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Transcript of Torrent Cluster System
Ion Torrent™ Informatics Solutions
Francisco Hernandez-Guzman, PhD, MBA
Product Manager - Bioinformatics
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Ion Torrent™ Informatics solutions
Our software solutions support all of the Ion
Torrent instruments including the new
Ion S5™/S5™ XL systems.
The simplest NGS software supporting various
diverse sequencing applications.
Pre-installed software using pre-set parameters
and workflows for optimized results.
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End-to-end informatics solutions
DESIGN
Custom targeted
sequencing panel design
for any genome
Ion AmpliSeq™ Designer
Sequencing data analysis
and management
Torrent Suite™ Software
ANALYZE REPORT
Variant annotation,
sample comparison and
report compilation
Ion Reporter™ Software
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Ion AmpliSeq™ Designer
Customize
Targets Construct
Library
Prepare
Template
Run
Sequence
Annotate
Results
Ion S5™ Systems or
Ion PGM™ System
Ion Chef™ System or
Ion OneTouch™ 2 System
Ion AmplISeq™ Library Kit or
Ion AmpliSeq™ Custom Panels
Ion AmplISeq™ Designer
Enter genes online in minutes Torrent Suite™ Software Ion Reporter™ Software
Analyze Data
Ion AmpliSeq™ Designer
Create/order panels in minutes
Customize
Targets
www.ampliseq.com
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Access pre-designed panels
Ion AmpliSeq Designer
Ready-to-Use and Community Panels
Broad set of Mendelian diseases research panels • Cardiovascular, hematology, neurological and more…
Noonan research panel
Tuberculosis research panel
Ready-to-Use panels:
• Oncology Research
• Inherited Disease Research
• Exome Sequencing
• More…
Community Research panels:
• Oncology Research
• Developmental Disorders
• Dementia Research
• More…
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Easily create/add/review/order your own designs
Ion AmpliSeq Designer
Custom targeted sequencing panels for any genome
Convenient one-stop shop enables easy ordering for all Ion AmpliSeq kits-
from custom designs to ready-to-use panels
Order 1 2 3 4 Create: Add: Review:
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Customize designs for your research
Custom Gene Fusions
Copy Number Variation
Ag Bio /GBS
Design custom panels for a variety of applications:
Hotspot variant detection
Gene Expression
Start with a little as 1ng of DNA or 500pg of RNA
Includes design options optimized for:
cfDNA FFPE or degraded DNA or RNA
Targeted re-sequencing
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Torrent Suite™ Software
Customize
Targets Construct
Library
Prepare
Template
Run
Sequence
Ion S5™ Systems or
Ion PGM™ System
Ion Chef™ System or
Ion OneTouch™ 2 System
Ion AmplISeq™ Library Kit or
Ion AmpliSeq™ Custom Panels
Ion AmpliSeq™ Designer
Create/order panels in minutes
Annotate
Results
Analyze Data
Ion Reporter™ Software
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Expanded capabilities with plug-ins available through the Ion Community
Intuitive web interface makes it fast and easy to plan, monitor, and view sequencing runs with any Ion Torrent instrument
Plan, Monitor & Review Sequencing Results
Torrent Suite Software and Torrent Server
Easy-to-use software for automated sequencing data analysis
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Set Up with Pre-configured Templates
Now with Whole Transcriptome
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Monitor Progress of Ion S5 Runs
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Monitor Progress of Ion AmpliSeq on Ion Chef™ Runs
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Access RNA Application-specific Plugins
Whole Transcriptome (RNASeqAnalysis) Ion AmpliSeq Transcriptome (ampliSeqRNA)
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Torrent Storage™ / Torrent Cluster™ Systems
Torrent Storage™ Devices Secure data storage and archiving
Fast and easy data retrieval—locally store and organize your sequencing data on-site
Scalable solutions—customize a storage solution with the ability to to expand storage as needed
Dependable data storage—store valuable sequencing data with individual disk failure tolerance to prevent data loss
Torrent Cluster™ System Multiple instrument data analysis
Customizable solutions—flexible modular design allows compute and storage customization
White glove service and support—our bioinformatics and HPC teams design, configure, verify, install, and support your Torrent Cluster™ System
Scalable HPC and storage— independently scale compute or storage components as needed
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Ion Reporter™ Software
Customize
Targets Construct
Library
Prepare
Template
Run
Sequence Analyze Data
Ion S5™ Systems or
Ion PGM™ System
Ion Chef™ System or
Ion OneTouch™ 2 System
Ion AmplISeq™ Library Kit or
Ion AmpliSeq™ Custom Panels
Ion AmplISeq™ Designer
Enter genes online in minutes Torrent Suite™ Software
Annotate
Results
Ion Reporter™ Software
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Full spectrum of algorithms and research applications
Ion Reporter Analysis Workflows Pre-configured and customizable for optimal results
Gene Fusion Analysis Detect and annotate known and
non-targeted gene fusions
Aneuploidy (PGS) Analysis Detect aneuploidies and large chromosome abnormalities
16S Metagenomics Analysis Determine the microbial diversity in samples
CNV Analysis Identify copy number variations (CNV) in Ion AmpliSeq™ workflows
Inherited Disease Trio Analysis Explore variants within a pedigree
Tumor -Normal Analysis Identify somatic mutations using advanced statistical approaches
Somatic and germline detection and annotation of SNPs, Indels, CNVs, Fusions
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Ion S5 System: full support in Ion Reporter
Ion Reporter Software supports analysis of Ion S5 sequencing Automated analysis of all 5-series chip types
All chip types and kits are all supported (5-series, 3-series, P-series) Use the same analysis workflows for Ion S5 data as used for Ion PGM™ and Ion Proton™ data.
