper. These genes are included in the Advanta Immuno-Oncology Gene Expression Assay. The team subsequently used these results to develop a gene signature based on a subset of the panel, effectively predicting therapeutic response that provides data that could potentially be used for developing future diagnostics tests.

Achieve greater overall productivity

The Advanta Immuno-Oncology Gene Expression Assay is optimized to run on the industry-proven Biomark HD system. This automated system enables researchers to easily run up to 96 samples at once with limited hands-on time, while delivering trusted performance. Together with the capability to sensitively detect biomarkers across defined T cell subsets, immune regulation, immune cell fate, cytokines, chemokines and more with exceptional cost-efficiency, this new assay offers an ideal solution to meet the rigorous demands of translational research studies.

Advanta IO Gene Expression Assay ordering information

Contact us to learn more about the Biomark HD system and the Advanta Immuno-Oncology Gene Expression Assay.

fluidigm

For Research Use Only. Not for use in diagnostic procedures.

Next-generation sequencing (NGS) has been instrumental in advancing the understanding of human health and disease. Growing demand for sequencing around the world is driving the need for workflow improvements and cost efficiencies.

Enter Juno™, the industry’s only fully programmed benchtop nanofluidics system, built to scale genomics workflows to optimum efficiency. The platform’s newest commercial application is targeted DNA sequencing library prep, which includes everything needed to prepare NGS-ready libraries including integrated custom assay design services.

High capacity

Juno library prep is optimized for use with Illumina® sequencing systems, bringing new sequencing efficiencies to labs running targeted NGS assays on the mid- to high-throughput scale. With processing capacity of up to 192 samples per run, sample throughput is at least twice that of other systems available today. One operator with a single Juno instrument can prepare up to 1,536 NGS-ready targeted DNA libraries weekly. For labs processing smaller batch sizes, Juno provides the same benefits of expedient turnaround time and walkaway workflow, yielding highly consistent NGS-ready amplicon libraries.

Flexibility

Juno library prep chemistry enables a range of assay panel options. You can amplify up to 4,800 amplicons per sample, access expert design services and ready-to-use primer delivery. Plus, the ability to add amplicon assays over time ensures your panel content stays up to date. Additionally, Juno targeted DNA library prep for NGS can operate overnight without monitoring, maximizing productivity over 24 hours.

“We are pleased to announce the Juno Targeted DNA Sequencing Library Preparation System as an expansion of our growing portfolio of automated genomic workflows that increase laboratory efficiency for medium-to-high-throughput pipelines,” said Steve McPhail, General Manager of Clinical and Applied Markets at Fluidigm. “We are now able to offer our customers a significant improvement over the largely manual, low-throughput and laborious NGS library preparation workflows used today.”

Learn more about new Juno Targeted DNA Sequencing Reagents.

Every year since 2012, the mass cytometry community has gathered to share its research findings and technical know-how in an atmosphere fostering support and collaboration. On June 9 of this year, the Museum of Science in Boston was the scene for the 6th Annual Mass Cytometry Summit, our largest ever with more than 200 attendees.

Watch a video of mass cytometry users sharing their thoughts on the Summit.

fluidigm

“The mass cytometry community is very dynamic and people are really open to exchanging ideas and protocols. Initially, most mass cytometry information was coming from the US. Now you can find people interacting all across the globe.”
—Hervé Luche, R&D manager, Centre d'ImmunoPHEnomique, Marseille

Researchers presented talks on topics ranging from new mass cytometry applications to best practices and data analysis approaches. Highlights included Ruth Montgomery from Yale and Stephen Oh from Washington University presenting on their use of mass cytometry in translational studies; Adeeb Rahman from Icahn School of Medicine at Mount Sinai presenting his innovative approach for a mass cytometric surrogate of light scatter; and Vinko Tosevski from the University of Zurich sharing his facility’s highly effective workflow for Cytobank data analysis. An informative panel discussion sparked lively audience engagement on integrating mass cytometry services into both academic and pharmaceutical institutions.

