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 S5 or Ion S5 XL Systems with optimized Precision ID library preparation, template preparation and sequencing kits, and forensically relevant panels.

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Let the evidence speak for itself. You can choose from a suite of targeted Precision ID panels for the NGS solution for your cases. Short tandem repeat (STR) panels provide high-resolution genotyping of STRs for analysis of complex mixtures. Ancestry-informative or phenotypic single nucleotide polymorphism (SNP) analysis may help generate investigative leads when suspects are unknown. Identity-testing SNPs can associate a degraded crime scene sample to a known reference when partial results are obtained with autosomal STR analysis. Mitochondrial DNA (mtDNA) from samples recovered at mass disasters and from other unidentified remains can be routinely analyzed to assist in human identification, and help establish links to related family members.

With as little as 1 ng 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.

Solutions for forensic DNA analysis

Applied Biosystems Precision ID panels enable analysis of up to hundreds of forensically targeted markers such as STRs, SNPs, or the mtDNA genome.

The Ion Chef System simplifies the workflow for targeted sequencing, providing a walk-away solution for automated library preparation, template preparation, and chip loading.

The Ion S5 and Ion S5 XL Systems provide the simplest DNA-to-data workflow for targeted sequencing—so you can spend less time doing repetitive lab work.

Simplest targeted NGS workflow

Simplest targeted NGS workflow

Precision ID panels for human identification

Number of samples per run

Category

Panel

Ion S5 Chips

Ion PGM Chips

   

Ion 520 Chip

Ion 530 Chip

Ion 314 Chip

Ion 316 Chip

Ion 318 Chip

STR

Precision ID GlobalFiler NGS STR Panels*

8

32

2

8

16

SNP

Precision ID Ancestry Panel**

48

192

4

24

48

Precision ID Identity Panel

64

264

6

32

64

mtDNA

Precision ID mtDNA Whole Genome Panel

16

64

2

8

16

Precision ID mtDNA Control Region Panel§

96

384

8

64

96

* Minimum 500x coverage. 
** Average 594x coverage.
† Average 738x coverage for autosomal SNPs and 236x coverage for Y SNPs. 
‡ 1,750x coverage of the mitochondrial genome. 
§ 1,750x coverage of the control region.

Analyze DNA mixtures more efficiently

The Precision ID GlobalFiler NGS STR Panels include the same 21 autosomal STRs along with Y markers and amelogenin sex markers found in the Applied Biosystems GlobalFiler PCR Amplification Kit.

In place of SE33, the Precision ID GlobalFiler NGS STR Panels contain additional multiallellic STR markers, including Penta D and Penta E in the v2 panel for the Ion S5 System, to aid in mixture interpretation of complex casework samples.

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 v2 is specifically designed for sequencing on the Ion S5 and Ion S5 XL Systems. Library preparation can be performed manually, on a robotic platform, or on the Ion Chef System, with template preparation optimized for the Ion Chef System.

The Precision ID GlobalFiler NGS STR Panel is currently available for use with manual library preparation, template preparation on the Ion Chef System or the Ion OneTouch 2 System, and sequencing only on the Ion PGM System. 

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.

Identify missing persons or analyze remains

The   Applied Biosystems Precision ID mtDNA Whole Genome Panel is an innovative approach to mitochondrial DNA sequencing specifically developed for forensic applications. This mtDNA tiling approach includes two primer pools of 81 small amplicons in each pool, with an average size of 163 bp, to assist with obtaining optimal mitochondrial genome coverage data from highly compromised, degraded samples such as hair shafts, teeth, and bones.

Whole genome coverage of 4 samples of ancient tooth and bone samples was generated using 1 ng of input DNA, automated library preparation using the Ion Chef System, and sequencing on the Ion S5 System. The small amplicon design and inclusion of degenerate primers in the Precision ID mtDNA Whole Genome Panel increases success with degraded and low-starting-template DNA.

The Applied Biosystems Precision ID mtDNA Control Region Panel is based on the same mtDNA tiling approach used in the Precision ID mtDNA Whole Genome Panel. This targeted control region panel contains two smaller sets of primer pools with 7 amplicons each that span the 1.2 kb control region, which encompasses HV-I, II, and III, with the same optimal coverage for degraded forensic samples.

