Sheri J. OlsonDirector, Product Management – CaseworkHuman Identification

Introducing the Applied BiosystemsTM

Precision ID NGS System for Human Identification

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Current challenges for forensic scientists

Unknown tissue/body fluid originUnknown tissue/body fluid origin

Complex kinship cases and/or familial

searches

Complex kinship cases and/or familial

searches

Laborious sequencing of mtDNA by CE

Laborious sequencing of mtDNA by CE

Difficult mixture interpretationsDifficult mixture interpretations

Partial or no profiles from highly degraded

or trace samples

Partial or no profiles from highly degraded

or trace samples

No STR profile matches

in DNA database

No STR profile matches

in DNA database

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NGS is a KEY to getting more information for forensics

Massively Parallel Sequencing Massively Parallel Sequencing

Sequencing allows greater depth of genetic

information

Sequencing allows greater depth of genetic

information

Multiplexing hundreds of the same markers

i.e. SNPs

Multiplexing hundreds of the same markers

i.e. SNPs

Multiplex different types of markers: SNP+ STRMultiplex different types of markers: SNP+ STR

Simultaneously analyze multiple samples

(barcoding)

Simultaneously analyze multiple samples

(barcoding)

Target small amplicons to recover DNA with challenging samples

Target small amplicons to recover DNA with challenging samples

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Low input validated workflows

I don’t want to have to re-

map my entire lab workflow

Easy sequencing workflow for a forensic lab

Easy to use and interpret data

analysis

Data storagesolutions for cloud & non-cloud labs

Forensicallyrelevant content

for my region

Forensic customers needs for NGS

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Future of Forensics: CE + NGS = Integrated forensics workflow

DNAExtraction

DNAExtraction

QuantificationBy qPCR

QuantificationBy qPCR

50-70% ofCasework

MixturesDegraded

Investigative leads

STR by CESTR by CE

ConvergePlatform

ConvergePlatform

AnalysisGMID-XAnalysisGMID-X

Brings CE + NGS data together

Precision IDNGS SystemPrecision IDNGS System

NGS will not

displace CE for the

foreseeable future

Position NGS for

difficult samples

Integrate NGS into

current workflow

Create integrated

NGS workflow

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HID NGS System: Simplest sequencing workflow

Genomic DNA Construct library Prepare template Massively parallel

sequencingAnalyze data

Ion Chef™ SystemIon S5™ and S5™ XL Sequencing Systems

Torrent Suite™ Software and Converge

Applied Biosystems™ Precision ID SystemApplied Biosystems™ Precision ID System

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Dual Function:

-Ion AmpliSeq Library (15 mins)

Template Preparation (15 mins)

Sequencing

Precision ID System: The future of forensics

PipetteSample and primer

pools into the Ion

Chef™ for library

prep

Pipettelibrary into the

Ion Chef™ for

templating,

enrichment, chip

loading

Transfer Chip to Ion S5™ for

Sequencing

Load Cartridge into

the Ion Chef™

Load Cartridge into

the Ion Chef™

Ion Chef™ System Ion S5/S5 XL System

Only 3-5 pipetting steps per sample from DNA to data

Optimized workflow efficiency for targeted sequencing

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Precision ID System: Ion Chef Automated Workflow

Run Ion AmpliSeq™ Panel on Ion Chef™ System

Target Amplification

Digestion and Ligation

Equalizer

Run Templating on Ion Chef™ System

Bead templation

Enrichment

Chip Loading

Load Sequencer

Remove chips from Chef and load onto Ion PGM™ or Ion

Proton™ Instrument

Remove chips from Ion Chef

System and load onto Ion PGM

System or Ion S5 System

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Automated Workflows For Walk-Away ConvenienceSingle use reagent cartridges –prepackaged and ready to go

Automated system cleaning –following an instrument run, clear the deck and

start the system cleaning function to minimize

potential contamination

Intuitive graphic user interface –after loading your library, samples, reagents and

consumables on the deck, simply select the run

parameters on the touch-screen interface and hit

‘go’.

On board reagent tracking –2D bar codes associated with all reagents and

consumables minimize the potential for user

error and ensure every run is set up correctly.

Confidence In Sequencing Results

Ion Chef™ automation helps to eliminate much of the day to day variation that exists in manual lab workflows to provide consistent results run-to-run & day-to-day

Precision ID System: Ion Chef™ System

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Precision ID System: Ion S5™ and S5™ XL Systems

• Simplest NGS workflow for targeted sequencing

• <15mins to set up a sequencing run

• <45mins total hands-on time from DNA to data with

Ion Chef™ System

• Fastest run time

• 3.5 hours from sequence to BAM files.

