Statistically Significant Results without the Headache. Q&A with Sarah Church, Ph.D., Senior Scientist at NanoString.
Talking to Sarah, whether during social gatherings or within the office walls, is always a pleasure. Dr. Church is a Senior Scientist at NanoString and one of the warmest people you can run into in the hallway.
She is also one of the exceptional minds behind the nCounter® “360 Series Panel Collection”─ a series of oncology-focused gene expression panels providing a 360-degree view of tumor, microenvironment, and immune response ─ as well as our new 360 Data Analysis Reports – reports that can be purchased to expedite research to insight. Data Analysis Reports are available for a subset of the 360 panels- namely the PanCancer IO360® and Breast Cancer 360® panels. These two panels contain valuable signatures, and scientists who take advantage of the additive reports receive an interactive, customizable, and publication-ready Data Analysis Report containing a variety of plots (heatmaps, volcano plots, box plots, forest plots, swimmer plots, Kaplan-Meier curves, and ROC curves) and signature scores annotated by the response, grouping variable, and/or survival status.
We recently talked with Sarah over Zoom and asked her some questions about the role of the PanCancer IO 360™ gene expression panels coupled with the power of a fast, robust, and reliable data analysis service. Here are her thoughts.
NS: What are your background and your role at NanoString?
SC: I’m a translational research scientist. I earned my Ph.D. studying immunotherapies and then spent a postdoctoral fellowship looking at different types of immune biomarkers in the tumor microenvironment. Here at NanoString, I am part of the Translational Science Team. I work on multiple collaborations that utilize our products, including the PanCancer IO 360™ Gene Expression Panel and the GeoMx® Digital Spatial Profiling technology.
NS: You played a central role in the inception of the oncology 360 Collection. How does this collection differ from the other oncology panels?
SC: The 360 collections are designed to examine the tumor microenvironment. The PanCancer IO 360 (IO 360) Panel focuses on tumor and immune cell interactions and includes our tumor inflammation signature, which was developed as a predictor for anti-PD-1 therapies. This panel has a number of signatures in it and focuses on clinically relevant biology, so it’s great for both biomarker discovery and profiling clinical samples.
NS: Can you walk us through the different 360 Panels?
SC: We have three different 360 Panels: IO 360, Breast Cancer 360™ (BC 360), and Tumor Signaling 360. The IO 360 Panel is meant for profiling the immune and tumor microenvironment across all solid tumor types. The BC 360 Panel is used to study breast cancer and includes the PAM50 signature, the tumor inflammation signature, and several different signatures that are intrinsic to breast cancer tumors. The Tumor Signaling 360 Panel is new and contains different pathways of tumor signaling intrinsic to the tumor itself. It differs from the IO 360 panel in that it is focused on the tumor environment in FFPE samples.
NS: We also offer a Data Analysis Service (DAS) with two of our 360 Panels. What is it, and what is the benefit to our customers? Why should a researcher consider adding a data analysis report to their purchase?
SC: The BC 360 and the IO 360 Panels have the option of being purchased with our Data Analysis Service, which allows customers to submit their data to NanoString and receive back a report. We generate a data analysis report that provides different signature scores, and within the report, we can compare outcomes across different clinical annotations such as response, grouping, variable, time courses, or survival data. The report is interactive and generates publication-ready figures. The scientist also has the ability to request up to five additional signatures be included in the analysis, which can include single genes from either the BC 360 Panel, the IO 360 Panel, or a customized signature of their design.
NS: Who are the scientists behind this service, and what is their level of expertise?
SC: Our Translational Science Team is comprised of (currently) five PhD-level scientists with expertise in immuno-oncology and breast cancer biology. Each report also includes a scientific consultation session with our team.
NS: Can this report actually improve the quality of a customer’s data? If so, how?
SC: The report has great figures that incorporate the quality controls within the customer’s data based on gene expression controls and internal nCounter controls. The information about the controls is accessible and easily reviewed by the user so they can review how their data are performing within the analysis parameters.
NS: Can you share an example of how the DAS and Report helped simplify and streamline data interpretation for a customer?
SC: One of the great things about the signatures included in the 360 reports is that they really bolster the statistical power of your data. Instead of being dependent on the variability of one gene acting as a control, the Report aggregates data based on different pathways and signatures to simply data extraction and visualization. This is particularly powerful when comparing these data to clinical outcomes. We worked with a pharma company that used the IO 360 Report to look at the different signatures and how those signatures might predict a response to their drug. Using the IO 360 Report, they quickly and clearly saw that one of the signatures within the report was highly correlative with responders to their drug treatment. They were then able to file a patent and use it in future studies.
NS: What would you tell a friend or colleague about why they should use the DAS and Report?
SC: One of the biggest benefits of the 360 Reports is that individual scientists can assess the data and results without engaging an expert in bioinformatics and biostatistics. The reports make it quick and easy for any researcher to analyze and interpret their data.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.