Precision ID NGS System for Human Identification: Targeted Sequencing for Forensic DNA Analysis

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.

• Automates library generation, equalization, and pooling for 1- and 2-pool designs for up to 8 samples in a single instrument run
• Operates with a very low inter-run cross-contamination rate of <0.01%
• Helps reduce sources of variability for forensic scientists of any experience level
• Supports all Ion Torrent semiconductor chips and sequencing chemistries

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.

Simplicity: ready, set, sequence

• Less than 15 minutes of sequencer hands-on time
• Less than 45 minutes of hands-on time for a DNA-to-data targeted sequencing workflow

Speed: because every hour counts

• <2.5 hours for a sequencing run
• From DNA to data in less than 2 days with an overnight Ion Chef templating run

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.

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.

Precision ID mtDNA panels

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.

Precision ID Ancestry panel

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

Precision ID Identity panel

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

Precision ID GlobalFiler NGS STR panel

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

Community panels

Ion AmpliSeq PhenoTrivium Panel

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

Ion AmpliSeq VISAGE-Basic Tool Research Panel

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

Ion AmpliSeq DNA Phenotyping Panel

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

Ion AmpliSeq MH-74 Plex Research Panel

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

Ion AmpliSeq HID Y-SNP Research Panel v1

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