Jonathan Irish, PhD, Vanderbilt University, led the panel discussion “Meeting the Challenge of Integrating Mass Cytometry at Your Institution” at the 6th Annual Mass Cytometry Summit. Panelists included, from left to right, Ruth Montgomery, PhD, Yale School of Medicine; Mike Lee, MS, University of California, San Francisco; Carina Torres, BS, Eli Lilly; Mike Leipold, PhD, Stanford University; John Daley, BS, Dana-Farber Cancer Institute.

Scientists from around the world participated, representing top-tier research institutions and major pharmaceutical companies. Attendees interacted and networked during breaks and meals on the banks of the Charles River at the Museum of Science outdoor pavilion.

“The Mass Cytometry Summit gives a unique way to interact with other researchers in a relaxed environment: It’s easy to meet new people and establish collaborations.”
—Denis Schapiro, PhD, University of Zurich

Many speakers graciously agreed to share their talks with the mass cytometry community. Watch their on-demand presentations.

fluidigm

For Research Use Only. Not for use in diagnostic procedures.

Enabling multiparameter profiling of precious samples, mass cytometry has been instrumental in achieving new research breakthroughs in areas such as immunology, cancer immunotherapy, drug discovery, vaccine development and more around the world.

Watch the webinars below to learn how researchers are utilizing Helios™, a CyTOF system, and mass cytometry applications to further their research.

	Finding Pathologic T Cells in Rheumatoid Arthritis by Mass Cytometry Deepak Rao, MD, PhD  Rheumatologist Co-Director, Human Immunology Center Brigham and Women's Hospital Watch
	Querying Cytokine-Signaling Networks in Myeloproliferative Neoplasms Stephen Oh, MD, PhD  Assistant Professor of Medicine, Division of Hematology  Washington University School of Medicine  Watch
	Enhancing Checkpoint Blockade in Lymphoma with In Situ Vaccination Joshua Brody, MD  Assistant Professor, Hematology and Medical Oncology Director, Lymphoma Immunotherapy Program Icahn School of Medicine at Mount Sinai Watch
	Decoding Tumors with Mass Cytometry Jonathan Irish, PhD Assistant Professor of Cancer Biology, Assistant Professor of Pathology, Microbiology and Immunology Vanderbilt University Watch
	Defining the Phenotypic and Functional Immune Microenvironment in AML Evan Lind, PhD Assistant Professor, Department of Molecular Microbiology and Immunology and Department of Cell, Development and Cancer Biology Oregon Health & Science University Watch
	Towards an Assay of Global Immune Competence Holden Maecker, PhD Associate Professor (Research) of Microbiology and Director, Human Immune Monitoring Center Stanford University Watch
	Signatures of Protective NK Cell Responses Catherine Blish, MD, PhD Assistant Professor, Department of Medicine and Immunology, Stanford University School of Medicine Assistant Director of the Stanford Medical Scientist Training Program Watch

Fluidigm

For Research Use Only. Not for use in diagnostic procedures.

The C1™ system provides the widest range of automated single-cell applications in the industry, from gene expression profiling to genomic and epigenetic analysis. With more than 150 peer-reviewed publications, the C1 system has empowered significant research breakthroughs in the understanding of cell diversity and function in cancer, neurology, immunology and cardiovascular and stem cell biology.

The key to successful single-cell studies is preparing high-quality suspensions with maximum cell viability and minimum cell stress and debris. Whether you are working with cultured cells or with samples freshly isolated from tissue, cell quality is a critical factor for ensuring optimal results in single-cell datasets.

Now you can load enriched cell populations obtained by flow cytometric cell sorting directly into the C1 IFC (integrated fluidic circuit) to obtain rare subpopulations of cells with high purity and viability.

Benefits of this new application include:

To learn more, download the application note Cell Sorting Directly to the C1 IFC and the associated C1 cell sorting workbook today.