Digital Spatial Profiling Frequently Asked Questions

 

General Questions

 

1. What are the advantages of utilizing the NanoString® GeoMx™ Digital Spatial Profiler (DSP) compared to alternative spatial profiling options?

Unlike other platforms, NanoString's digital spatial profiling technology enables analysis of both protein and RNA expression of FFPE samples. The platform also allows for high-plex analysis of precious and limited samples as it is non-destructive (the sample may be reanalyzed with alternative approaches such as whole exome sequencing (WES), RNAscope®, immunohistochemistry, etc.), and only a single section is required. In addition, researchers can select from a host of curated disease- and pathway-focused panels with the potential for customizationincluding the new, comprehensive 1,800 Cancer Transcriptome Atlas (CTA) panel covering >50 cancer-related pathways.

 

2. What is the sensitivity/limit of detection using the GeoMx platform?

The limit of detection is dependent upon the expression level of the target. However, cell mixing experiments have demonstrated that as few as 1.6% of positive cells can be detected in a population of negative cells.

 

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Region of Interest (ROI) Selection

 

3. How many regions of interest (ROIs) can be selected per sample?

Over 96 ROIs may be selected per slide.

 

4. What is the size of each region of interest (ROI)?

Each ROI can be as large as a 700 µm diameter area, or as small as a single cell (10 µm). However, while sensitivity is sample- and transcript/protein-dependent, ROIs with at least 40 cells typically offer the best results.

 

5. How are regions of interest (ROIs) selected?

There are several approaches for defining ROIs, including placing geometric shapes around specific areas (“geometric profiling”), tiling a grid across the entire slide ("gridded profiling"), profiling using immunofluorescence/RNAscope patterns (“segment profiling”), placing concentric circles surrounding a histological landmark (“contour profiling"), or any combination of these approaches. Researchers should submit a circled, adjacent H&E section together with the unstained section(s) to facilitate ROI selection.

 

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Panel Selection

 

6. Which proteins/RNAs are included in each panel?

Please visit here for the gene list for each targeted panel or here for the 1,800 gene Cancer Transcriptome Atlas (CTA) panel. However, please note that new panels are being added, and content is subject to change. For the most up-to-date gene list, please contact us via email at NGS@genewiz.com, or call us toll-free at 877-GENEWIZ (436-3949) ext. 1.

 

7. What are GeoMx assay cores and modules?

GeoMx assays are pre-validated and modular to provide flexibility, and support a range of research needs. For protein profiling, select one ~20-plex core and up to six optional 10-plex modules to analyze expression of your proteins of interest. For RNA profiling, select a core panel with the possibility of adding custom, user-defined probes. Note that it is not possible to run a module without running a core, or to combine protein and RNA cores/modules on the same slide.

 

8. What is the Cancer Transcriptome Atlas?

The Cancer Transcriptome Atlas (CTA) is a ~1,800 gene panel designed for comprehensive profiling of tumor biology, the tumor microenvironment, and immune response. It contains genes from over 50 pathways,  including coverage of global immune response, microenvironment activity, and tumor reactivity to explore all aspects of cancer biology. Furthermore, you can customize by supplementing up to 30 additional targets of interest.

 

9. Can I create my own custom panel?

Yes, it is possible to customize pre-existing panels by spiking-in custom reagents, as well as potentially designing an entirely new panel for your own purposes. Please contact us via email at NGS@genewiz.com, or call us toll-free at 877-GENEWIZ (436-3949) ext. 1 to learn more.

 

10. I have a proprietary or custom antibody. Can it be used on the GeoMx platform?

Yes, GENEWIZ may facilitate custom protein barcoding through NanoString. Once you have your labeled antibody, NanoString will ship it to GENEWIZ to process your samples.

 

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Sample Preparation

 

11. How do I prepare my FFPE slides for submission?

Please provide FFPE slides on positively-charged glass slides, or FFPE blocks ready to be sectioned. GENEWIZ will provide a document outlining all aspects of sample preparation with your quote.

 

12. Can you return my FFPE slides/blocks after processing on the GeoMx?

One of the advantages of using the GeoMx platform is that it is non-destructive, and slides may be reused for other applications (e.g. immunostaining, WES/panel sequencing, etc.). Upon request, GENEWIZ will return all slides after processing. If providing FFPE blocks, please note that they may be exhausted after sectioning, but GENEWIZ will take every effort to preserve material and return blocks after processing.

 

13. Can frozen tissues be submitted?

Yes. Although the GeoMx platform is designed for FFPE samples, it is also compatible with frozen tissues. Please specify in your quote request if you would like to submit frozen tissue sections.

 

14. How do I contact GENEWIZ for a technical consultation about my project?

GENEWIZ's NGS Team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. Contact the team directly by emailing us at NGS@genewiz.com, or calling us toll-free at 877-GENEWIZ (436-3949) ext. 1.

 

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Data Analysis & Delivery

 

15. Can you perform CLIA- or GLP-grade analysis on the GeoMx platform?

Digital spatial profiling using the GeoMx platform is currently provided on a research use only (RUO) basis. Please contact our CLIA Team by emailing us at CLIA@genewiz.com, or calling us toll-free at 877-GENEWIZ (436-3949) ext. 1 if you're interested in clinical-grade digital spatial profiling. 

 

16. What data delivery methods are available?

GENEWIZ will recommend the best data delivery option based on your specific project details. Data delivery options include:

  • Secure File Transfer Protocol (SFTP)
  • Customer cloud account
  • External hard drive (additional charges may apply)

 

17. How will my data be delivered?

If your results are being shipped to you via hard drive, you can track its shipment using the tracking number provided to you in the delivery email sent from GENEWIZ.

If your results are being delivered via another data delivery method, such as AWS S3, Aspera, or other cloud-based methods, please refer to the delivery email sent from GENEWIZ for detailed information on the transfer, and consult with your IT department to ensure compliance with your institution’s policies.

If your results are being sent via a secure File Transfer Protocol (sFTP), please refer to GENEWIZ’s sFTP Data Download Guide for instructions on how to download your data and troubleshooting tips.

 

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Ordering & Processing

 

18. How do I request a quote? 

For a quick tutorial, watch the video below. Select the Spatial Genomics icon to reach the quote request form. 

 

 

19. What happens after I submit a quote request form?

Our NGS team will review your inquiry, follow up with a quote, and guide you through the next steps. 

 

20. How do I confirm a quote?

For a quick tutorial, watch the video below. 

 

 

21. How do I submit the GENEWIZ Sample Submission Form to provide detailed information about my samples?

Please watch the video below for a brief tutorial on how to submit your Sample Submission Form. 

 

 

22. How can I monitor the progress of my project?

The status of your order, including an estimated date of delivery, can be viewed anytime through your GENEWIZ account. Visit the Order Summary page of your project to find the current order status. Watch the video below for a brief tutorial.  

 

 

23. How long does GENEWIZ hold samples?

We hold samples for 1 year after project completion. Please contact us if you would like samples retained for a longer period or shipped back to you. 

 

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Have a specific question?

Email | NGS@genewiz.com

Phone | 1-877-GENEWIZ (436-3949), ext. 1

 

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