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Illumina’s Cancer Research Portfolio and Dedicated Workflows
Michael Sohn
Clinical Sales Specialist Spain&Italy 2017
For Research Use Only. Not for use in diagnostic procedures.
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Moving From Single Gene to Multi-Gene
Small tissue samples:
Lung biopsies Fine Needle Aspirates
An increasing number of variants of known significance
More variants to query More tests to be performed
The Challenge
How to find more with less?
Image from Chen et al., J Thorac Dis. 2013 Jun;5(3):E93-7. doi: 10.3978/j.issn.2072-1439.2013.04.17. Figure 2
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A potential future:
Broad panel adoption ensures coverage of future relevant biomarkers
Targeted Panels Broad Panels Genomes and
Exomes
A portion of translational biomarkers may become clinically relevant
Relevant Biomarkers
Translational Biomarkers
http://www.nature.com/nrc/journal/v16/n5/full/nrc.2016.35.html
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http://www.nature.com/nrc/journal/v16/n5/full/nrc.2016.35.html
Further along…
Genome/exome adoption may become necessary to cover ever expanding number of relevant biomarkers
Targeted Panels Broad Panels Genomes and
Exomes
Relevant Biomarkers
Translational Biomarkers
Biomarkers across
the genome may
become relevant
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TruSight Tumor 170 Content
Gene List and Variant Classification
● RAF1 ● CCDN3
● FGF19
● LAMP1
● TFRC
● ABL1
● AXL
● EML4
● ETS1
● ETV1
● ETV4
● ETV5
● EWSR1
● FLI1
● KIF5B
● NTRK1
● NTRK2
● NTRK3
● PAX3
● PAX7
● PPARG
● TMPRSS2
● ALK
● AR
● BRAF
● BRCA1
● BRCA2
● CDK4
● EGFR
● ERBB2
● ESR1
● FGFR1
● FGFR2
● FGFR3
● FGFR4
● JAK2
● KIT
● MET
● MYC
● PDGFRA
● PDGFRB
● PIK3CA
● RET
● RPS6KB1
● AKT2
● ATM
● CCND1
● CDK6
● CHEK1
● CHEK2
● ERBB3
● ERCC1
● ERCC2
● FGF1
● FGF2
● FGF3
● FGF4
● FGF5
● FGF6
● FGF7
● FGF8
● FGF9
● FGF10
● FGF14
● FGF23
● KRAS
● MDM4
● NRAS
● PIK3CB
● PTEN
● RICTOR
● AKT3
● BCL2
● CCNE1
● CSF1R
● ERG
● FLT1
● FLT3
● KDR
● KMT2A (MLL)
● MDM2
● MYCL1
● MYCN
● MLLT3
● MSH2
● NOTCH1
● NOTCH2
● NOTCH3
● AKT1
● APC
● ARID1A
● ATR
● BAP1
● BARD1
● BCL6
● BRIP1
● BTK
● CARD11
● CCND2
● CD79A
● CD79B
● CDH1
● CDK12
● CDKN2A
● CEBPA
● CREBBP
● CTNNB1
● DDR2
● DNMT3A
● EP300
● ERBB4
● EZH2
● FAM175A
● FANCI
● FANCL
● FBXW7
● FOXL2
● GEN1
● GNA11
● GNAQ
● GNAS
● HNF1A
● HRAS
● IDH1
● IDH2
● INPP4B
● JAK3
● MAP2K1
● MAP2K2
● MCL1
● MLH1
● MPL
● MRE11A
● MSH3
● MSH6
● MTOR
● MUTYH
● MYD88
● NBN
● NF1
● NPM1
● PALB2
● PIK3CD
● PIK3CG
● PIK3R1
● PMS2
● PPP2R2A
● PTCH1
● PTPN11
● RAD51
● RAD51B
● RAD51C
● RAD51D
● RAD54L
● RB1
● SLX4
● SMAD4
● SMARCB1
● SMO
● SRC
● STK11
● TERT
● TET2
● TP53
● TSC1
● TSC2
● VHL
● XRCC2
Amplifications
Fusions &
Splice Variants Small Variants
● NRG1
● ROS1
For Research Use Only. Not for use in diagnostic procedures.
