Question: How do I facilitate a fast advanced custom panel design turn around?
Answer: Familiarize yourself with and provide appropriately formatted input files (including references and files related to advanced custom targets) and optimize your gene list. Appropriately formatted input files and optimized gene list can reduce weeks of design time to days (and in some cases hours). Below are two things you can do to speed up the process.
1. Prepare your input files
- Single cell references (additional information)
- Required to optimize optical utilization
- The closer they match your xenium samples the more likely you are to succeed with better data quality
- You can use public data but you may need to reformat the data to match what the panel design tool is expecting
- Advanced custom target input files (additional information)
- All advanced custom targets require FASTA input
- Some targets such as SNVs require additional files
- Follow the guidance in the advanced custom panel design technote when selecting targets and building required input files
2. Optimize the gene list for your panel by creating a mock panel (additional information)
- Once you have your single cell reference files formatted correctly you can use XPD to iteratively optimize your gene list for standard gene expression (mouse & human panels only)
- Optimizing includes adding and subtracting genes as well as adjusting number probe sets per gene target based on TP10k values
- Steps in the process
- Submit your advanced customer design request using your design ID (i.e. CDP #) associated with the “Advanced Custom Upgrade” PO
- You will be sent an email that will be used for future correspondence about your design
- Start a mock standard gene expression panel design without providing a design ID (i.e. CDP #)
- Select addon or standalone panel with standard genes (matching what you will be using for your advanced custom design) and upload your gene list and reference(s)
- Not selecting advanced targets will allow you to optimize your gene gene list in the Xemium Panel Design tool.
- After optimizing do not finalize the panel but download the final summary file and the optimized gene list and send these as an attachment to the email you received from your advanced custom panel design request
In summary, providing an optimized gene list as well as properly formatted input files ensures a fast panel design turn around, once the process starts. If you have already submitted your request, that’s okay. You can reply to the email you received regarding your request and provide the optimized gene list as an attachment. You can also attach most advanced custom target inputs in email as well. For large files like single cell references you can send them to us using the transfer utility here.