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.
Summary:
Circular RNAs (circRNAs) were recently discovered as a novel class of noncoding RNA that are widely expressed in various tissues. Although the function of the vast majority of circRNAs remains unknown, several of them have already been associated with human disease. Currently there is lack of essential approaches to study circRNAs. A target-enrichment sequencing method suitable for high-throughput screening of circRNAs and their linear counterparts in large sample sets were developed using AmpliSeq technology.
Circular RNAs (circRNAs) were recently discovered as a novel class of noncoding RNA that are widely expressed in various tissues. Although the function of the vast majority of circRNAs remains unknown, several of them have already been associated with human disease. Currently there is lack of essential approaches to study circRNAs. A target-enrichment sequencing method suitable for high-throughput screening of circRNAs and their linear counterparts in large sample sets were developed using AmpliSeq technology.
Authors: Ammar Zaghlool1,2, Adam Ameur1,2, Chenglin Wu3,4, Jakub Orzechowski Westholm3,4, Adnan Niazi1,2, Manimozhi Manivannan5, Kelli Bramlett5, Mats Nilsson3,4, Lars Feuk1,2
Affiliation:1Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
2Science for Life Laboratory Uppsala, Sweden
3Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
4Science for Life Laboratory Stockholm, Sweden
5Clinical Sequencing Division, Life Science Solutions Group, Thermo Fisher Scientific, San Francisco, CA, USA
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.
Summary:
The Ion AmpliSeq™ Transcriptome Mouse Gene Expression Research Panel is used to measure expression levels of 23,930 RefSeq genes using only 1 pool. The panel targets 20,767 well annotated RefSeq genes and 3,163 coding and non-coding genes with provisional annotation based on Genome Reference Consortium Mouse Reference 38 (GRCm38). All amplicons are of approximately 150 bases in length. We recommend sequencing 8 samples on a Ion 540™ Chip or Ion PI™ Chip.
Sensitive measurement of gene expression fold change between samples
Amplicons designed to be most inclusive for transcripts of the target gene
Requires only 10 ng of FFPE total RNA (no rRNA depletion or polyA+ selection required)
Manual library kit and Ion Chef ready library kit configurations available.
Compatible with Ion Chef™ or Ion OneTouch™ Systems for template prep and the Ion S5™ or Ion Proton™ Systems for sequencing
Genome
GRCm38
Design Date
June 2017
Recommended Application
Gene Expression
Recommended Configuration
Sample per Chip: 8 per 540 chip
Or
8 per PI chip
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.
Summary:
The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements.
The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements. The assay is designed to efficiently capture all three complementarity determining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy.
Note: The amplicon count and number of pools are dummy values.
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.
Summary:
The Oncomine™ Immune Response Research Assay is a targeted gene expression assay that enables immuno-oncology research through the quantitative evaluation of the expression of markers associated with different leukocyte subsets, antigen presentation, checkpoint pathways, and tumor progression.
The Oncomine™ Immune Response Research Assay is a targeted gene expression assay that enables immuno-oncology research through the quantitative evaluation of the expression of markers associated with different leukocyte subsets, antigen presentation, checkpoint pathways, and tumor progression. The assay measures the expression of genes involved in tumor-immune interactions, including the low-expressing genes involved in inflammatory signaling.
Note: The amplicon count and number of pools are dummy values.
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.
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
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.
Summary:
Coronaviruses have been implicated in severe acute respiratory syndromes. The Ion AmpliSeq™ SARS-CoV-2 Research Panel is a quick, accurate and cost-effective tool to detect SARS-CoV-2 Virus responsible for Coronavirus disease 2019 (COVID-19).
An updated version of this panel is now available to cover emerging SARS-CoV-2 variants with higher sensitivity. Learn more about it here. The Ion AmpliSeq SARS-CoV-2 Research Panel consists of two 5X primer pools that target 237 amplicons specific to the SARS‑CoV‑2 (the virus that causes COVID-19) for viral surveillance and epidemiology research.
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.
Summary:
The panel was developed as a quick, accurate and cost effective method to identify the present of Ebola virus (EBOV). The panel contains 150 amplicons in 2 pools on the Ebola genome.
As of August 2015, there were over 15,000 infection cases and over 5000 deaths due to 2014 Ebola outbreak in West Africa countries with intense transmission. The panel was developed as a quick, accurate and cost effective method to identify the present of Ebola virus (EBOV). The panel contains 2 pools, 150 amplicons on Ebola genome. The reference genome came from UCSC Ebola virus Sierra Leone 2014 genome portal http://genome.ucsc.edu/ebolaPortal/. For more information see Virological.org website http://virological.org/c/ebolavirus.
Design Date
Nov 2014
Publication: In Progress Author: Kate Rhodes (kate.rhodes@thermofisher.com) Affiliation: Ion Torrent, Thermo Fisher Scientific
Recommended Application
Identification of Ebola virus
Recommended Configuration
Sample per Chip: 13 per 318 chip
Minimum coverage: 2000x
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.
Summary:
Genes in this panel are involved in Cell Cycle & Proliferation, Virology, Signal Transduction.