• Lowest capital investment

• Single platform for all targeted applications with

flexibility to scale from 5M - 80M reads

• Lowest DNA/RNA input requirements

• 1-10ng using Ion AmpliSeq™ technology

• <1ng for HID applications – coming soon

• Easy setup and training

• Single day installation and plug and play cartridge-

based reagents

Simplest and Fastest targeted sequencing system with the lowest capital investment

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Temp Controlled Chip Clamp

Wash Solution

&

Waste Cartridge(behind W2 Solution)

Sequencing Reagent

Cartridge

Large HD Touchscreen

Automated

Cleaning Solution

Standard Power

Gas

Water

S5 & S5XL Plug and Play Reagents

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Precision ID System – Built for Forensics

For challenging casework samples with a standardized HID-specific NGS system

Similar to CE WorkflowLeverage existing HID workflow- Sample Collection, Extraction and Quant

More information per sample / caseHID Individual Panels (PGM & S5/XL)-Specific markers for specific questions:

STRs, SNPs, Mito, Body Fluid, etc.

HID Solution Panels (S5/XL only)-Sets of markers for HID applications:

Mixtures, Investigative Leads, DVI, etc.

Instruments, Kits, SW &

HID Protocols

NEW - NGS Forensic

panel content

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Precision ID System: Targeted information to resolve challenges

mtGenome orCR mtDNA

STRsIdentity & Y SNPs

Degraded & Trace DNA

Complex Kinship & Familial Cases

Missing Persons & Remains

Analyze

STRs Identity SNPs

More Investigative Leads Ancestry & Phenotype

SNPsBody Fluid

Generate

Mixture Interpretation STRsImprove

Molecular Autopsy Body Fluid

Time of DeathInherited Diseases

Examine

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About 15% of casework samples yield partial or

no STR profiles due

to DNA degradation*

MiniFiler™ PCR kit is limited by the number of loci obtained

Touch and aged samples

highlight need for robust adjunct technology

Identity SNP information can

assist with increasing PI

Analyze highly degraded DNA or trace DNA

* Based on survey results conducted by Life Technologies in Feb 2013.

Precision ID Identity PanelPrecision ID Identity Panel

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Identify degraded casework samples in less than a day

• Ready-to-use panel consists of 124 SNPs

• Pi ranges from 1x10-31 – 6x10-35

• Small amplicon size (average132;141 nt) for degraded DNA

• Only 1 ng DNA recommended

• 99.99% of concordance for 43 Ken Kidd SNPs

Precision ID Identity Panel

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Precision ID SNP Genotyper for Identity panel

• RMP estimates from the 1000 genomes frequency data.

• Raw genotypes can reference own personal frequency database.

Random Match Probability (RMP) Autosomal Genotypes

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Y Genotypes

note: not all snps are displayed here

Y Clades

ISOGG 2014 tree.

Precision ID SNP Genotyper for Identity panel

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• No suspect and no STR profile matches in DNA database

• Ancestry or phenotype such as eye, hair, or skin color information can provide investigative leads to law enforcement officers

Help generate more investigative leads

Precision ID Ancestry PanelPrecision ID Ancestry Panel

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Precision ID Ancestry Panel

Obtain biogeographic ancestry information for investigative leads

• Ready-to-use panel consists of 165 autosomal SNPs

• Suitable for casework samples or degraded DNA

• Small amplicon size (average122;130 nt)

• Only 1 ng DNA recommended

• 99.77% of concordance for 55 Ken Kidd SNPs

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Precision ID SNP Genotyper for Ancestry panel

Admixture prediction

Population likelihoods

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Bone, teeth, and hair are the typical

biological sources left from missing

persons or remains

Bone, teeth, and hair are the typical

biological sources left from missing

persons or remains

Precision ID can streamline the

mtGenome sequencing workflow –

built for degraded samples

Precision ID can streamline the

mtGenome sequencing workflow –

built for degraded samples

Analyze missing person or remains

Average ampliconlength is 163nt

Average ampliconoverlap of 11nt

Precision ID mtGenome & CR PanelsPrecision ID mtGenome & CR Panels

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New Chemistry Improvements: Ion Chef™ Library & Templating on Ion S5™

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Example: A 20 allele is not always just a 20…

Individual A 20 repeats: TCTA [GGAA]13 [GGCA]7Individual B 20 repeats: TCTA [GGAA]14 [GGCA]6