Automatically upload and launch Ion S5 analyses Easy uploading from Torrent Suite and launching of analysis workflows simplifies routine data generation
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16S workflow improvements
Ion Reporter Software version 5.0 : 16S workflow Harnessing algorithms from the QIIME software, primer-specific results export
Alpha diversity rarefaction curves at Species, Genus, and Family-level Beta diversity relative differences between multiple samples
Primer set-specific results export lets you easily independently explore fasta results from each V-region primer set in the Ion™ 16S Metagenomics kit
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Aneuploidy Improvements
Ion Reporter Software v. 5.0 New workflow for our new Ion ReproSeq™ PGS kits and new PGS visualization and reporting
1 2 3 View batches of results, filter on quality metrics, New PGS sample attributes:
Drill down to detailed information on any sample:
Customized Reports on batches or single samples:
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Oncology Research: Oncomine™ Focus Assay support
Ion Reporter Software 5.0 and Oncomine Assays New somatic CNV detection and Fusions details and algorithms
CNV algorithm improvements to handle sample and lab variation automatically Fusion call improvements 1) “Overall Fusions Call” summarizing results, and 2) enhanced calling and QC metrics
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Customize Table Preferences for any application
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Thermo Fisher Cloud integration of Ion Reporter
Share & collaborate
Store, organize & manage data.
Design Experiment
Analyze Data
Confirm Results via Cross-platform analysis
Experiment Setup & Monitor runs
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Secure on-site data analysis
Ion Reporter™ Server Combined software and hardware solution
Maintain a secure environment - controlled, local access on a HIPAA compatible* server
*Designed to the same robust data security standards as are described in the HIPAA rules, standards, and implementation guides
Accelerate clinical research- automated analysis pipelines with fast upload and analysis times
Control software versions – update on your timeline
Archive and Restore Samples and Analyses - back up and retrieve from Torrent Storage devices.
Multiple Organizations – create multiple independent Organizations on your Ion Reporter Server
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COMING SOON
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Ion Torrent next-generation sequencing product portfolio
Supporting genomic analysis applications from basic research to molecular diagnostics
Ion PGM, Ion Proton, Ion Chef and Introducing the Ion S5 Series Systems
For Research Use Only
Ion PGM™ Dx System For In Vitro Diagnostic Use
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Coming soon (December 2015):
Ion PGM™ Dx System with Combined Functions Software
Ion PGM™ Dx System
IVD Mode
Empowering clinical customers to bring NGS into their laboratories, using a combined function platform that offers
a secure IVD Mode for molecular diagnostic tests and an Assay Development Mode* for clinical research.
Product Concept: Combined Function System
Assay Development Mode (RUO)
• Will enable users to run a variety of assays for clinical research
• Will expand system functionality
• Will enable a mechanism in partnership with Thermo Fisher Scientific to build menu and develop IVD assays
The content provided herein may relate to products that have not been officially released and is subject to change without notice.
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Questions?
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
© 2015 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the
property of Thermo Fisher Scientific and its subsidiaries unless otherwise
specified.
