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The Applied Biosystems Precision ID NGS System for human identification can help you solve tough cases by getting more information from your challenging samples. Now you have help moving those unknown samples from storage to investigative leads. Adopting next-generation sequencing (NGS) for forensic DNA analysis in your laboratory is simpler than ever when you combine the Ion Chef System and Ion GeneStudio S5 Systems with optimized Precision ID library preparation, template preparation and sequencing kits, and forensically relevant panels.
With as little as 125 pg of DNA input, you can process unsolved and missing persons cases with NGS in your lab today, with as few as 5 pipetting steps and 45 minutes of hands-on time.
Construct library | Prepare template | Run sequence | Analyze data |
Precision ID panels and Ion AmpliSeq Community panels | Ion Chef System
| Ion GeneStudio S5 System
| Converge Software |
The Applied Biosystems Precision ID Library Kits are specifically designed for rapid generation of targeted sequencing libraries from Precision ID panels. The kits are built on Ion AmpliSeq chemistry, which enables scalable multiplex PCR reactions from tens to thousands of amplicons in a single well using as little as 125 pg of starting DNA. These kits also enable the preparation of barcoded libraries using Ion Xpress Barcode Adapters 1-96 Kits or the IonCode Barcode Adapters 1-384 Kit. The barcoded libraries can be combined and loaded onto a single Ion chip to minimize the sequencing run time and costs, and allow for accurate sample-to-sample comparison. Precision ID Library Kits are for use with manual procedures or with high-throughput robotics platforms.
The Precision ID DL8 Kit is designed for use with the Ion Chef System for automation of Ion AmpliSeq library construction. Leveraging the automation capabilities of the Ion Chef System, this kit enables the reproducible preparation of Precision ID amplicon libraries, with less than 15 minutes of hands-on time and only 3 liquid transfer steps. Compatible with 1- and 2-pool panel designs, the kit automates the preparation of libraries from 8 samples in a single run, delivering a single tube of pooled libraries ready for downstream templating and sequencing.
The Ion S5 Precision ID Chef & Sequencing Kit is fully optimized for templating and sequencing of all available HID NGS panels (STR, SNPs, and mitchondrial DNA) on the Ion GeneStudio S5 Systems. The kit is available in two formats: two runs per initialization for higher-throughput labs and one run per initialization for less frequent analyses.
Save time at the bench, help improve your laboratory’s productivity, and standardize your results. The Ion Chef System for human identification performs the repetitive lab work without the need for complex robotics and confusing scripts. Paired with Ion Torrent next-generation sequencing platforms, the Ion Chef System automates Precision ID library preparation, template generation, and chip loading with push-button simplicity—enabling DNA to data in as little as 45 minutes of hands-on time.
Suitable for scientists and researchers in forensic human identification, the Ion Chef System offers automated workflows that help enable gains in laboratory efficiency. Unleash the power of the Precision ID NGS System with Ion Chef System automation, paired with Ion AmpliSeq technology which is used in the Precision ID Panels for human identification.
Comparison of reproducibility across several next-generation sequencing metrics (number of reads, base coverage and loading efficiency) for Ion libraries processed (templating and chip loading) using the Ion Chef and Ion OneTouch 2 Systems. While both systems exhibit excellent reproducibility, the Ion Chef System demonstrates lower coefficient of variation (CV) % values across all metrics.
Want to sequence SNP panels on Monday, mtDNA panels on Wednesday, and STR panels on Thursday? The Ion GeneStudio S5 Systems, an integral part of the Precision ID NGS System, let you leverage a single benchtop instrument that scales to your application and throughput needs. The Ion GeneStudio S5 Systems provide the simplest DNA-to-data workflow for targeted sequencing with industry-leading speed and affordability, and the flexibility to multiplex and optimize the number of samples and panels on a single chip.
Ion GeneStudio S5 System | Ion GeneStudio S5 Plus System | Ion GeneStudio S5 Prime System | ||||||||
Ion 510 Chip | Ion 520 Chip | Ion 530 Chip | Ion 510 Chip | Ion 520 Chip | Ion 530 Chip | Ion 510 Chip | Ion 520 Chip | Ion 530 Chip | ||
Reads | 2-3 million | 4-6 million | 15-20 million | 2-3 million | 4-6 million | 15-20 million | 2-3 million | 4-6 million | 15-20 million | |
Turnaround time (sequencing + analysis) | mtDNA whole genome panel | - | 7.5 hr | 10.5 hr | - | 3.5 hr | 5 hr | - | 3 hr | 4 hr |
mtDNA control regions panel | 4.5 hr | 7.5 hr | - | 3 hr | 3.5 hr | - | 3 hr | 3 hr | - | |
Ancestry panel | 4.5 hr | 7.5 hr | 10.5 hr | 3 hr | 3.5 hr | 5 hr | 3 hr | 3 hr | 4 hr | |
Identity panel | 4.5 hr | 7.5 hr | 10.5 hr | 3 hr | 3.5 hr | 5 hr | 3 hr | 3 hr | 4 hr | |
STR panel | - | 12.5 hr | 22.5 hr | - | 4.5 hr | 5.5 hr | - | 4 hr | 5 hr |
New to next-generation sequencing? Watch the demos for each step of the Ion Torrent next-generation sequencing workflow.
Converge Software is an all-in-one modular enterprise platform from Thermo Fisher Scientific that integrates forensic DNA data management and analysis into a single software package designed to increase the efficiency of forensic DNA laboratories. With the Converge NGS analysis module, laboratories are now able to examine the mitochondrial genome to identify remains when there is poor quality or no autosomal DNA available for analysis, STR markers to help determine the number of contributors in a mixture analysis, and targeted and forensically relevant single nucleotide polymorphism (SNP) markers to help generate investigative leads. Additionally, full auditing functionality is included for chain-of-custody requirements.