Ion AmpliSeq™ RNA MAPK Pathway Research Panel targets 197 genes in MAPK pathway that is commonly involved in cell signaling process such as growth, differentiation and proliferation.
Design Date
June 2016
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 (~900,000 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
197 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Signaling Pathway Research
Ion AmpliSeq™ RNA Human Oncology Pathways Research Panel
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.
Summary:
Genes in this panel are involved in key pathways of cancer.
Ion AmpliSeq™ RNA Human Oncology Pathways Research Panel targets 605 genes related to DNA repair, angiogenesis, cell adhesion, extracellular matrix, cell cycle and apoptosis, and many of the genes encoding kinases and transcription factors that have been found to be differentially expressed between different stages of cancer.
Design Date
June 2016
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 (~3M 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
605 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Oncology Research
Ion AmpliSeq™ RNA Inflammation Response Research Panel
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.
Summary:
Genes in this panel are involved in key pathways of inflammation response including chemokines.
Ion AmpliSeq™ RNA Inflammation Response Research Panel targets 683 genes in key pathways of inflammation response including chemokines.
Design Date
June 2016
Publication:
Assembly of Inflammation-Related Genes for Pathway-Focused Genetic Analysis
Matthew J. Loza, Charles E. McCall, Liwu Li, William B. Isaacs, Jianfeng Xu, Bao-Li Chang
PLoS ONE. 2007; 2(10): e1035. Oct 2007
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 (~3M 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
683 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Inflammation Response Research and Immune Response Research
Ion AmpliSeq™ RNA WNT Signaling Pathway Research Panel
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.
Summary:
Genes in this panel are involved in regulating WNT pathway, Biomarker-Related Pathway(s), Extracellular Matrix & Cell Adhesion, Oncology, Apoptosis.
Ion AmpliSeq™ RNA WNT Signaling Pathway Research Panel targets 169 genes that regulate the production of WNT signaling molecules, interactions with receptors on target cells, and signal transduction.
Design Date
June 2016
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 (~800,000 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
169 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Signaling Pathway Research
Ion AmpliSeq™ RNA Pancreatic Adenocarcinoma Research Panel
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.
Summary:
Genes in this panel are involved in Pancreatic carcinoma.
Ion AmpliSeq™ RNA Pancreatic Adenocarcinoma Research Panel targets 92 known genes over-expressed in Pancreatic carcinoma including the RTKs, EGFR and/or its family members (like Her2), and TGF-BetaRs. The activation of RTKs trigger a signaling cascade, which involves SOS, Src, GRB2, and MAPK activation, ultimately resulting in a cellular proliferative response.
Design Date
June 2016
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 (~400,000 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
92 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Pancreatic Adenocarcinoma Research
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.
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; http://www.sciencedaily.com/releases/2009/10/091005161322.htm
6. Gene May Cause Some Breast Cancers to Metastasize; BreastCancer.org; http://www.breastcancer.org/research-news/20090105
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.
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.
Summary:
Genes in this panel involves long non coding RNAs that are known tumor suppressors.
Ion AmpliSeq™ Long Non-coding RNA (lncRNA) Research Panel targets 418 lncRNAs involved in key biological processes. Specific targets included in the panel are known tumor suppressors GAS5, NEAT1, CAHM, MIR31HG and MIR7-3HG as well as known oncogenes HOTAIR, MALAT1, H19, XIST, HULC, TUG1, SNHG16, and LINC00152.
Design Date
June 2016
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 (~2M 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
418 genes
# of Primer Pools
1
Input RNA
1-100ng, FFPE compatible
Disease Research Area: Long Non-coding RNA Research
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.
Summary:
Genes in this panel are involved in characterisation of undifferentiated stem cells or their differentiated derivatives.
Ion AmpliSeq™ RNA Stem Cell Research Panel targets 930 gene expression markers to characterize human embryonic stem (hES) cell identity and assess phenotypic variations between embryonic stem cell isolates. The majority of the gene content (609) of this panel comes directly from the work of the I.S.C.I. consortium and characterisation of human embryonic stem cell lines by the International Stem Cell Initiative. Remaining genes were included based on the following criteria:
• Expression in human embryonic carcinoma cells (hEC), primordial germ cells, or hES cells
• Known role in maintenance of pluripotency in hES cells
• Identification in microplate-based experiments as being correlated with the stem cell state
• Expression known to be characteristic of specific differentiation lineages in the post implantation embryo and mature tissues
Design Date
June 2016
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 (~4M 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
930
# of Primer Pools
1
Input RNA
1-100ng, FFPE compatible
Disease Research Area: Stem Cell Research
Ion AmpliSeq™ Transcriptome Human Gene Expression Research Panel A26325
The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.
Summary:
The Ion AmpliSeq™ Transcriptome Human Gene Expression Research Panel is used to measure expression levels of over 20,800 RefSeq genes using only 1 pool. The panel targets 18,574 coding genes and 2,228 non-coding genes based on UCSC hg19 annotation. This panel contains 20,802 amplicons of approximately 150 bases in length, in a single pool.