• NGS STR solution can provide both allele number and base sequence for each repeat structure

• Additional resolution for individuals with the same allele repeat number using sequence dissimilarity within the repeat and flanking sequence

Enable more efficient analysis of DNA mixtures

D2S1338 Repeat Structure

Precision ID GlobalFiler™ STR NGS PanelPrecision ID GlobalFiler™ STR NGS Panel

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Precision ID STR Genotyper Dashboard

Sample

Dashboard

Sample Details

25

Precision ID STR Genotyper: The value of NGS

Homozygous at allele 14

Different sequence variations

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• NGS tools to assist sudden unexplained death (SUD) and Sudden Cardiac Death (SCD) investigations

• Assistance with post-mortem for patients who have died suddenly of unknown causes

13 Inherited Disease panels available

Examine molecular autopsy

Ion AmpliSeq™ Cardiovascular Research PanelIon AmpliSeq™ Hematology Research Panel

Ion AmpliSeq™ Inherited Disease Panel

Ion AmpliSeq™ Cardiovascular Research PanelIon AmpliSeq™ Hematology Research Panel

Ion AmpliSeq™ Inherited Disease Panel

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TSS & Converge

Streamlined data management, centralized analysis, reporting & storage.

Torrent Suite

Software

Coming soonComing soon

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Precision ID GlobalFiler™ NGS Mixture ID Panel

Precision ID GlobalFiler™ Mixture ID Panel – Early Access May 2017• For low level mixtures (LCN, Touch/Volume/Property/Serious Crime)• To determine how many contributors in a mixture sample

• Panel content:• Contains same GlobalFiler NGS STR Panel loci• Select set of identity SNPs added – to increase PI for degraded samples

• Select set of microhaplotypes added – to help identify # of contributors in a mixture

• Optimized for:• S5 / S5XL only• Converge SW• <1ng automated library prep on Ion Chef

• Panel to be put through SWGDAM Guided Validation

More information per sample / case

HID Individual Panels-Specific markers for specific questions: PGM / S5/XL

STRs, SNPs, Mito, Body Fluid, etc.

HID Solution Panels

-Sets of markers for HID applications: S5/S5XL

Mixtures, Investigative Leads, DVI, etc.

NEW - NGS Forensic

panel content

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Types of AmpliSeq™ Panels

• Pre-designed / ready to use Panels (HID Panels)

• Community – user created panels that can be shared within a community

• Custom – user created panels for specific researcher purposes

Ion Ampliseq Designer – design assistance and chip calculator

AmpliSeq.com

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Sign up for a free account on Ion Community!

https://ioncommunity.thermofisher.com

Ion Community is a great place to learn about getting started with Ion technology, access product resources, & share ideas with fellow Ion users.

Browse applications spaces, download product user guides, ask a question or sign-up for product updates in this interactive online community

• HID NGS Space on Ion Community

• https://ioncommunity.thermofisher.com/community/applications/hid

Ion Community.com

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New Training Delivery: Customer Experience Centers

Guilford, CT ‘Ion East’ Oyster Point, SSF CA

Customer Experience Centers: Targeted NGS Training Offerings

• Tailor training to meet internal technical

teams and customers’ needs

• Develop HID U. courses for new users, prospective customers, TL’s, etc.

• Engage new HID customers with specialized, onsite demo workshops

• Access NGS training data / case examples via Torrent marketing server

• View updates to panels and Converge software

Ten Centers Globally

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• STR genotyping/sequencing• SNP genotyping (large multiplex)• Whole mtGenome sequencing

• mRNA (tissue/body fluid ID, etc.)

• STR genotyping• SNP genotyping (small multiplex)

• mtDNA Sequencing (control region)

3500/xl Genetic Analyzer

NGS and CE: a powerful combination for forensics

Complement existing forensic DNA analysis workflows with NGS capabilities.

Ion S5™ and Ion PGM ™ Systems

Expanding your Casework Workflow with the Proven Performance of CE & the Power of NGS

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Ion AmpliSeq Identity panel, Ion AmpliSeq Ancestry Panel, and QuantiFiler Trio kit, QuantiFiler HP kit are For Research, Forensic or Paternity Use Only.

When used for purposes other than Human Identification, the instrument and the modules of the cited software are for Research Use Only. Not for use in diagnostic procedures.

©2016 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

Go to thermofisher.com/HID-NGSFollow us at human_id

Thank you for your attention!Answers that empower

3500Analysis

Ion S5 and S5 XL Sequencing

Systems

Maximize results with the

proven performance of

CE and the power

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