Analysis of the mtGenome can be challenging due to complex alignments, the presence mtDNA heteroplasmy, and insertions and deletions present throughout the genome that may impact the accuracy of variant calling. NGS reads from the BAM files are first mapped to nodes in PhyloTree and then realigned using a custom Smith–Waterman alignment algorithm that integrates PhyloTree and EMPOP information into the scoring function. Variants are called with reference to the rCRS. Additionally, the closest haplogroup is calculated, and variants are evaluated based on their occurrence in the haplogroup as well as other general metrics including frequency, strand bias, and coverage. Variants can be viewed in a variety of formats, including a circular plot, linear view, grid, or IGV format. In addition, profiles can be compared as well as downloaded in CODIS format.
With an interface similar to that of Applied Biosystems GeneMapper ID-X Software, you will be able to quickly evaluate sequencing data using familiar process quality values (PQV) and flags such as allele number (AN), off-ladder allele (OL), peak height ratio (PHR), below stochastic threshold (BST), and control concordance (CC) (use figure). Preconfigured analysis settings are provided within the NGS module and may be modified by the laboratory as needed.
Converge Software SNP analysis provides a variety of metrics to monitor sequencing quality, including coverage of aligned reads to a hotspot, strand bias, number of reads containing each base at the hotspot, genotype call and quality, and major allele frequency. Tertiary ancestry analysis consists of generating an estimation of admixture prediction and population likelihoods with variability estimates based on bootstrapping analysis (Alexander et al., Genome Research, 2009). Identity analysis calculating random match probability (RMP) can be based on genotype frequencies generated from 1000 Genomes data or from user-supplied population frequency data as well as a Y haplogroup prediction.
Kocsis, Balázs et al. (2024) Internal validation of the Precision ID GlobalFiler NGS STR panel v2 kit with locus-specific analytical threshold, and with special regard to mixtures and low template DNA detection. Forensic Science International: Genetics, Volume 74, 103159
Liu, J et al. (2023) Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing. Forensic Sci Int. 348:111708.
Faccinetto, C et al. (2021) Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel. Int J Legal Med 135(6):2295-2306.
Ta, MTA at al. (2021) Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5 system. Int J Legal Med. 135(6):2285-2294.
Resutik, P et al (2023) Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference. Forensic Sci Int Genet. 64:102850.
Truelsen D et al (2021) Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations. Sci Rep;11(1):18595
Köksal, Z et al (2023) Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals. Forensic Sci Int Genet 67:102934
Jin, S et al (2018) Implementing a biogeographic ancestry inference service for forensic casework. Electrophoresis. 39(21):2757-2765
Yang, SB et al (2023) Forensic genetic analysis of single-nucleotide polymorphisms and microhaplotypes in Koreans through next-generation sequencing using precision ID identity panel. Genes Genomics. 45(10):1281-1293
Zupanič Pajnič, I et al (2023) Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med. 137(4):1007-1015
Tiedge, TM et al (2021) High-throughput DNA sequencing of environmentally insulted latent fingerprints after visualization with nanoscale columnar-thin-film technique. Sci Justice. 61(5):505-515
Turchi, C et al (2020) Assessment of the Precision ID Identity Panel kit on challenging forensic samples. Forensic Sci Int Genet. 49:102400
Ohuchi, T et al (2022) Allele frequencies of 31 autosomal short tandem repeat (auSTR) loci obtained using the Precision ID GlobalFiler NGS STR Panel v2 in 322 individuals from the Japanese population. Leg Med (Tokyo). 59:102151
Zupanič Pajnič, I et al (2022) Isometric artifacts from polymerase chain reaction-massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology? .Electrophoresis. 43(13-14):1521-1530
Ragazzo M et al (2020) Interpreting Mixture Profiles: Comparison between Precision ID GlobalFiler NGS STR Panel v2 and Traditional Methods. Genes (Basel). 11(6):591
Zupanič Pajnič, I et al (2020) Identifying victims of the largest Second World War family massacre in Slovenia. Forensic Sci Int. 306:110056
Diepenbroek, M et al (2023) Phenotype predictions of two-person mixture using single cell analysis. Forensic Sci Int Genet 67:102938
Diepenbroek, M et al (2020) Evaluation of the Ion AmpliSeq PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes (Basel) 11(12):1398
Diepenbroek, M et al (2021) Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing. Genes (Basel). 12(9):1362
Xavier, C et al (2020) Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA. Forensic Sci Int Genet. 48:102336
Inkret, J, et al (2023) A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology. Genes (Basel). 14(7):1449
Kukla-Bartoszek, M et al (2020) The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system. Forensic Sci Int Genet. 47:102301
Melchionda, F et al (2022) Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples. Genes (Basel). 13(10):1688
Breslin, K et al (2019) HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet. 43:102152
Oldoni, F et al (2020) Population genetic data of 74 microhaplotypes in four major U.S. population groups. Forensic Sci Int Genet. 49:102398
Oldoni, F et al (2020) A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures. Forensic Sci Int Genet. 49:102367
Köksal, Z et al (2022) Testing the Ion AmpliSeq HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Forensic Sci Int Genet. 59:102708
Ochiai, E et al (2016) Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeq Identity Panel. Leg Med (Tokyo). 22:58-61
Wang M et al (2019) Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system. Forensic Sci Int Genet. 38:70-76
Ralf, A et al (2019) .Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing. Forensic Sci Int Genet 41:93-106
For Research Forensic or Paternity Use Only. Not for use in diagnostic procedures. For licensing and limited use restrictions visit HIDlicensing.