This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq HID Y-SNP Research Panel enables analyses of 859 Y-SNPs to infer 640 Y haplogroups. Preliminary forensic developmental validation testing revealed the performance of this Y-SNP MPS tool is highly accurate, is sensitive and robust.
Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. The Ion AmpliSeq HID Y-SNP Research Panel enables analyses of 859 Y-SNPs to infer 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that the performance of this Y-SNP MPS tool is highly accurate, sensitive and robust. For further details, including analysis recommendation, see Ralf et al, Forensic Science International: Genetics 2019
Design Date
Jan 2019
Publication: Ralf et al, Forensic Science International: Genetics 2019
Author: Manfred Kayser (m.kayser@erasmusmc.nl)
Affiliation: Erasmus MC University Medical Center
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ PhenoTrivium Panel contains ancestry, DNA phenotyping and male lineage markers for a total of 200 autosomal SNPs and 120 Y chromosomal SNPs in a single panel. Diepenbroek et al show that reliable ancestry and phenotype predictions can be obtained with the Ion AmpliSeq™ PhenoTrivium Panel down to 125 pg of genomic DNA (gDNA) and the added benefits of combining ancestry, phenotype and male lineage predictions on casework samples.
Growing research on the application of alternative markers in the field of forensic genetics has aided in identifying methods to obtain more genetic information from challenging samples. The use of biogeographical ancestry, DNA phenotyping and lineage markers can provide investigative leads in cold cases and cases where there are no suspects. The Ion AmpliSeq™ PhenoTrivium Panel contains ancestry, DNA phenotyping and male lineage markers for a total of 200 autosomal SNPs and 120 Y chromosomal SNPs in a single panel. Diepenbroek et al show that reliable ancestry and phenotype predictions can be obtained with the Ion AmpliSeq™ PhenoTrivium Panel down to 125 pg of genomic DNA (gDNA) and the added benefits of combining ancestry, phenotype and male lineage predictions on casework samples.
Design Date
December 2020
Publication:
Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples, Genes (2020). M. Diepenbroek, B. Bayer, K. Schwender, R. Schiller, J. Lim, R. Lagacé, K. Anslinger
Affiliation: Marta Diepenbroek (Marta.Diepenbroek@med.uni-muenchen.de)
References
Department of Forensic Genetics, Institute of Legal Medicine, Ludwig Maximilian University of Munich
Recommended ApplicationForensic Genetics: Bio-geographic ancestry inference, DNA Phenotyping, Investigative Leads
Recommended Configuration
Sample per Chip: 16-24 samples/530 Chip
Sample Type
Human genomic DNA, compatible with degraded DNA and forensic samples
Number of sample in publication
~178 Samples
Observed Performance
Marker Call Rate: 98.75%
Input DNA required
1 ng per sample but
reliable ancestry & phenotype predictions down to 125 pg of DNA
Disease Research Area: Forensics, Human Identification, Biogeographical Ancestry, DNA Phenotyping, Investigative Leads
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ MH-74 Plex Research Panel is a 157 – 325 bp assay covering 74 microhaplotypes (230 SNPs) selected from a set of 130 microhaplotypes previously characterized by the Kidd Laboratory.
