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.
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:
Noonan syndrome is a relatively common autosomal dominant congenital disorder. The noonan Panel assesses 14 genes known to be related with this disorder: A2ML1, BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1 and SPRED1. This panel contains 268 amplicons in 2 pools.
Noonan syndrome is a relatively common autosomal dominant congenital disorder with a high phenotypic variability. It is a clinically and genetically heterogeneous disorder that belongs to the group of Rasopathy diseases, caused by mutations in genes dysregulating the RAS/MAPK pathway.
The Noonan Research Gene Panel has been developed in collaboration with an European consortia composed by Marco Tartaglia(1), Jose Luis Costa (2), Kornelia Neveling and Marcel Nelen (3) . 1) Istituto Superiore di Sanità, Rome, Italy, 2) Ipatimup, Porto 3) Human Genetics, Radboud UMC Nijmegen .
The panel assesses 14 genes known to be related with this disorder. A2ML1, BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1, SPRED1. In a first study of 60 archived samples we showed that very high sensitivity and specificity are achievable. For further details see ASHG 2014 poster “Development and verification of a Noonan genes Ion AmpliSeq™ panel” M. Nelen et al.
Design Date
Publication: ASHG 2014 Poster "Development and verification of a Noonan genes Ion AmpliSeq™ panel" Author: Marcel Nelen (Marcel.Nelen@radboudumc.nl) Affiliation: Dept. of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 8 per 318 chip
Minimum coverage: 684
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.
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 variants in genes associated with antimicrobial resistance in Mycobacterium tuberculosis (TB). The panel assesses 8 genes related to antimicrobial resistance (embB, eis, gyrA, inhA, katG, pncA, rpoB, rpsL). This panel uses 109 amplicons in 2 pools.
Tuberculosis (TB) remains one of the main infectious diseases affecting developing countries. According to WHO, globally in 2013 there were 9 million people who fell ill with TB. Furthermore, an estimated 480,000 people developed multidrug-resistant TB (MDR-TB), and there were an estimated 210,000 deaths from MDR-TB. The TB Research Panel has been developed in collaboration with leading public health institutes. The panel assesses 8 genes related to antimicrobial resistance (embB, eis, gyrA, inhA, katG, pncA, rpoB, rpsL). For further details see ASM 2015 poster “Strain-Typing and Antibiotic Resistance Profiling From Research Samples Using Highly Multiplexed Targeted Library Construction with High Throughput Semi-Conductor Based Sequencing” J. Bishop et al.
Design Date
Dec 2013
Publication: Bishop et al. Poster session presented at 115th General Meeting of the American Society for Microbiology; 2015 May 30- June 2; New Orleans, LA. (Poster link) Author: John Bishop (john.bishop@thermofisher.com) Affiliation: Ion Torrent, Thermo Fisher Scientific
Recommended Application
Identification of gene variants correlating with antimicrobial resistance in Mycobacterium tuberculosis
Recommended Configuration
Sample per Chip: 36 per 318 chip
Minimum coverage: 1000x
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.
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:
Ion AmpliSeq™ Pharmacogenomics Panel is a single pool of primers used to perform multiplex PCR for preparation of amplicons libraries from genomic “hot spot” regions that play critical role in DME genes.The panel is a part of sample to answer workflow designed for a next-generation sequencing (NGS) platform from Thermo Fisher Scientific, to interrogate SNP, indels and copy number variations (CNV) in the DME genes.
Ion AmpliSeq™ Pharmacogenomics Panel is a single pool of primers used to perform multiplex PCR for preparation of amplicons libraries from genomic “hot spot” regions that play critical role in DME genes.The panel is a part of sample to answer workflow designed for a next-generation sequencing (NGS) platform from Thermo Fisher Scientific, to interrogate SNP, indels and copy number variations (CNV) in the DME genes. The panel focuses on 136 well documented SNP and indel variants and captures CYP2D6 copy number variations at both the gene level and for exon 9 rearrangement enabling the screening of broad selection of haplotypes including *36. In addition, Ion AmpliSeq™ Pharmacogenomics Research Panel includes 9 specially designed primer pairs for sample Identification.