Generate more investigative leads

Precision ID Ancestry Panel

Ion AmpliSeq technology enables simple, fast target selection of hundreds of SNPs using multiplex PCR. Thousands of primer pairs can be used in a single tube for target amplification followed by next-generation sequencing (NGS) on the Applied Biosystems Precision ID NGS System. Utilizing this technology for human identification (HID) applications, the   Precision ID Ancestry Panel can provide you with biogeographic ancestry information and guide your investigation process. Alternatively, it may help identify or stratify the subjects for your research projects.

This ready-to-use panel includes 165 autosomal markers that provide biogeographic ancestry information. 55 of these markers were selected based on a publication by Dr. Kenneth Kidd [1], and 123 markers were selected based on a publication by Dr. Michael Seldin [2]. Ion AmpliSeq technology makes it possible to multiplex 165 PCR reactions in one tube with only 1 ng of input DNA. With small amplicon sizes, the panel is also optimized for degraded DNA samples.

24 samples of known genotype were analyzed after one run on the Ion PGM System using the Ion 318 Chip v2. The sequencing reads were analyzed using Torrent Suite Software, Variant Caller 4.0, and the HID SNP Genotype plug-in. Results from the study demonstrated a concordance rate of 99.77% for the 55 SNPs from Dr. Kenneth Kidd at an average read depth of ~1,250x per SNP.


Analyze highly degraded or trace DNA

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 [3] and the SNPforID Consortium [4,5].

32 samples were analyzed after one run on the Ion PGM System using the Ion 318 Chip v2. The sequencing reads were analyzed using Torrent Suite Software, Variant Caller 4.0, and the HID SNP Genotyper plug-in. A set of 46 SNPs (all 43 unlinked SNPs from Dr. Kenneth Kidd and 3 additional SNPforID SNPs) were evaluated in a concordance study with results demonstrating a concordance rate of 99.99% at an average read depth of ~750x per autosomal SNP and ~350x per Y SNP .

The 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 10’s to 1,000’s of amplicons in a single well using just 1 ng 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 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.

The Ion PGM Hi-Q STR Chef Kit and the Ion PGM Hi-Q STR Sequencing Kit are designed specifically for robust and highly accurate sequencing of STR (short tandem repeat) libraries prepared from the Precision ID GlobalFiler NGS STR Panel using the Ion Chef System or Ion OneTouch 2 System, respectively, and sequenced on the Ion PGM System. 

Automate library and template preparation with the Ion Chef System

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.

Ion Chef System templating and chip loading workflow
1 Library Preparation


Ion Chef

 

  • Load reagents & consumables
  • Load library samples
  • Set run parameters

       

 
2 Automated template preparation and chip loading
Ion Chef System

 

  • Library amplification
  • ISP recovery & enrichment
  • Chip loading

 

 
3 Sequencing


Ion PGM, Ion S5

Run sequence on either:

  • Ion S5 System
  • Ion PGM System

 

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

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.

Fast, flexible, and simple next-generation sequencing for forensics with the Ion S5 and Ion S5 XL Systems

  • Simple workflow
  • Fast sequencing
  • Lower weekly throughput

  • Simple workflow
  • Faster data analysis
  • Higher weekly throughput

Want to sequence SNP panels on Monday, mtDNA panels on Wednesday, and STR panels on Thursday? The Ion S5 Systems, an integral part of the Precision ID NGS System, or the Ion PGM System let you leverage a single benchtop instrument that scales to your application and throughput needs. The Ion S5 and Ion S5 XL 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 to 5.5 hours for a sequencing run
  • From DNA to data in just over a day

 

Ion S5 System

Ion S5 XL System

Ion 520 Chip

Ion 530 Chip

Ion 520 Chip

Ion 530 Chip

Reads

 

3–5 million

15–20 million

3–5 million

15–20 million

 

Run time

SNP panels

2.5 hr

2.5 hr

2.5 hr

2.5 hr

Precision ID mtDNA Whole Genome Panel

2.5 hr

2.5 hr

2.5 hr

2.5 hr

Precision ID mtDNA Control Region Panel

2.5 hr

2.5 hr

2.5 hr

2.5 hr

 

Analysis time (aligned BAM)

