Agilent NGS Innovations for Cancer Research
Tim Wise
Genomics Product Specialist
Diagnostics and Genomics Group
PR7000-0837
Agilent acquires Cartagenia enabling
clinical analysis of genomic data
2005 2009 2012 2000
Agilent ships first
DNA microarrays
Agilent acquires Dako, leader in cancer
diagnostics
Diagnostic and Genomics Group formed to
lead Agilent’s entry into clinical sciences
2015
Array-based comparative genomic
hybridization introduced
Agilent begins transformation into
a life sciences company
NGS enters new era with Agilent’s
selective sequencing technology
SureSelect
Agilent Technologies Delivering innovations that advance human health
ISH product portfolio enables
higher resolution ISH
2016
Agilent announces investment in
Lasergen to move NGS
technology forward
2017
Agilent acquires Multiplicom to expand
clinical genomics workflow solutions
Agilent acquires Halo Genomics to grow
sequencing technology portfolio
2011
PR7000-0837
Precision Medicine and
Personalized Therapy
Agilent in the Fight Against Cancer Agilent expertise spans the entire spectrum of technologies
FFPE Sample
Handling
Molecular
Assays
• True leader in
target enrichment
• Fast and easy customization of molecular assays to fit your needs
• History of translational
success with arrays
• A growing menu of FISH and CISH probes for FFPE samples
• FFPE-compatible target enrichment platform and QC assays
• Unmatched CDx development expertise
• Trusted partnerships with major pharmaceutical companies
Tissue-based
Diagnostics
• Integrated automation for tissue-based staining
• Continuous and flexible loading of IHC and ISH assays
• Rich portfolio of antibodies and ISH probes
Companion
Diagnostics
Next
Generation
Sequencing
Data Analysis
Pipelines
Companion
diagnostics
FFPE to
Molecular
Assays
Staining
solutions
Molecular
Assay
Expertise
Genomics and Molecular
Analysis Routine Diagnostics
For Research Use Only.
Not for use in diagnostic procedures.
PR7000-0837
Fight Cancer Molecular Dx is revolutionizing cancer treatment
Number of actionable mutations
in lung cancer is constantly
increasing
• MDx(1) techniques have significantly
increased the understanding of the
underlying driver mutations
• An increasing number of these
mutations have become actionable with
new drugs (e.g. Iressa, Xalkori and
Tarceva)
• By using NGS and FISH together,
almost all of the currently actionable
mutations in lung cancer can be
identified
(1) Molecular Diagnostic
Few actionable mutations
by PCR & Sanger
2000
Many actionable mutations
by NGS & FISH
2014
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Agilent NGS products by workflow
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
DNA Targeted-Seq: SureSelect + HaloPlex
Methylation Targeted-Seq:
SureSelect RNA Targeted-Seq:
SureSelect
Whole genome sequencing:
SureSelect QXT
Transcriptome sequencing:
SureSelect strand-specific
A Broad NGS Portfolio to Advance Constitutional and Cancer Research
SureDesign
SureCall
Cartagenia Bench Consortium
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Target Enrichment: Focus on what Matters
Key Goals of Target Enrichment
• Focus on a subset of the genome
• Achieve greater depth in targeted regions
- Discover more mutations, SNPs and Indels
• Lower sequencing costs and obtain faster time to result
gDNA
Enriched Targets
SureSelect HaloPlex
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Two target enrichment platforms
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
• Hybridization-based enrichment (1.5 days)
• Most published, gold standard platform
• Uniform enrichment for large and/or custom panels
• Molecular Barcodes with HS-XT coming in May
• Advanced amplicon-based enrichment (<1 day)
• Ideal balance of workflow and performance
• <1% allele frequency detection with molecular
barcodes
Molecular
barcode
Tailoring and updating gene panel content
- Minimal optimization
- Catalog quality
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
SureSelect ClearSeq Cancer Research Panels
COMPREHENSIVE
FOCUSED
Fully customizable! Power up a catalog product with additional content, or
design using your own targets.
ClearSeq
AML
ClearSeq
Cancer
(Hotspots)
Flexibility
Kinome
OR
ClearSeq Comprehensive Cancer targets 151 genes
New in May
HS-XT with
Molecular Barcodes
Higher Sensitivity
for minor allele
frequency detection
below 1%
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
High-output Desktop
RESEARCH AND
TRANSLATIONAL CLINICAL RESEARCH
SureSelect
Human All Exon V6
OneSeq Constitutional
Research Panel
SureSelect
Clinical Research Exome v2
SureSelect
Focused Exome
ClearSeq
Inherited Disease
Capture Size
and # Genes
58Mb
whole exome
28Mb
genomewide backbone +
disease-focused mutation
panel
66Mb
whole exome
16Mb
~5700 genes
10.5Mb
~2800 genes
Key Features
Best uniformity
Best exome-wide
breadth and depth of
coverage
Copy number and LOH in
addition to SNPs and Indels
Increased depth in
disease-associated regions
Includes intronic disease-
associated regions
Desktop exome
Targets ONLY disease-
associated targets
ONLY targets genes
known to cause
inherited disorders
Agilent SureSelect Exomes A range of options for the flexibility you need
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
SureSelect Human All Exon V6 Bridging the gap
Coverage gaps in exome sequencing
Most comprehensive content
All Exon V6 + COSMIC
All Exon V6 + UTR
All Exon V6 + Custom
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
SureSelectXT HS
Coming Soon!
What is it?
• Agilent’s highest sensitivity hybrid capture-based library prep and target
enrichment solution for NGS
What does it do?
• 10 ng input
• Optimized for high-quality intact DNA, low- and high-quality FFPE DNA
• Molecular barcode (MBC) tagged libraries increase positive predictive value (PPV)
• Higher complexity libraries with higher percentage reads in targeted regions
• 90 minute hybridization and master-mixed reagents for faster, more efficient workflow
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
SureSelect XT RNA Enrichment:
Using All Exon
V6 + UTR
FFPE Direct to Capture
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
SureSelect XT RNA Enrichment:
Strand Specific
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Sample prep QC
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
Sample prep QC: save operational cost & ensure data quality
2100 Bioanalyzer: widely accepted QC standard
• Up to 12 samples, manual
4200 tapestation: New release
• 96 sample walkaway operation
• Scalable throughput at a constant cost
• Ready-to-use consumables
NGS FFPE QC kit
• Qualify and quantify amplifiable
DNA in challenging samples
• Help optimize library prep workflow
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Analysis, interpretation and reporting
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
Cartagenia bench lab for molecular pathology
• Variant assessment and reporting
• Key features
• fast turnaround time
• Molecular profile in tumor-type context
• Clinical grade reports
SureCall: Make NGS analysis easy, fast, and accurate
• Alignment and variant calling
• Simple 3-step workflow
• Fast time-to-results
Analysis Reporting
For Research Use Only. Not for use in diagnostic procedures marketed in the USA as exempt Class I Medical Device and in Europe and Canada as a Class I Medical Device
PR7000-0837
Sequencer
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
• Houston, Texas based
• Proprietary “lightning terminators”
sequencing chemistry
• $80M investment in Lasergen (48% stake)
• To provide end-to-end NGS workflow
solution
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.
Agilent NGS for pathology
Automation
Library Prep /
target enrichment QC Sequencing Analysis
Interpretation /
Reporting
Questions?
For customers in a clinical
environment, ask your
Agilent / Cartagenia
representative for more
information about our new
Alissa interpretation &
reporting solution.
PR7000-0837
For Research Use Only.
Not for use in diagnostic procedures.