Introducing the Applied Biosystems TM Precision ID NGS System for Human Identification

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1 Introducing the Applied Biosystems TM Precision ID NGS System for Human Identification Sheri J. Olson Director, Product Management Casework Human Identification

Current challenges for forensic scientists Difficult mixture interpretations Partial or no profiles from highly degraded or trace samples No STR

2 Current challenges for forensic scientists Difficult mixture interpretations Partial or no profiles from highly degraded or trace samples No STR profile matches in DNA database Unknown tissue/ body fluid origin Complex kinship cases and/or familial searches Laborious sequencing of mtdna by CE 2

3 NGS is a KEY to getting more information for forensics Sequencing allows greater depth of genetic information Multiplexing hundreds of the same markers i.e. SNPs Multiplex different types of markers: SNP+ STR Simultaneously analyze multiple samples (barcoding) Target small amplicons to recover DNA with challenging samples Massively Parallel Sequencing 3

Forensic customers needs for NGS Low input validated workflows Easy sequencing workflow for a forensic lab I don t want to have to remap my entire

4 Forensic customers needs for NGS Low input validated workflows Easy sequencing workflow for a forensic lab I don t want to have to remap my entire lab workflow Data storage solutions for cloud & non-cloud labs Easy to use and interpret data analysis Forensically relevant content for my region 4

5 Future of Forensics: CE + NGS = Integrated forensics workflow 50-70% of Casework STR by CE Analysis GMID-X DNA Extraction Quantification By qpcr Converge Platform Mixtures Degraded Investigative leads Precision ID NGS System Brings CE + NGS data together NGS will not displace CE for the foreseeable future Position NGS for difficult samples Integrate NGS into current workflow Create integrated NGS workflow 5

6 HID NGS System: Simplest sequencing workflow Applied Biosystems Precision ID System Ion Chef System Ion S5 and S5 XL Sequencing Systems Torrent Suite Software and Converge Genomic DNA Construct library Prepare template Massively parallel sequencing Analyze data 6

Precision ID System: The future of forensics Ion Chef System Ion

Template Preparation (15 mins) Sequencing Only 3-5 pipetting

for targeted sequencing Pipette Sample and primer pools into the

Pipette library into the Ion Chef for templating, enrichment,

7 Precision ID System: The future of forensics Ion Chef System Ion S5/S5 XL System Dual Function: -Ion AmpliSeq Library (15 mins) Template Preparation (15 mins) Sequencing Only 3-5 pipetting steps per sample from DNA to data Optimized workflow efficiency for targeted sequencing Pipette Sample and primer pools into the Ion Chef for library prep Load Cartridge into the Ion Chef Pipette library into the Ion Chef for templating, enrichment, chip loading Load Cartridge into the Ion Chef Transfer Chip to Ion S5 for Sequencing 7

Precision ID System: Ion Chef Automated Workflow Run Ion

System Load Sequencer Target Amplification Bead templation

load Ion onto PGM Ion PGM or Ion Proton Instrument System or

8 Precision ID System: Ion Chef Automated Workflow Run Ion AmpliSeq Panel on Ion Chef System Run Templating on Ion Chef System Load Sequencer Target Amplification Bead templation Remove chips chips from from Ion Chef and System load onto and load Ion onto PGM Ion PGM or Ion Proton Instrument System or Ion S5 System Digestion and Ligation Enrichment Equalizer Chip Loading 8

Precision ID System: Ion Chef System Automated Workflows For Walk-Away Convenience Single use reagent cartridges prepackaged and ready to go Automated system cleaning following an instrument run,

9 Precision ID System: Ion Chef System Automated Workflows For Walk-Away Convenience Single 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 9

Precision ID System: Ion S5 and S5 XL Systems Simplest and Fastest targeted sequencing system with the lowest capital investment Simplest NGS workflow for

10 Precision ID System: Ion S5 and S5 XL Systems Simplest and Fastest targeted sequencing system with the lowest capital investment 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 cartridgebased reagents 10

Sequencing Reagent Cartridge Wash Solution & Waste

11 S5 & S5XL Plug and Play Reagents Large HD Touchscreen Temp Controlled Chip Clamp Standard Power Gas Water Sequencing Reagent Cartridge Wash Solution & Waste Cartridge (behind W2 Solution) Automated Cleaning Solution 11

Precision ID System Built for Forensics For challenging casework samples with a

Workflow Leverage existing HID workflow - Sample Collection, Extraction and Quant NEW - NGS

S5/XL) -Specific markers for specific questions: STRs, SNPs, Mito, Body Fluid, etc.