SNP panels

5 hr

8 hr

1 hr

2.5 hr

Precision ID mtDNA Whole Genome Panel

5 hr

8 hr

1 hr

2.5 hr

Precision ID mtDNA Control Region Panel

5 hr

8 hr

1 hr

2.5 hr

Small sample input: because every sample matters

  • As little as 1 ng low-quality DNA needed to generate human identification profiles

Scalability: single sequencer, multiple applications

  • Analyze SNPs, mtDNA, STRs and mRNA targets
  • Multiple chip formats and read lengths to match your throughput needs 
  • Read lengths of 200 or 400 bp
  • Flexible multiplexing of samples and panels on a single chip

Simple data analysis and storage

  • Plan, monitor, track, and analyze your runs in Torrent Suite Software
  • Integrate, annotate, and interpret variants with easy-to-use Torrent Browser plug-ins

Service and support

  • More than 3,700 global sales, service, and technical support specialists are available to assist you in person, by phone, or online—including our Human Identification Professional Services (HPS) team that can help you successfully navigate the validation process required to bring new technologies into your lab.

New to next-generation sequencing? Watch the demos for each step of the Ion Torrent next-generation sequencing workflow.

See the Ion S5 System in action ›

Converge Software with an NGS Analysis module is required to generate profiles from the Precision ID GlobalFiler NGS STR Panel v2. The integrated HID STR genotyper functionality provides information on STR allele calls, STR sequence motifs, known SNPs in flanking regions, and isometric heterozygotes. 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). Preconfigured analysis settings are provided within the NGS module and may be modified by the laboratory as needed. Additionally, full auditing functionality is included for chain-of-custody requirements.

Raw data, base calling, variant calling, and genotyping are processed on the Ion S5 Sequencer; or, in the case of the Ion S5 XL System, transferred to a dedicated Ion S5 Torrent Server for faster analysis. Torrent Suite Software is used to plan runs and for plug-in analysis.

Torrent Variant Caller is a genetic variant caller for Ion Torrent sequencing platforms, and is specially optimized to exploit the underlying flow signal information in the statistical model to evaluate variants. Torrent Variant Caller is designed to call SNPs, multi-nucleotide polymorphisms (MNPs), insertions, deletions, and block substitutions.

The HID SNP Genotyper plug-in is designed to be an integrated tool, providing streamlined analysis and reporting for the Precision ID Identity Panel and Ancestry Panel. It uses the Torrent Variant Caller to identify genotypes at specific hotspot locations and performs biogeographical ancestry prediction, Y lineage prediction, andrandom match probability (RMP) computation.

Webinars

Adapting next-generation sequencing (NGS) for forensics is not a paradigm shift —Dr. Bruce Budowle, University of North Texas Health Science Center

Introducing mitochondrial DNA sequencing by NGS technology —Dr. Walther Parson, Institute of Legal Medicine at Innsbruck Medical University

Accelerate your forensic DNA analyses with Ion Torrent NGS automation —Joseph Chang, Thermo Fisher Scientific

Customer videos

MPS of STRs in forensic DNA analysis

Forensic scientists need to differentiate genetic profiles from complex forensic DNA mixtures, such as those commonly associated with crime scenes. But complicating factors, such as DNA degradation, mixtures and/or insufficient starting material, may prevent an estimated 30–40% of samples from generating conclusive results when using traditional capillary electrophoresis–based approaches. Now, by using the Applied Biosystems Precision ID GlobalFiler NGS STR Panel v2 and Converge Software 2.0, labs can effectively retrieve more information from these mixed, degraded or limited DNA samples.

Watch video
Mitochondrial DNA analysis in human identification

Imagine that you have a small, aged bone fragment or charred remains after a fire, a tooth that has been buried and exposed to the environment for years to decades, or possibly a single hair shaft. How would you even begin to make an identification to reconnect these remains with family members? Walther Parson, PhD from the Institute of Legal Medicine, Innsbruck Medical University discusses a number of cases his lab has worked on, using mtDNA analysis to make critical identifications.

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Next-generation sequencing for forensic DNA analysis

Next-generation sequencing and the ability to multiplex many markers for a single sample has gained acceptance within the forensic community. There are a number of SNP classifications that are currently being investigated, including identity SNPs, phenotypic SNPs, and biogeographic ancestry SNPs. Executive Director Soizic Le-Gunier discusses how Institute Genetics Nantes Atlantique (IGNA) uses the various technology options, and how SNP genotyping will have an impact in the future.

Watch video