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:
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 Ion AmpliSeq™ Hearing Loss Research Panel v1 was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with hearing loss. The panel assesses 63 genes known to mutations causal of hearing. This panel contains 2,064 amplicons in 2 pools.
Because of the extreme genetic heterogeneity of deafness, interpreting genetic information is difficult. Research using targeted exon sequencing by massively parallel DNA sequencing is a powerful strategy to discover rare variants in genes associated with Mendelian disorders such as deafness. This panel was developed as a quick, accurate and cost-effective method to identify genetic mutations associated with hearing loss. The panel assesses 63 genes known to mutations causal of hearing, which we routinely screen with the Invader method and Taqman® method. We obtained very high sensitivity and specificity with this panel in a study of more than 100 archived samples. For further details see Miyagawa et al, Plos One 2013.
Design Date
April 2013
Publication: Miyagawa et al, Plos One 2013 Author: Maiko Miyagawa, Shinya Nishio, Takuo Ikeda, Kunihiro Fukushima and Shin-ichi Usami Affiliation: Shinshu University
Recommended Application
Germ line mutation detection
Recommended Configuration
Sample per Chip: 6–8 per 318 chip
Minimum coverage: 100x
* average coverage was 248.7x for 6 sample per 318 chip
Sample Type
Genome DNA
Number of sample in Publication
~100 samples (included previous panel)
Observed Performance
Average panel uniformity: 95.6%
Reads on-targets: 90.7%
* average of 100 trial samples
