Ion Research Panels:

Panel Name Research Area Genome Number of amplicons per pool
(# of tubes)
Tags Actions
Ion AmpliSeq™ RNA Breast Cancer Research Panel
Breast Cancer Research Human (RefSeq) Pool 1: 1174 amplicons
(1 tube)
Community Panel
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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


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: Genes shown to have a role in breast cancer development and progression.

Ion AmpliSeq™ RNA Breast Cancer Research Panel targets 1174 genes known to be associated with breast cancer development and progression. The gene list was derived from the following eight publications.

Design Date June 2016 Publications 1. Differential expression of breast cancer-associated genes between stage- and age-matched tumor specimens from African- and Caucasian-American Women diagnosed with breast cancer; J M Grunda, A D Steg, Q He, M R Steciuk, S Byan-Parker, M R Johnson and W E Grizzle; BMC Research Notes 2012, 5:248
2. A Molecular Role for lysyl oxidase in breast cancer invasion; Kirschmann DA, Seftor EA, Fong SF, Nieva DR, Sullivan CM, Edwards EM, Sommer P, Csiszar K, Hendrix MJ; Cancer Res. 2002 Aug 1;62(15):4478-83
3. Down-Regulation of HP1Hs Expression Is Associated with the Metastatic Phenotype in Breast Cancer1; D A. Kirschmann, R A. Lininger, L Gardner, E A Seftor, V A Odero, A M Ainsztein, W C Earnshaw, L L Wallrath, and M J Hendrix; Cancer Research 60, 3359–3363, July 1, 2000
4. Differential Gene Expression in Primary Breast Tumors Associated with Lymph Node Metastasis; Ellsworth RE, Field LA, Love B, Kane JL, Hooke JA, Shriver CD; Int J Breast Cancer, 2011; 2011:142763.
5. Gene That Regulates Breast Cancer Metastasis Identified; Science Daily;
6. Gene May Cause Some Breast Cancers to Metastasize;;
7. A Six-Gene Signature Predicting Breast Cancer Lung Metastasis; Landemaine T, Jackson A, Bellahcène A, Rucci N, Sin S, Abad BM, Sierra A, Boudinet A, Guinebretière JM, Ricevuto E, Noguès C, Briffod M, Bièche I, Cherel P, Garcia T, Castronovo V, Teti A, Lidereau R, Driouch K; Cancer Res, 2008 Aug 1; 68(15):6092-9
8. Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis; N S Crawford, X Qian, A Ziogas, A G Papageorge, B J Boersma, R C Walker, L Lukes, W L Rowe, J Zhang, S Ambs, D R Lowy, H Anton-Culver, K W Hunter; PLOS Genetics.
Recommended Application Gene Expression Recommended Configuration Compatible with all Ion Sequencing platform and chips.

We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~5M total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type RNA
Number of Targets 1,174 genes # of Primer Pools 1 Input DNA 1-100ng, FFPE compatible
Disease Research Area: Breast Cancer Research