This panel provides the following benefits:
A targeted ready-to use panel with high value pharmacogenomics content
Panel customization flexibility to create a ‘design of choice’
Genotyping and copy number assay in a single workflow for fastest turnaround time
Exceptional performance on buccal swab samples with minimal sample input of only 10ng
High coverage and unbiased amplification offering outstanding accuracy, minimizing a need for sample reruns
Ready-to-use automation scripts availability for sequence-ready library construction
Sample multiplexing flexibility to run 8 or up to 96 samples in a single batch
Straightforward data analysis with Integrated analysis software solution
Sample mis-identification detection capability for QA and accurate sample reporting
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.
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:
This Mendelian Disease (single gene disorders) panel was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with inherited cardiovascular defects. The panel assesses 404 genes known to harbor mutations affecting cardiovascular functioning.
It can be difficult to identify specific genetic causes of cardiovascular diseases because of pleiotropy, locus heterogeneity and accessibility of gene tests. The panel was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with inherited cardiovascular defects. The panel assesses 404 genes known to harbor mutations affecting cardiovascular functioning. In addition to targeting all coding regions, an additional 94 non-coding disease-causing loci are targeted, as well as special coverage of two repeat expansion regions, in genes DMPK and CACNA1A.
Design Date
December 2013
Avg Amplicon Length
254 bp
Insert Size
206 bp
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 2 per 318 chip
Average coverage: 314x
Sample Type
Standard
Design Statistics
Number of genes in panel: 404
Average gene coverage: 99.4%
Non-coding hotspots: 94
Observed Performance
Uniformity of coverage: 90.1%
% reads on target: 97%
Positive predictive value: 99.5%
Input DNA required
10ng per tube
2 pool
20 ng total
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.
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:
This Mendelian Disease (single gene disorders) panel was developed as a quick, accurate and cost effective method to identify genetic mutations associated with inherited hematological disorders. The Hematology panel assesses 394 genes known to harbor mutations affecting cardiovascular functioning.
Research to identify a specific genetic cause of hematological disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of gene tests. The panel was developed as a quick, accurate and cost effective method to identify genetic mutations associated with inherited hematological disorders. The Hematology panel assesses 394 genes known to harbor mutations affecting the blood. In addition to targeting all coding regions, an additional 161 non-coding disease-causing loci are targeted.
Design Date
August 2013
Avg Amplicon Length
253 bp
Insert Size
205 bp
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 2 per 318 chip
Average coverage: 445x
Sample Type
Standard
Design Statistics
Number of genes in panel: 394
Average gene coverage: 99.5%
Non-coding hotspots: 161
Observed Performance
Uniformity of coverage: 93.8%
% reads on target: 97%
Positive predictive value: 99.5%
Input DNA required
10ng per tube
2 pool
20 ng total
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.
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:
This Mendelian Disease (single gene disorders) panel was developed as a quick, accurate and cost effective method to identify genetic mutations associated with inherited neurological disorders. The panel assesses 751 genes known to harbor mutations affecting the functioning of the brain and nervous system.
Research to identify specific genetic causes of neurological disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of gene tests. This panel was developed as a quick, accurate and cost effective method to identify genetic mutations associated with inherited neurological disorders. The panel assesses 751 genes known to harbor mutations affecting the functioning of the brain and nervous system. In addition to targeting all coding regions, an additional 101 non-coding disease-causing loci are targeted, as well as 14 repeat-expansion regions in genes AFF2, AR, ATN1, ATXN7, ATXN8OS, ATXN3, CACNA1A, CSTB, DMPK, HTT, JPH3, PABPN1, PPP2R2B, TBP.
Design Date
December 2013
Avg Amplicon Length
254 bp
Insert Size
205 bp
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 2 per 318 chip
Average coverage: 165x
Sample Type
Genomic DNA, including FFPE (mtDNA also tested)
Design Statistics
Number of genes in panel: 751
Average gene coverage: 99.4%
Non-coding hotspots: 107
Observed Performance
Uniformity of coverage: 91.9%
% reads on target: 97%
Positive predictive value: 99.9%
Input DNA required
10ng per tube
2 pool
20 ng total
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.
