Fixed Panel Results Files
Target Mutations
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
- Gene symbol
- Accession id
- COSMIC id
- CDS Mutation - Change occurred in the nucleotide sequence
- AA Mutation - Change occurred in the peptide sequence as a result of the mutation
- Strand (+/-)
- Coordinates (hg19)
- Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
- Insert Sequence
- Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
