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Precision ID NGS System for human identification

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Targeted sequencing for forensic DNA analysis

The Applied Biosystems™ Precision ID NGS System for human identification can help you solve tough cases by getting more information from your challenging samples. Adopting NGS (next-generation sequencing) for forensic DNA analysis in your laboratory is now simpler than ever, when you combine the Ion Chef™ System and Ion S5™ or Ion S5™ XL Systems with forensically relevant Precision ID panels that utilize Ion AmpliSeq™ technology.

With as little as 1 ng of DNA input, you can quickly and easily analyze your challenging casework samples with as few as 5 pipetting steps and 45 minutes of hands-on time. 

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

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

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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

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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

 

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

STR

Precision ID GlobalFiler NGS STR Panel§

2

8

16

* 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.
§ Minimum 500x coverage.

Analyze DNA mixtures more efficiently

The Applied Biosystems™ Precision ID GlobalFiler™ NGS STR Panel includes the same 21 autosomal STRs, along with a Y indel and amelogenin sex markers found in the GlobalFiler DNA amplification kit. Instead of using SE33, this panel includes 9 additional multiallelic STR markers (for a total of 33 targets) to aid in mixture interpretation for complex casework samples. Using minimal input of 1 ng of DNA, this targeted forensic marker panel enables sample extraction to genotypes in less than two days using the HID STR Genotyper plug-in.

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

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.

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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.


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].

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.

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

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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 
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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.
See the Ion S5 System in action ›
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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.

By expanding the functionality of the current on-board software, plug-ins offer a powerful means to manage a full range of HID applications. Torrent Suite Software allows you to customize your analysis at the end of each run through the use of different plug-ins available in the Ion Community.

  • Torrent Variant Caller (TVC) is a genetic variant caller and is specially optimized to exploit the underlying flow signal information in the statistical model to evaluate variants. TVC can be used to analyze mtDNA data at both the whole genome and control region panels.
  • HID SNP Genotyper is a plug-in 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 the genotypes at specific hotspot locations, performs bio-geo ancestry Y lineage prediction, and computes Random Match Probability (RMP).
  • The Ion S5 systems with the HID SNP Genotyper plug-in display results on an admixture predication map, thereby facilitating analysis.
  • The HID STR Genotyper plug-in analyzes sequencing data from short tandem repeat regions and generates allele calls along with their sequence content. Interactive allele coverage charts and quality metrics for each locus simplify the complexity of analyzing STRs using next-generation sequencing. The allele calls can then be exported and utilized for further downstream applications like mixture analysis or database searches.

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