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 Ophthalmic Research Panel (Mendelian disease panel affected by single gene disorders), was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with inherited blindness or other impairments of vision. The panel assesses 316 genes known to harbor mutations causal of vision impairment.
It can be difficult to identify specific genetic causes of vision impairment because of pleiotropy, locus heterogeneity and accessibility of gene tests. The panel was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with inherited blindness or other impairments of vision. The panel assesses 316 genes known to harbor mutations causal of vision impairment. In addition to targeting all coding regions, an additional 50 non-coding disease-causing loci are targeted, as well as special coverage of two repeat expansion regions, in genes CNBP and ATXN7.
Design Date
December 2013
Avg Amplicon Length
253 bp
Insert Size
205 bp
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 2 per 318 chip
Average coverage: 406x
Sample Type
Standard
Design Statistics
Number of genes in panel: 316
Average gene coverage: 99.4%
Non-coding hotspots: 50
Observed Performance
Uniformity of coverage: 97.6%
% reads on target: 98%
Positive predictive value: 99.0%
Input DNA required
10ng per tube
2 pool
20 ng total
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.
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™ Autism Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 236 genes associated with autism.
Research to identify specific genetic causes of autism is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Autism Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Deafness Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited deafness. The panel assesses 126 genes known to harbor mutations affecting the hearing function.
Research to identify specific genetic causes of hearing impairment is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Deafness Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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 Cardiac Arrhythmias and Cardiomyopathy Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with cardiac arrhythmias and cardiomyopathies. The panel assesses 92 genes known to harbor mutations affecting the functioning of the heart.
Research to identify specific genetic causes of heart disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Cardiac Arrhythmias and Cardiomyopathy Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Dermatology Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited dermatological impairment. The panel assesses 222 genes known to harbor mutations affecting the skin.
Research to identify specific genetic causes of dermatological impairment is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Dermatology Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Dysmorphia-Dysplasia Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited dysmorphia-dysplasia disorders. The panel assesses 519 genes known to harbor mutations causing dysmorphia or dysplasia.
Research to identify specific genetic causes of dysmorphia-dysplasia is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Dysmorphia-Dysplasia Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Endocrine Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited endocrine disorders. The panel assesses 340 genes known to harbor mutations affecting the functions of the endocrine system.
Research to identify specific genetic causes of endocrine disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Endocrine Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Epilepsy Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 386 genes associated with epilepsy.
Research to identify specific genetic causes of epilepsy is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Epilepsy Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Gastrointestinal Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited gastrointestinal disorders. The panel assesses 194 genes known to harbor mutations affecting gastrointestinal functions.
Research to identify specific genetic causes of gastrointestinal disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Gastrointestinal Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Inborn Errors of Metabolism Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited metabolic disorders. The panel assesses 594 genes known to harbor mutations affecting metabolic function.
Research to identify specific genetic causes of metabolic disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Inborn Errors of Metabolism Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
Number of amplicons
9,681
Avg Amplicon Length
254 bp
Insert Size
207 bp
Recommended Application
Germ line mutation detection
Compatible platforms
Ion S5™ System, Ion PGM™ System, Ion Proton™ System
Sample Type
Standard
Design Statistics
Number of genes in panel: 594
Average gene coverage: 99.2%
Observed Performance
Uniformity of amplicon coverage: 95.8%
% reads on target: 97%
Input DNA required
10 ng per pool
20 ng total
2 pools
Disease Research Area: Inherited Metabolic Disorders
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.
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™ Inherited Cancer Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 134 genes associated with inherited cancers.
Research to identify specific genetic causes of inherited cancers is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Inherited Cancer Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Comprehensive Ovarian Cancer Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 41 genes associated with inherited ovarian cancer.
Research to identify specific genetic causes of inherited ovarian cancer is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™Comprehensive Ovarian Cancer Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Primary Immune Deficiency Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with primary immunodeficiencies. The panel assesses 264 genes known to harbor mutations affecting the functioning of the immune system.
