Creating a custom panel

  • Updated

On the home screen, click Create Panel. CreatePanelButton.png

The custom panel creation screen will appear. Step0.png

Name the Panel

  • Panel Name: Provide a name for the panel. It can be up to 100 characters, consisting of letters, numbers, special characters, and spaces.
  • Description: Enter an optional description for the panel. It can be up to 250 characters, consisting of letters, numbers, special characters, and spaces.
  • Click Next.

Step 01 – Select Parameters

  • Assay Type: Preset. Currently, Tapestri Designer supports only the DNA assay.
  • Amplicon Length Range: The amplicon length range is preset to 175 – 275 bp.
  • Genome: Select the genome of choice from the drop-down menu. Tapestri Designer provides catalog human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38). Additionally, you may upload your own by following the steps provided here. Any previously uploaded genomes will be listed in the menu.
  • Click Next.

Step 02 – Upload Targets

Enter the targets for the custom panel by uploading a .csv. Alternatively, paste or type the target information. 

Important: The .csv must use a comma (“,”) as the separator. The EU semicolon separator (“;”) will not work. Download sample file template

Upload File: To upload a file, drag and drop it into the box. Or click Choose File to locate the file. If the .csv file has a header row, click the File has a header (skips the first line) checkbox to ignore that information. The file should have two columns with an optional third – target type, target ID, and target name (optional). Step02-UploadFile.png

  • Add Targets: Click Add Targets to paste or manually enter the targets. If the pasted targets have a header row, click the File has a header (skips the first line) checkbox to ignore that information.

Step02-AddTargets.png

Target Formats

Targets must be in this format: target type, target ID, and target name (optional). 

Example Tapestri Designer input

gene, TP53, p52_mutation
region, chr10:106721610-106721610, variant ABC
dbSNP, rs4880, SOD2 mutation
COSMIC, COSM1041, my variant
hgvs, PIK3CA:C.1633G>A, PIK3CA

Notes 

  • The spaces after the commas are optional. 
  • Only the hg19 catalog genome supports all targets. Please use ‘region’ targets for all other genomes.
  • Gene names are case sensitive.
  • Duplicate targets are not allowed.

For more information about target types and a sample .csv file, refer to Target types.

  • After uploading the targets, click Next.

Step 03 – Review Targets

After entering the target information, the targets will be preprocessed to resolve them to chromosomal regions. The status of your panel will be Preprocessing.

  • Click the Refresh icon to see the latest results.

Once the targets have been preprocessed, the panel status will change to Draft.

If the panel contains any targets with errors, those targets need to be edited or removed to proceed further.

                                                                      EditTarget.png

  • To edit a target, such as the type, name, or ID, click the edit icon next to the target. Click the green check mark to accept the change, or the red “x” to revert the change.
  • To delete a target, click the trashcan icon, and click Delete Target.

Possible Errors

Invalid ID: The format of the ID is invalid. Change the ID to match the required format.

Duplicate Target: Neither duplicate target ID nor Names are allowed. Edit or delete the target.

Invalid Region Target: Region targets are validated to check the chromosome length constraint. Regions with either start or stop values greater than the chromosome length are marked invalid.

Incorrect Target ID Format: If the target ID contains an additional space, it is marked invalid. For example, Chr13: 28674559-28674790 is invalid.

Incorrect Target ID or Name: Target IDs and names cannot contain commas. When added, they are removed from the targets before creating the panel.

Masked Regions: If the target has many masked regions (Ns in reference .fasta for the target), the panel will fail. Avoid adding region targets with these.

SearchTarget.png

  • Add Target: To add more targets, click Add Target

In the pop-up screen, select the Target Type, enter Target ID and an optional Target Name. Repeat this process for any additional targets you want to add. AddTargetModal.png

  • Search: Type in either a type, name, or ID to display a list of only those targets.

  • Bulk Actions: Click the checkbox to the left of each target to enable the bulk actions menu.
  • Sort: Sort the targets by any column in ascending or descending order by clicking the header name.

Step 04 – Submit Panel

Panels created using the hg19 (GRCh37) catalog reference may have overlapping targets with Mission Bio’s catalog panels. If your panel contains overlapping targets, you can explore the catalog panels in Step 04. Step04.png 

  • To compare the catalog panels, select the checkbox to the left of each catalog panel. A Compare Target Overlap table listing each of the custom panel’s targets and the overlap with the catalog panel will appear. Information for up to three catalog panels can be displayed in the table at one time. CompareTargetOverlap.png
  • If a catalog panel meets your needs, save time by using that panel. Click Explore to the right of the catalog panel name to display the panel details page where you can request a quote.
  • Submit: If no panel overlapped with your custom panel or the coverage did not meet your needs, click Submit to submit your panel.

In Progress

Once you submit your custom panel, the Panels Details page will display with a status of In Progress. It will also display in the dashboard on the Tapestri Designer home page as In Progress. You will receive an email confirming that you submitted a panel for processing.

During the processing, amplicons are generated to cover the targets, and the coverage percentage is calculated. When the design is complete, you will receive another email.

Note: After submitting the panel for processing, no further editing is possible. To include more targets, click on the three vertical dots in the Custom Panels dashboard next to the Panel name. Select Copy Targets. This will create a new custom panel where you can add more targets. Only the targets are copied, not the amplicons.

ContextMenu.png

Ready

When the processing is complete, you will receive notification that the results are ready via an email, which includes the panel details. The status in the dashboard will change to Ready.

Download the files created by Designer during processing to view the details or use as input into Tapestri Pipeline.

If the panel details page is still open when you receive the email, click the Refresh button to update the information.

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