Ion AmpliSeq HID community panels are designed with input from forensic scientists and verified for performance, providing expanded applications in targeted sequencing for human identification applications. These panels can be ordered through ampliseq.com and are compatible with the Applied Bioystems Precision ID sequencing workflow. Whether you select from our menu of predesigned panels described below or create a custom panel with your specific content, your panel will enable high coverage and performance. In addition, the Converge NGS SNP module software supports custom panel analysis through the inclusion of user-defined markers and population frequencies.

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Ion Ampliseq VISAGE-Basic Tool Research Panel

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Forensic DNA phenotyping can provide investigative leads on externally visible characteristics (EVCs) and biogeographical ancestry (BGA) to assist in investigations where there is no database hit or CE-STR analysis fails. The Ion AmpliSeq VISAGE (Visible Attributes through Genomics)-Basic Tool Research Panel consists of 153 SNPs, allowing prediction of EVCs and biogeographical ancestry, and incorporating 41 SNPs of the HIrisPlex-S assayand 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.

Pool1: 146 amplicons

Sample type: human genomic DNA, compatible with degraded DNA and forensic samples

Input DNA: 1 ng per sample but full profile recovery demonstrated down to 100 pg of DNA

Recommended configuration:
Sample per chip: 16 samples/Ion 530 Chip

 

 

Observed performance:
Marker call rate: 100%
Reproducibility: 100%

 

 

Citation
1Chaitanya, 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.

Design date:
June 2020
Publication:
Xavier, et al. Forensic Science International: Genetics 2020
Recommended applications:
Forensic genetics: bio-geographic ancestry inference, DNA phenotyping
 

Ion Ampliseq DNA Phenotyping Panel

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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.

Pool1: 17 amplicons (1 tube)

Sample type: DNA

Input DNA: 1 ng

Recommended configuration:
Sample per chip: 32 samples per Ion 318 or Ion 520 chip
Minimum coverage: 1000X
Observed performance:
Panel uniformity: 99%
Reads on-targets: 93%

 

Design date:
March 2015
Publication:
Walsh et al, Forensic Science International: Genetics 2013
Recommended applications:
Forensic genetics: visible traits inference
 

Ion AmpliSeq PhenoTrivium Panel

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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 show that reliable ancestry and phenotype predictions can be obtained with the panel down to 125 pg of genomic DNA (gDNA) and the added benefits of combining ancestry, phenotype, and male lineage predictions on casework samples.

Pool1: 311 amplicons

Sample type: human genomic DNA, compatible with degraded DNA and forensic samples

Input DNA: 1 ng per sample but reliable ancestry & phenotype predictions down to 125 pg of DNA
Recommended configuration:
Sample per chip: 16-24 samples/Ion 530 Chip
Observed performance:
Marker call rate: 98.75%

 

Design date:
December 2020
Publication:
Diepenbroek, et al. Genes 2020, 11(12)

Recommended applications:
Forensic genetics: bio-geographic ancestry inference, DNA phenotyping, investigative leads

 

Ion AmpliSeq HID Y-SNP Research Panel v1

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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.

Pool1: 602 amplicons (1 tube)

Sample type: human genomic DNA, compatible with degraded DNA and forensic samples

Input DNA: 1 ng per sample, but accurate haplogrouping demonstrated down to 25 pg of DNA

Recommended configuration:
Sample per chip: 24 per Ion 318 Chip
Average coverage/marker: 175X
*Also compatible with Ion 510, 520 and 530 chips
Observed performance:
Marker call rate: 97.3%
Precision: 100%

 

Design date:
Jan 2019
Publication:
Ralf et al, Forensic Science International: Genetics 2019
Recommended applications:
Forensic genetics: paternal lineage identification and paternal bio-geographic ancestry inference

Ion AmpliSeq MH-74 Plex Research Panel

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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 Laboratory. 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.

Pool1: 74 amplicons

Sample type: human genomic DNA, compatible with degraded DNA and forensic samples

Input DNA: 1 ng per sample, but sensitivity as low as 50 pg

Recommended configuration:
Sample per chip: 16 samples/Ion 530 Chip
Observed performance:
Marker call rate: 100%

 

Design date:
December 2020
Publication:
Oldoni, et al. Forensic Science International: Genetics 2020
Recommended applications:
Forensic genetics: bio-geographic ancestry inference, DNA mixtures