The content provided herein may relate to products that have not been officially
released and is subject to change without notice
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Appendix
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Top points to remember:
Free access
Intuitive interface
DNA or RNA
Any Genome*
Annotation support
= flexibility + ease-of-use
Ion AmpliSeq™ Designer
* Any genome with a full or partial reference genome Annotation supported for Human and mouse only.
www.ampliseq.com
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Barcode-aware Torrent Variant Caller™ Plugin
My custom CHP params
My custom params 2
My custom params 2
Testing new params
Generic - PGM - Somatic - Low
Run the plugin with different
parameters and BED files per
barcode
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Simplify your path to research results
Ion Reporter™ Software
Automated variant detection, annotation and reporting
Security for your data with controlled access, role-based logins and locked workflows
Automate and simplify data analysis with pre-configured analysis workflows optimized for a variety of applications
Quickly focus on biological relevance with rich annotations from >25 public databases and advanced filtering capabilities
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Application-focused Improvements
Ion Reporter™ Software 5.0 More Improvements for all Applications
PDF Report improvements • New interactive Preview screen • Customize report sections • X of Y page numbering • Template choice persists with workflow
My Variants improvements • Upload vcf files into MyVariants • Display all My Variants and details in
new expandable table
Expanded Filter chain creation Construct customized nested filter chains using intuitive new interface
Improved Fusion calling • Fusions’ Present / Absent / No call based
on isoform presence or absence and 3'/5' imbalance values
• Sample QC based on Total mapped reads • Barcode Crosstalk QC for Fusion calls • Overall Fusion Call • Reason for No Calls given in the Detection
column
Customize Analysis Results table • Add, Hide, Reorder and Resize any
column in the Summary tab • Save in “Table Preferences” list • Workflow adopts selected Preferences.
Organize data by “Projects” Use the “Project” attribute to group samples
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Oncomine Knowledgebase Reporter (RUO Workflow)
Oncomine® Knowledgebase Reporter
Ion Reporter™
Workflow*
Lab Generated
Report*
Research
Laboratory
• FDA labels • NCCN Guidelines • Clinical trial evidence
*For Research Use Only. Not for use in diagnostic procedures.
Genetic variants
Associated published
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Ion PGM Dx System
Ion PGM Dx Torrent Suite v5.0 Report
Coming Soon (December 2015)…
System functionalities in Assay Development Mode*
Functional Capabilities
Assay Development Mode
Application types • Germline or Somatic • SNPs, Indels, CNVs
• RNA Fusions • 16S Metagenomics
Pre-loaded templates
• 10 preloaded template files for Oncomine™ assays and AmpliSeq™ panels
Workflows • Ion OneTouch™ Dx instruments • Ion Chef™ System
Reagents / Consumables
• Ion PGM™ Dx Consumables* • Ion PGM™ Select Consumables • Ion Hi-Q™ Consumables
Chips • Ion 318™ Dx Chip • 3-series BC Chips (314 / 316 / 318)
For Research Use Only. Not for use in diagnostic procedures. *The content provided herein may relate to products that have not been
officially released and is subject to change without notice.
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Combined Function Software Expands Capabilities of PGM
Dx System - Comparing IVD to Assay Development Mode
Functional Capabilities
IVD Mode Assay Development Mode
Application Template (Support Custom
Panel)
• Germline DNA Validated (SNP/Indels)
• Germline DNA Validated (SNP/Indels) • Germline DNA (SNP/Indels/CNV) • DNA and Fusions (SNP/Indels/CNV/Fusion) • RNA Fusions • Somatic DNA (SNP/Indels/CNV) • 16S™ Metagenomics • Generic Sequencing Application
Existing Factory Assay
• NA • Oncomine™ Focus Assay (OCP 50) • Solid Tumor DNA Panel • Solid Tumor RNA Panel • Ion AmpliSeq™ Colon and Lung Cancer Panel v2 • Ion AmpliSeq™ RNA Lung Fusion Panel • Ion AmpliSeq™ Cancer Hotspot Panel v2 • Ion AmpliSeq™ BRCA Community Panel • Ion AmpliSeq™ AML Community Panel • Ion AmpliSeq™ CFTR Panel • 16S Metagenomics Kit
Sample Type DNA from whole blood Both DNA and RNA derived from blood, FFPE, bacteria culture
Workflow 200bp on OT 200bp & 400bp on OT and Chef
Reagent PGM Dx Consumables PGM Dx Consumables; PGM Select Consumables; Hi-Q™ Consumables
Chips 318 Dx Chip 318 Dx Chip; 318 Select Chip; 3-series BC chips (314/316/318)