12 Precision ID System Built for Forensics For challenging casework samples with a standardized HID-specific NGS system Instruments, Kits, SW & HID Protocols Similar to CE Workflow Leverage existing HID workflow - Sample Collection, Extraction and Quant NEW - NGS Forensic panel content More information per sample / case HID 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. 12

13 Precision ID System: Targeted information to resolve challenges Degraded & Trace DNA STRs Identity SNPs Analyze Complex Kinship & Familial Cases STRs Identity & Y SNPs Missing Persons & Remains mtgenome or CR mtdna Generate More Investigative Leads Ancestry & Phenotype SNPs Body Fluid Improve Mixture Interpretation STRs Examine Molecular Autopsy Body Fluid Time of Death Inherited Diseases 13

14 Analyze highly degraded DNA or trace DNA 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 Precision ID Identity Panel 14 * Based on survey results conducted by Life Technologies in Feb 2013.

15 Precision ID Identity Panel Identify degraded casework samples in less than a day Ready-to-use panel consists of 124 SNPs P i ranges from 1x x10-35 Small amplicon size (average132;141 nt) for degraded DNA Only 1 ng DNA recommended 99.99% of concordance for 43 Ken Kidd SNPs 15

Raw genotypes can reference own personal frequency

16 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 16

17 Precision ID SNP Genotyper for Identity panel Y Genotypes Y Clades note: not all snps are displayed here ISOGG 2014 tree. 17

18 Help generate more investigative leads 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 Precision ID Ancestry Panel 18

Precision ID Ancestry Panel Obtain biogeographic ancestry information for investigative leads Ready-to-use panel consists of 165 autosomal SNPs

19 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 19

20 Precision ID SNP Genotyper for Ancestry panel Admixture prediction Population likelihoods 20

streamline the mtgenome sequencing workflow built for degraded samples Average

21 Analyze missing person 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 Average amplicon length is 163nt Average amplicon overlap of 11nt Precision ID mtgenome & CR Panels 21

22 New Chemistry Improvements: Ion Chef Library & Templating on Ion S5 22

within the repeat and flanking sequence Example: A 20 allele is not always just a 20 Individual A 20 repeats: TCTA [GGAA]

23 Enable more efficient analysis of DNA mixtures 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 Example: A 20 allele is not always just a 20 Individual A 20 repeats: TCTA [GGAA] 13 [GGCA] 7 Individual B 20 repeats: TCTA [GGAA] 14 [GGCA] 6 D2S1338 Repeat Structure Precision ID GlobalFiler STR NGS Panel 23

24 Precision ID STR Genotyper Dashboard Sample Dashboard Sample Details 24

25 Precision ID STR Genotyper: The value of NGS Homozygous at allele 14 Different sequence variations 25

26 Examine molecular autopsy 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 Ion AmpliSeq Cardiovascular Research Panel Ion AmpliSeq Hematology Research Panel Ion AmpliSeq Inherited Disease Panel 26

27 TSS & Converge Torrent Suite Software Coming soon 27 Streamlined data management, centralized analysis, reporting & storage.

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

28 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 NEW - NGS Forensic panel content 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. 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 28

29 AmpliSeq.com 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 29

30 Ion Community.com Sign up for a free account on Ion Community! 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 30

New Training Delivery: Customer Experience

CA Customer Experience Centers: Targeted NGS

internal technical teams and customers needs

courses for new users, prospective customers, TL

Engage new HID customers with specialized, onsite

31 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 31

3500/xl Genetic Analyzer Ion S5 and Ion PGM Systems STR genotyping SNP genotyping (small multiplex) mtdna Sequencing

32 NGS and CE: a powerful combination for forensics Complement existing forensic DNA analysis workflows with NGS capabilities. 3500/xl Genetic Analyzer Ion S5 and Ion PGM Systems STR genotyping SNP genotyping (small multiplex) mtdna Sequencing (control region) STR genotyping/sequencing SNP genotyping (large multiplex) Whole mtgenome sequencing mrna (tissue/body fluid ID, etc.) Expanding your Casework Workflow with the Proven Performance of CE & the Power of NGS 32

Thank Answers you that for empower your attention! Questions?

power of NGS! Ion S5 and S5 XL Sequencing Systems Go to thermofisher.

AmpliSeq Ancestry Panel, and QuantiFiler Trio kit, QuantiFiler HP kit are

When used for purposes other than Human Identification, the instrument

Not for use in diagnostic procedures. 2016 Thermo Fisher Scientific Inc.

33 Thank Answers you that for empower your attention! Questions? 3500 Analysis Maximize results with the proven performance of CE and the power of NGS! Ion S5 and S5 XL Sequencing Systems Go to thermofisher.com/hid-ngs Follow us at human_id 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 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 33

Expand your forensics workflow with the Precision ID NGS System for human identification

Expand your forensics workflow with the Precision ID NGS System for human identification Integrate NGS into your forensic DNA lab workflow The Applied Biosystems Precision ID NGS System for human identification