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

With as little as 125 pg of DNA input, you can quickly and easily analyze these commonly used forensic markers in less than 2 days.

The Precision ID GlobalFiler NGS STR Panel provides both allele number and base sequence for each repeat structure, offering enhanced mixture resolution and increased Probability of Identity (PI) estimates.

Precision ID Identity Panel

Single-nucleotide polymorphisms (SNPs) provide a variety of new, important information for human identification purposes, in addition to short tandem repeats (STRs). Due to the shorter amplicons required for sequencing, SNPs enable high recovery of information from degraded samples—such as from mass disaster victims.

The  Applied Biosystems Precision ID Identity Panel includes 124 autosomal markers, and provides discrimination of individuals similar to STR genotype match probabilities used by forensic analysts (between 1 x 10-31 and 6 x 10-35). The high discrimination power is achieved by using 34 upper Y-clade SNPs and 90 autosomal SNPs that have high heterozygosity and low Fixation Index (Fst), described in publications by Kenneth Kidd of Yale University and the SNP for ID Consortium.

The Converge Software NGS Data Analysis module contains parameters for analyzing the Precision ID Identity Panel, generating random match probabilities (RMPs) from either the 1000 Genomes Project dataset using 85 unlinked identity SNPs, as well as Y haplogroup determination from the 34 upper Y-clade SNPs or customer supplied population frequency data.

Ion AmpliSeq community panels are designed with input from leading scientists and verified for performance, providing expanded applications in targeted sequencing for forensics.  These panels can be ordered through ampliseq.com and are compatible with the Applied Bioystems Precision ID sequencing workflow.  In addition, the Converge NGS SNP module software can support custom panel analysis through the inclusion of user-defined markers and population frequencies.  

Current HID community panels include the Ion AmpliSeq DNA Phenotype Panel (Walsh et al., Forensic Science International: Genetics 2013) and Ion AmpliSeq HID Y-SNP Research Panel V1 (Ralf et al., Forensic Science International: Genetics 2019). 

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In addition, custom Ion AmpliSeq panels can be designed with your specific content using the Ion AmpliSeq Designer at ampliseq.com.

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.

Adapting next-generation sequencing (NGS) for forensics is not a paradigm shift —Dr. Bruce Budowle, University of North Texas Health Science Center
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Introducing mitochondrial DNA sequencing by NGS technology —Dr. Walther Parson, Institute of Legal Medicine at Innsbruck Medical University
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Accelerate your forensic DNA analyses with Ion Torrent NGS automation —Joseph Chang, Thermo Fisher Scientific
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Mitochondrial DNA analysis

Diepenbroek, M., Amory, C., Niederstätter, H. et al. Genetic and phylogeographic evidence for Jewish Holocaust victims at the Sobibór death camp. Genome Biol 22, 200 (2021). https://doi.org/10.1186/s13059-021-02420-0
Performance of the Early Access AmpliSeq Mitochondrial Panel with degraded DNA samples using the Ion Torrent platform. Wai, K. T., Barash, M. and Gunn, P. (2018), ELECTROPHORESIS. doi:10.1002/elps.201700371
Evaluation of the precision ID whole mtDNA genome panel for forensic analyses Strobl, Christina et al. Forensic Science International: Genetics , Volume 35 , 21 – 25

STR analysis

Muller P et al. (2018) Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the Ion S5 System. Forensic Sci Int Genet 36:95–103.
Alonso A, Barrio PA, Muller P, et al. (2018) Current state‐of‐art of STR sequencing in forensic genetics. Electrophoresis doi:10.1002/elps.201800030
Wang Z et al. (2017) Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler NGS STR Panel and the Ion PGM System. Forensic Sci Int Genet 31:126–134

Ancestry SNP analysis

Al-Asfi M, McNevin D, Mehta B et al. (2018) Assessment of the Precision ID Ancestry panel. Int J Legal Med doi: 10.1007/s00414-018-1785-9.
Pereira V et al. (2017) Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 28:138–145.
Hollard C, Keyser C, Delabarde T et al. (2017) Case report: on the use of the HID-Ion AmpliSeq Ancestry Panel in a real forensic case. Int J Legal Med 131:351–358.
Tasker E et al. (2017) Analysis of DNA from post-blast pipe bomb fragments for identification and determination of ancestry. Forensic Sci Int Genet 28:195–202.

Identity SNP analysis

Liu J et al. (2018) Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. Forensic Sci Int Genet 35:141–148.
Meiklejohn KA et al. (2017) Evaluation of the Precision ID Identity Panel for the Ion Torrent PGM sequencer. Forensic Sci Int Genet 31:48–56.
van der Heijden S et al. (2017) Comparison of manual and automated AmpliSeq workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet 31:118–125.