The Ion AmpliSeq™ Transcriptome Human Gene Expression Research Panel is a revolutionary offering allowing for the simultaneous measurement of the expression levels of over 20,800 human RefSeq genes in a single pool. The panel targets 18,574 coding genes and 2,228 non-coding genes based on UCSC hg19 annotation. We recommend sequencing 8 samples on a Proton PI™ Chip.
Sensitive measurement of gene expression fold changed between samples
Amplicons designed to be most inclusive for transcripts of the target gene
Requires only 10 ng of FFPE total RNA (no rRNA depletion or polyA+ selection required)
Create libraries using the Ion AmpliSeq™ Kit Plus reagents and Ion Xpress™ Barcode Adapters
Compatible with Ion Chef™ or Ion OneTouch™ Systems for template prep and the Ion Proton™ or Ion PGM™ Systems for sequencing
This panel contains 20,802 amplicons (41,604 primers), approximately 150 bases in length, in a single pool.
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel Files
CSV file
The CSV file in this panel contains the assay names and references of the 61 unique gene fusions, 5
expression control genes, and 4 genes containing 5’ and 3’ imbalance assays. As indicated in the reference column, some EML4-ALK assays target fusions transcripts having updates to annotation in COSMIC v67 (denoted as COSFXXXX.1)
README
The README text file provides information
about the panel design and analysis software solution.
Summary:
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel is designed to target a set of known fusion transcripts as well as expression imbalances between the 3’ and 5’ regions of the genes. The panel contains 85 amplicons in a single pool. (**Note: The trial kit version is not available for EMEA countries**)
This panel targets over 70 known fusion transcripts for the ALK, RET, ROS1, and NTRK genes. In addition, the panel contains amplicons to analyze the expression imbalance between the 3’ and 5’ regions of these genes, which allows the discovery of novel mutations associated with the ALK gene. It also includes 5 positive controls, which help determine RNA quality and overall assay performance.
Design Date
July 2014
Recommended Configuration
Sample per Chip: 16 per 318 chip
Sample Type
FFPE samples
Recommended Application
Gene Fusion Detection
Observed Performance
Sensitivity to detect targeted fusion transcript when present in only 1% of input RNA. Over 90% concordant with cytogenetic methods for ALK fusion detection.
The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.
Apoptosis_Designed.bed
This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.
Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.
Apoptosis_Primer.bed
This file provides similar but more detailed information than the file Apoptosis_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).
Apoptosis_DataSheet.csv
This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.
Summary:
The Ion AmpliSeq™ RNA Apoptosis Panel is a screening tool designed against 267 genes involved in the cellular apoptosis pathway. Included are genes associated with death receptor mediated apoptosis, cmyc, and p53 mediated apoptosis. This panel contains 267 amplicons in 1 pool.
The Ion AmpliSeq™ RNA Apoptosis Panel is a screening tool designed against 267 genes involved in the cellular apoptosis pathway. Included are genes associated with death receptor mediated apoptosis, cmyc, and p53 mediated apoptosis.
Measure gene expression fold changes between samples
Amplicons are designed to be most inclusive for transcripts of the target gene
Each reaction requires only 500 pg of unfixed RNA or 5 ng of fixed (FFPE) RNA
Prepare amplicon libraries with the Ion AmpliSeq™ RNA Library Kit and sequence on the Ion Personal Genome Machine™ (PGM™) or Proton™ System
This panel contains 267 amplicons (534 primers), approximately 150 bases in length, in a single pool. Learn more
For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.
Targets
267
Amplicon length
Average 150 bp
Primer pool size
534 individual primers, 267 primer pairs
The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.
Cancer50_Designed.bed
This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.
Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.
Cancer50_Primer.bed
This file provides similar but more detailed information than the file Cancer50_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).
Cancer50_DataSheet.csv
This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.
Summary:
The Ion AmpliSeq™ RNA Cancer Panel is a screening tool designed against 50 oncogenes/tumor suppressor genes found in the COSMIC database. This panel has been developed as an RNA complement to the DNA focused Ion AmpliSeq™ Cancer Hotspot Panel v2. This panel contains 50 amplicons in 1 pool.
The Ion AmpliSeq™ RNA Cancer Panel is a screening tool designed against 50 oncogenes/tumor suppressor genes found in the COSMIC database. This panel has been developed as an RNA complement to the DNA focused Ion AmpliSeq™ Cancer Hotspot Panel v2. The panel is a single pool of primers representing 50 oncogenes and tumor suppressor genes with coverage of KRAS, BRAF, and EGFR genes.
Measure gene expression fold changes between samples
Amplicons are designed to be most inclusive for transcripts of the target gene
Each reaction requires only 500 pg of unfixed RNA or 5 ng of fixed (FFPE) RNA
Prepare amplicon libraries with the Ion AmpliSeq™ RNA Library Kit and sequence on the Ion Personal Genome Machine™ (PGM™) or Proton™ System
This panel contains 50 amplicons (100 primers), approximately 150 bases in length, in a single pool.
For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.
Learn more
Targets
50
Amplicon length
Average 150 bp
Primer pool size
100 individual primers, 50 primer pairs