Research to identify specific genetic causes of primary immunodefieciency disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Primary Immune Deficiency Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Pulmonary Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited pulmonary disorders. The panel assesses 131 genes known to harbor mutations affecting the functioning of the lungs.
Research to identify specific genetic causes of pulmonary disorders is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Pulmonary Research Panel v2 was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
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.
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™ Renal Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited renal disorders. The panel assesses 154 genes known to harbor mutations affecting the functioning of the kidneys.
The Ion AmpliSeq™ Renal Research Panel v2 provides a quick, accurate and cost effective way to identify genetic mutations associated with inherited renal disorders. The panel assesses 154 genes known to harbor mutations affecting the functioning of the kidneys.
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.
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:
This panel amplifies regions covering germline mutations of 25 hereditary cancer-related genes which have a central role in DNA repair and the mismatch repair pathway. This panel is designed to augment a separate BRCA1/2 analysis.
Approximately 5–10% of all breast and/or ovarian cancer cases are considered as inherited. BRCA1 and BRCA2 tumor suppressor genes account for a high penetrance of hereditary cases, but familial cases without mutations in these genes can also occur. Despite their low penetrance, other hereditary cancer-related genes are known to be associated with breast and ovarian cancer risk. This panel amplifies regions covering germline mutations of 25 hereditary cancer-related genes which have a central role in DNA repair and the mismatch repair pathway (APC, ATM, BARD1, BMPR1A, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, SMAD4, STK11, and TP53). This panel is designed to augment a separate BRCA1/2 analysis.
Design Date
MARCH 2015
Publication: Hirotsu et al., Multigene panel analysis identified germline mutations of DNA repair genes in breast and ovarian cancer. Molecular Genetics & Genomic Medicine(2015); 3(5): 459–466
Author: Dr. Hirotsu et al.,
Affiliation: Yamanashi Prefectual Central Hospital (Japan)
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.
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:
This panel was developed as a research method to identify genetic mutations associated with inherited breast and ovarian cancers. The panel assesses 11 genes known to harbour mutations related to breast and/or ovarian cancer.
Approximately 7-10% of breast and ovarian cancers are hereditary.
BRCA 1 & BRCA 2 tumor suppressor genes account for a high number of these
cases, but it is known that other hereditary cancer related genes are
associated with the risk to develop breast and/or ovarian cancer.The panel
was developed as a research method to identify genetic mutations associated with
inherited breast and ovarian cancers. The panel assesses 11 genes known to
harbour mutations related to breast and/or ovarian cancer (ATM, BRCA1, BRCA2, CHEK2,
PALB2, RAD51C, RAD51D, NBN, CDH1, SMARCA4, TP53). The panel
was validated in 3 laboratories using 45 samples.
Design Date
June 2015
Recommended Application Germ line mutation detection
Recommended
Configuration
Sample Type High molecular weight DNA
PGM
Sample per Chip:
4 per 318 chip
Minimum coverage: 1517x
S5
Sample per Chip:
9 per 540 chip
Minimum coverage: 4600x
Number of sample in
Study
45 samples
Observed
Performance
Input DNA required
10ng per tube
PGM
Panel uniformity: 94.49%
Reads on-targets: 96.29%
S5
Panel uniformity: 89.71%
Reads on-targets: 87%
Disease Research Area: Breast and Ovarian cancer 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.
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™ DNA Phenotyping Panel is used to predict hair and eye color using 24 phenotype SNPs from the HIrisPlex system. This panel targets 23 SNPs and one indel from the following genes: MC1R, SLC45A2, ASIP/PIGU, EXOC2, HERC2, IRF4, KITLG, OCA2, TYR, SLC24A4, and TRYP1.
