Ion Research Panels:

Panel Name Research Area Genome Number of amplicons per pool
(# of tubes)
Tags Actions
Ion AmpliSeq™ Cardiovascular Research Panel
Inherited Disease Human (hg19) Pool1: 5222 amplicons
Pool2: 5208 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ Hematology Research Panel
Inherited Disease Human (hg19) Pool1: 3722 amplicons
Pool2: 3712 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ Neurological Research Panel
Inherited Disease Human (hg19) Pool1: 9045 amplicons
Pool2: 9032 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ Ophthalmic Research Panel
Inherited Disease Human (hg19) Pool1: 3619 amplicons
Pool2: 3604 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The 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.
Ion AmpliSeq™ Autism Research Panel
Inherited Disease Human (hg19) Pool1: 3604 amplicons
Pool2: 3590 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ Autism Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 236 genes associated with autism.
Ion AmpliSeq™ Deafness Research Panel v2
Inherited Disease Human (hg19) Pool1: 1770 amplicons
Pool2: 1750 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Cardiac Arrhythmias and Cardiomyopathy Research Panel
Inherited Disease Human (hg19) Pool1: 1103 amplicons
Pool2: 1095 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The 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.
Ion AmpliSeq™ Dermatology Research Panel v2
Inherited Disease Human (hg19) Pool1: 2496 amplicons
Pool2: 2468 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Dysmorphia-Dysplasia Research Panel v2
Inherited Disease Human (hg19) Pool1: 6288 amplicons
Pool2: 6270 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Endocrine Research Panel v2
Inherited Disease Human (hg19) Pool1: 3191 amplicons
Pool2: 3168 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Epilepsy Research Panel
Inherited Disease Human (hg19) Pool1: 4444 amplicons
Pool2: 4431 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ Epilepsy Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 386 genes associated with epilepsy.
Ion AmpliSeq™ Gastrointestinal Research Panel v2
Inherited Disease Human (hg19) Pool1: 2060 amplicons
Pool2: 2043 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Inborn Errors of Metabolism Research Panel v2
Inherited Disease Human (hg19) Pool1: 4855 amplicons
Pool2: 4826 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Inherited Cancer Research Panel
Inherited Disease Human (hg19) Pool1: 1676 amplicons
Pool2: 1664 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ Inherited Cancer Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 134 genes associated with inherited cancers.
Ion AmpliSeq™ Comprehensive Ovarian Cancer Research Panel
Inherited Disease Human (hg19) Pool1: 669 amplicons
Pool2: 662 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Primary Immune Deficiency Research Panel v2
Inherited Disease Human (hg19) Pool1: 2627 amplicons
Pool2: 2614 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Request Quote

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Pulmonary Research Panel v2
Inherited Disease Human (hg19) Pool1: 1693 amplicons
Pool2: 1672 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ Renal Research Panel v2
Inherited Disease Human (hg19) Pool1: 2175 amplicons
Pool2: 2157 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.
Ion AmpliSeq™ BRCA Reflex, Hereditary Cancer Research Panel
Inherited Disease Human (hg19) Pool1: 308 amplicons
Pool2: 302 amplicons
(2 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ BRCA Plus, Extended Hereditary Breast and Ovarian Research Panel
Inherited Disease Human (hg19) Pool1: 233 amplicons
Pool2: 233 amplicons
Pool3: 233 amplicons
(3 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ Inherited Disease Panel
4477686
Inherited Disease Human (hg19) Pool1: 3447 amplicons
Pool2: 3438 amplicons
Pool3: 3424 amplicons
(3 tubes)
DNA
Ready-to-Use Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ Inherited Disease Panel provides highly multiplexed target selection of all exons of over genes that are mutated in over 700 unique inherited diseases, according to the NCBI ClinVar database (May 2012). This panel contains 10,309 amplicons in 3 pools.
Ion AmpliSeq™ CFTR Panel
Inherited Disease Human (hg19) Pool1: 50 amplicons
Pool2: 52 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: 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.
Ion AmpliSeq™ Hearing Loss Research Panel v1
Inherited Disease Human (hg19) 1: 1036 amplicons
2: 1028 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

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

Variant Caller Plugin

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

Summary: The Ion AmpliSeq™ 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.