introducing the applied biosystems precision id ngs system...
TRANSCRIPT
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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
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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
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