The analysis of alternative marker types can complement CE-STR results for challenging samples, such as complex mixtures or degraded samples, to generate investigative leads. Microhaplotypes have arisen as an alternative marker to traditional STR-CE typing due to the additive enhanced mixture analysis and biogeographical ancestry prediction capabilities that favor its use for forensic samples. The Ion AmpliSeq™ MH-74 Plex Research Panel is a 157 – 325 bp assay covering 74 microhaplotypes (230 SNPs) selected from a set of 130 microhaplotypes previously characterized by the Kidd Laboratory1. Microhaplotypes were selected based on high Ae (effective number of alleles) and In (informativeness) values to enhance mixture deconvolution and biogeographic ancestry prediction capabilities. Oldoni et al demonstrate sensitivity down to 50 pg of genomic DNA (gDNA) and the utility of the assay in analyzing complex mixtures to complement CE-STR typing results
Design Date
December 2020
Publication:
A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures, Forensic Science International: Genetics (2020). F. Oldoni, D. Bader, C. Fantinato, S.C. Wootton, R. Lagacé, K.K. Kidd, D. Podini
Author: Daniele Podini (podini@gwu.edu), Kenneth K. Kidd (kenneth.kidd@yale.edu)
Affiliation: The George Washington University, Yale University School of Medicine
References
1K.K. Kidd, W.C. Speed, A.J. Pakstis, D.S. Podini, R. Lagace, J. Chang, S. Wootton, E. Haigh, U. Soundararajan, Evaluating 130 microhaplotypes across a global set of 83 populations, Forensic Sci. Int. Genet. 29 (2017) 29–37
Recommended ApplicationForensic Genetics: Bio-geographic ancestry inference, DNA Mixtures
Recommended Configuration
Sample per Chip: 16-24 samples/530 Chip
Sample Type
Human genomic DNA, compatible with degraded DNA and forensic samples
Number of sample in publication
~79 Samples
Observed Performance
Marker Call Rate: 100%
Input DNA required
1 ng per sample
Disease Research Area: Forensics, Human Identification, Biogeographical Ancestry
Ion AmpliSeq™ VISAGE (Visible Attributes through Genomics)-Basic Tool Research Panel
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ VISAGE-Basic tool research panel consists of 153 SNPs allowing for prediction of EVCs and biogeographical ancestry, incorporating 41 SNPs of the HIrisPlex-S assay1 and 115 BGA markers chosen for differentiation of seven continental populations. The assay design is beneficial for degraded samples with an average amplicon size of 175 bp
Forensic DNA phenotyping can provide investigative leads on externally visible characteristics (EVCs) and biogeographical ancestry (BGA) to assist investigators in investigations where there is no database hit or CE-STR analysis fails. The Ion AmpliSeq™ VISAGE-Basic tool research panel consists of 153 SNPs allowing for prediction of EVCs and biogeographical ancestry, incorporating 41 SNPs of the HIrisPlex-S assay1 and 115 BGA markers chosen for differentiation of seven continental populations. The assay design is beneficial for degraded samples with an average amplicon size of 175 bp. Preliminary validation of the assay shows high sensitivity with full profiles down to 100 pg of genomic DNA (gDNA) and 240 minutes of sonication.
Design Date
June 2020
Publication:
Development and Validation of the VISAGE AmpliSeq Basic Tool to Predict Appearance and Ancestry from DNA, Forensic Science International: Genetics (2020). C. Xavier, M. de la Puente, A. Mosquera-Miguel, A. Freire-Aradas, V. Kalamara, A. Vidaki, T. Gross, A. Revoir, E. Pospiech, E. Kartasinska, M. Spolnicka, W. Branicki, C. E. Ames, P. M. Schneider, C. Hohoff, M. Kayser, C. Phillips, W. Parson, on behalf of the VISAGE Consortium
Affiliation: VISAGE Consortium
References1Chaitanya, L. et al., The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci Int Genet, 2018. 35: p. 123- 135.
Recommended ApplicationForensic Genetics: Bio-geographic ancestry inference, DNA phenotyping
Recommended Configuration
Sample per Chip: 16 samples/530 Chip
Sample Type
Human genomic DNA, compatible with degraded DNA and forensic samples
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion Ampliseq™ DNA Phenotyping Panel is used to predict hair and eye color using 24 phenotype SNPs from the HIrisPlex system. This panel targets 23 SNPs and one indel from the following genes: MC1R, SLC45A2, ASIP/PIGU, EXOC2, HERC2, IRF4, KITLG, OCA2, TYR, SLC24A4, and TRYP1.
DNA phenotyping can be useful for generating investigative leads in cases where STR profiles have not resulted in a database match. The Ion Ampliseq™ DNA Phenotyping Panel is used to predict hair and eye color using 24 phenotype SNPs from the HIrisPlex system. This panel targets 23 SNPs and one indel from the following genes: MC1R, SLC45A2, ASIP/PIGU, EXOC2, HERC2, IRF4, KITLG, OCA2, TYR, SLC24A4, and TRYP1. Results suggesting probability of blue, intermediate, or brown eye color along with shade of black, brown, red, or blond hair are provided by the HIrisPlex prediction model (http://hirisplex.erasmusmc.nl/). For further details see Walsh et al, Forensic Science International: Genetics 2013
Design Date
March 2015
Publication:
Walsh et al, Forensic Science International: Genetics 2013
Recommended Application
Research Applications in human identification
Recommended Configuration
Sample per Chip: 32 samples per 318 or 520 chip
Minimum coverage: 1000x
