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 customization.

 

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.

 

Region of Interest (ROI) Selection

 

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

Up to 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).

 

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. Alternatively, researchers can submit a circled adjacent H&E section together with your unstained section(s), or allow GENEWIZ’s network of pathologists to select ROIs on your behalf.

 

Panel Selection

 

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

Please visit here for the gene list for each 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 at NGS@genewiz.com, toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 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 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. Can I create my own custom panel?

Yes, it is possible to customize pre-existing panels by spiking-in custom reagents, as well as designing an entirely new panel for your own purposes. Please contact us at NGS@genewiz.com, toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 ext. 1 to learn more.

 

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

Yes, a custom protein barcoding service is available through NanoString. Once you have your labelled antibody, please ship it to GENEWIZ along with your samples.

 

Ordering & Sample Preparation

 

10. 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.

 

11. 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.

 

12. 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.

 

13. 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 at NGS@genewiz.com, toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 ext. 1.

 

Data Analysis & Delivery

 

14. 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 at CLIA@genewiz.com, toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 ext. 1 if you're interested in clinical-grade digital spatial profiling. 

 

15. 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)

Please mention in the additional comments section of the quote request form if you have a specific preference for any of the above options.

 

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Have a specific question?

North & South America: Email |  Phone 1-877-436-3949, Ext. 1

Europe: Email |  Phone +49 341 520 122-41

 

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