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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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


Create/order panels in minutes

Customize

Targets

www.ampliseq.com

http://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 PGM™ System






Create/order panels in minutes

Annotate

Results

Analyze Data


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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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Customize

Targets Construct

Library

Prepare

Template

Run

Sequence Analyze Data


Ion PGM™ System





Ion AmplISeq™ Designer

Enter genes online in minutes Torrent Suite™ Software

Annotate

Results


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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


* Any genome with a full or partial reference genome Annotation supported for Human and mouse only.

www.ampliseq.com

http://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


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)

Torrent Cluster System

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