Ion Research Panels:

Panel Name Research Area Genome Number of amplicons per pool
(# of tubes)
Tags Actions
Ion AmpliSeq™ ERCC Companion Panel
A36552
RNA Research hg19 AmpliSeq Transcriptome ERCC v1 Pool 1: 10 amplicons
(1 tube)
RNA
Ready-to-Use Panel
Review panel Sign in to order

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.

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.

TS4 Refs

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.

BED Upload

BED Available

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:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: The Ion AmpliSeq™ ERCC Companion Panel is used to measure expression levels of 10 of the ERCC Spike-in reference RNAs in Mix 1, melding the convenience of ERCC controls with the power of AmpliSeq™.

The Ion AmpliSeq™ ERCC Companion Panel is used to measure expression levels of 10 of the ERCC Spike-in reference RNAs in Mix 1, melding the convenience of ERCC controls with the power of AmpliSeq™. The controls targeted by the panel help to assess the dynamic range and sensitivity of the library and sequencing run while consuming 2% or fewer of the reads. Quickly identify sample degradation or extraction issues.

Design Date June 2017
  • Observe up to a dynamic range of 13log2 from RNAs at known relative concentrations.
  • Targeted ERCCs were selected based on GC content and linearity by Taqman® assay.
  • Confirm R2 values > 0.9 in your experiment via this internal control.
  • Compatible with both Human and Mouse AmpliSeq™ Transcriptome kits in both manual and Ion Chef ready formats.
  • Conveniently assess ERCC performance using the available ERCC_analysis plugin; no change to the RNA reference sequence required.
Recommended Application Gene Expression Recommended Configuration Spike-in with AmpliSeq™ Transcriptome Panels

Sample per Chip: 8 per Ion 540/PI chip Or 16 per Ion 550 chip
Genome Use current reference sequence of choice for your panel
Number of pools 1 Number of Amplicons per pool 10 Input RNA required 1-2 μL of 1:1,000 or higher dilution of AmpliSeq™ ERCC Spike-In Mix 1
Disease Research Area: RNA Research