DNA phenotyping can be useful for generating investigative leads in cases where STR profiles have not resulted in a database match. The Ion Ampliseq™ DNA Phenotyping Panel is used to predict hair and eye color using 24 phenotype SNPs from the HIrisPlex system. This panel targets 23 SNPs and one indel from the following genes: MC1R, SLC45A2, ASIP/PIGU, EXOC2, HERC2, IRF4, KITLG, OCA2, TYR, SLC24A4, and TRYP1. Results suggesting probability of blue, intermediate, or brown eye color along with shade of black, brown, red, or blond hair are provided by the HIrisPlex prediction model (http://hirisplex.erasmusmc.nl/). For further details see Walsh et al, Forensic Science International: Genetics 2013
Design Date
March 2015
Publication:
Walsh et al, Forensic Science International: Genetics 2013
Recommended Application
Research Applications in human identification
Recommended Configuration
Sample per Chip: 32 samples per 318 or 520 chip
Minimum coverage: 1000x
This file contains all of the data for your 384 Well Plate. For each amplicon, you will find the pool information, its (row,column) coordinates, the AmpliconID, and the forward and reverse primers.
BRCA1_2.YYYYMMDD.concentration.tab
This file contains the concentration.
BRCA1_2.YYYYMMDD.designed.bed
Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.
BRCA1_2.YYYYMMDD.hotspotAnnot.csv
This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information:
* 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
* Insert Sequence
* Target URL – links to the COSMIC curated mutations database.
BRCA1_2.YYYYMMDD.hotspots.bed
The Hotspots 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*.
* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.
BRCA1_2.YYYYMMDD.primerDataSheet.csv
This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).
BRCA1_2.YYYYMMDD.results_coverage_details.csv
This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.
BRCA1_2.YYYYMMDD.results_coverage_summary.csv
In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.
BRCA1_2.YYYYMMDD.submitted.bed
This file contains the regions that were submitted to AmpliSeq for design.
JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs
plan.json
This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.
Data Analysis in the Torrent Browser
You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com.
1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
Summary:
Mutations in tumor suppressor genes BRCA1 and BRCA2 have been implicated in hereditary breast and ovarian cancer. The Ion AmpliSeq™ BRCA1/2 Panel utilizes 167 amplicons to analyze the coding regions of both BRCA1 and BRCA2 genes.
Description
Mutations in tumor suppressor genes BRCA1 and BRCA2 have been implicated in hereditary breast and ovarian cancer. Much research is currently being done today to better detect, treat, and prevent cancer by assessing mutations in those who carry mutations in BRCA1 and BRCA2. The Ion AmpliSeq™ BRCA1/2 Panel utilizes 167 amplicons to analyze the coding regions of both BRCA1 and BRCA2. Design and validation is currently in progress with Drs. Marjolijn Ligtenberg and Arjen Mensenkamp from Radboud University Nijmegen Medical Centre, The Netherlands, and with Drs. José Carlos Machado and José Luis Costa from The Institute of Molecular Pathology and Immunology of the University of Porto.
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.
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™ Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. This panel contains 207 amplicons in 1 pool.
The Ion AmpliSeq™ Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. Building on the mutations included in our original Ion AmpliSeq™ Cancer Panel, this latest Ion AmpliSeq™ ready-to-use panel provides:
Maintained compatibility with FFPE samples while expanding mutational content for broader coverage of additional genes and "hot spot" mutations
Extremely uniform coverage for more efficient sequencing and cost savings
Enhanced primer design with optimization of new primer sets and even lower strand bias for added confidence in accurate variant calling
Improved variant detection with Torrent Suite™ Software v3.0 and Variant Caller Plugin in low allele variant detection along with improved indel sensitivity
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.
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™ Colon and Lung Cancer Panel v2 is a single pool panel that analyses hotspot and targeted regions of 22 genes implicated in colon and lung cancers. This panel uses 92 amplicons for re-sequencing and analysis. (**Note: The trial kit version is not available for EMEA countries**)
Designed with leading researchers from the OncoNetwork Consortium, the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 is a single pool panel that analyse hotspot and targeted regions of 22 genes implicated in colon and lung cancers (KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, FGFR3, NOTCH1, ERBB4, FGFR1, FGFR2). It contains the same primer pairs of the Ion AmpliSeq™ Colon and Lung Cancer Panel v1 plus three new amplicons covering additional target regions for NRAS and ALK gene. NRAS exon 4 variants ( p.117, p.146) and ALK (G1269A, p.S1206Y)
Design Date
January 2014
Recommended Configuration
Sample per Chip: 8 per 316 chip
Minimum coverage: 500x
Each row contains details about the regions covered by the panel: the chromosome number, the start and ending positions, the gene ID associated to the region and the pool ID in which the primers are placed. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In; the primer pool information is used by the Coverage Analysis plugin to display a plot of the average number of reads per amplicon per pool:
CCP.YYYYMMDD.hotspots.bed
The Hotspots 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*.
* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.
CCP.YYYYMMDD.missed.bed
This file contains information about the regions that are missed by the design: the chromosome number and the (start,end) coordinates of the missed region.
CCP.YYYYMMDD.primerDataSheet.csv
This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).
CCP.YYYYMMDD.results_coverage_details.csv
This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.
CCP.YYYYMMDD.results_coverage_summary.csv
In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.
CCP.YYYYMMDD.submitted.bed
This file contains the regions that were submitted to AmpliSeq for design.
JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for Proton runs
plan.json
This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.
Data Analysis in the Torrent Browser
You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the CCP panel.
1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
Summary:
The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. With all-exon coverage of 409 genes, this panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing. The panel contains 15,992 amplicons in only 4 pools.
The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. Encompassing over 50% of the Wellcome Trust Sanger Institute Cancer Gene Census, this is the most comprehensive cancer gene panel available. With all-exon coverage of 409 genes, the Ion AmpliSeq™ Comprehensive Cancer Panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing.
The Ion AmpliSeq™ technology allows ultra-high multiplex PCR combined with targeted sequencing library construction in just 16 hours for over 400 genes. Utilizing only 10 ng of input DNA per primer pool for a total of 40 ng of input DNA, analysis of restricted samples like FFPE samples is possible. The Ion AmpliSeq™ Comprehensive Cancer Panel is optimized for library construction with the Ion AmpliSeq™ Library Kit 2.0. Libraries are then ready for template preparation on the Ion OneTouch™ System and sequencing on the Ion PGM™ Sequencer. The Ion AmpliSeq™ Comprehensive Cancer Panel is not compatible with Ion Ampliseq™ 2.0 Beta Kits.
Learn more
COSMIC mutation targets
15,749
Amplicon length
125–175 bp (average 155 bp)
Primer pool size
~16,000 primers in 4 tubes
Input DNA required
10 ng per pool, 40 ng per DNA sample
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.
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:
Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane regulator (CFTR) gene. The Ion AmpliSeq™ CFTR Panel is a 2 pool panel with 102 amplicons used for re-amplification and analysis of the coding region of the CFTR gene.
Description
Cystic fibrosis is one of the most common, fatal genetic diseases in the United States and is caused by mutations in the cystic fibrosis transmembrane regulator (CFTR) gene. While hundreds of mutations have been discovered in CFTR, sequencing can be cost prohibitive when running large numbers of samples using Sanger sequencing. The Ion AmpliSeq™ CFTR Panel provides a simple and affordable CFTR gene sequencing with dedicated analysis workflows for optimal variant calling in Ion Reporter™ Software 4.0. This panel allows you to analyze all coding exons, intron-exon boundaries and UTRs of CFTR with 102 amplicons, including the >160 mutations from CFTR2.org research database.
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.
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 TP53 gene codes the tumor suppressor protein p53 which has been extensible researched in the field of Human Oncology. The Ion AmpliSeq™ TP53 Panel is a 2 pool panel with 24 amplicons designed to analyze all coding exons of the TP53 gene.
Description
The tumor suppressor protein p53 is encoded by the TP53 gene, one of the most researched genes in human cancer. Genetic mutations in TP53 can impact gene expression of p53 and its downstream targets, and TP53 mutations are present in more than 50% of all types of human cancers. With input from Anne-Lise Børresen-Dale and her lab at the Norwegian Radium Hospital, Institute for Cancer Research, the Ion AmpliSeq™ TP53 Panel was designed and verified to analyze all coding exons of TP53 with 24 amplicons, enabling the advancement of cancer research in early detection, prevention, and therapy.
**Note that for the Ion AmpliSeq TP53 Panel, your order will contain only 750 pre-pooled reactions in tubes, no primer plates will be included in your order.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