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TruSight Tumor 170
Multi-Biomarker Cancer Panel
Single assay:
Detection of currently relevant DNA & RNA variants for multiple types of cancer
AKT1 ALK BRAF DDR2 EGFR ERBB2 FGFR1 FGFR3 KRAS MAP2K1 MET NRAS PIK3CA PTEN RET TP53 Lung *
BRAF CTNNB1 GNA11 GNAQ KIT MAP2K1 NF1 NRAS PDGFRA PI3KCA PTEN TP53 Melanoma
AKT1 AR BRCA1 BRCA2 ERBB2 FGFR1 FGFR2 PIK3CA PTEN Breast
BRAF KIT KRAS MET MLH1 PDGFRA TP53 Gastric AKT1
BRAF HRAS KRAS MET MLH1 MSH2 MSH6 NRAS PIK3CA PMS2 PTEN SMAD4 TP53 Colon
MSH6 PMS2 TSC1 Bladder BRAF
BRCA1 BRCA2 KRAS PDGFRA FOXL2 TP53 Ovary
For Research Use Only. Not for use in diagnostic procedures.
Variant detection from both DNA and RNA targets
*NCCN Clinical Practice Guidelines in Oncology for NSCLC v5 March 16, 2017 recommend broad molecular profiling.
AR
ERG
TMPRSS2
Prostate
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DNA Library Prep
RNA Library Prep
Enrichment
Sequencing
DNA Library Prep
RNA Library Prep
TST170 Enrichment
Sequencing
DNA Library Prep
RNA Library Prep
Exome Enrichment
Sequencing
DNA Library Prep
UMI Adapters
Enrichment
Sequencing
Building A Standard Solution for Tumor Profiling
TruSight® Oncology Library Prep and Enrichment
TruSight Oncology
Workflow TruSight Tumor 170 TruSight ctDNA Solutions ImmunoOncology
Post Analytic Variant Calling:
SNV Indels Fusions Splice Variants Copy Number Expression UMIs
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The Neoantigen Story: Assessing the Immunogenicity of Tumors
Schumacher and Schreiber, Science, 2015; 348(6230): 69-74
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Exome and RNA Sequencing To Understand Response To Checkpoint Blockade
Rizvi et al, Science, 2015; 348(6230):124-128; Snyder et al, N Engl J Med, 2014; 371: 2189-2199; McGranahan et al, Science, 2016;
351(6280): 1463-1469; Le et al, N Engl J Med, 2015; 372(26): 2509-2520; Tumeh et al, Nature, 2014; 515: 568-571; Van Allen et al, Science, 2015; 350 (6257): 207-211
For Research Use Only. Not for use in diagnostic procedures.
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Multi-Omics Approach
A holistic view
Whole-genome Sequencing
(WGS)
Targeted sequencing
Methylation
analysis RNA sequencing
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Liquid Biopsy
Potential applications
Vigilance
Asymptomatic screening,
risk assessment,
high-risk screening
Diagnosis
Includes prognostic testing
Therapy Selection, Response to Treatment, Resistance
Identify biomarkers predictive of
treatment, response to targeted therapy, and the emergence
of resistance
Monitoring
Assess response, progression, and
recurrence
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Liquid Biopsy
Illumina UMI Toolkit
Unique Molecular Identifiers (UMI) enable error correction
Raw reads
A G G G
● Adapters and indices required for the
generation of UMI- containing libraries
● Error-correction software
● Shipping Q4 2017
Introducing the lllumina UMI Toolkit
and
Collapsed, error corrected reads
G
For Research Use Only. Not for use in diagnostic procedures.
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Liquid Biopsy
ctDNA sequencing on NovaSeq™ Series
● ctDNA sequencing requires both – Breadth of targets
– Depth of coverage
● NovaSeq enables economical sequencing of broad panels
● Illumina UMI Toolkit + NovaSeq = New possibilities
For Research Use Only. Not for use in diagnostic procedures.
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TruSight Tumor 170 DNA panel run on NovaSeq at ~20Kx raw coverage per sample*
Variant Allele Frequency (titration) Sensitivity Error Rate
0.2% 94.4% (34/36) 0.000030%
0.4% 100% (36/36) 0.000026%
0.6% 100% (36/36) 0.000024%
0.2% 0.4% 0.6%
Expected Allele Frequency
0.2%
0.4%
0.6%
0.8%
Observed Allele Frequency 0.0%
High concordance between detected and expected allele frequency
Liquid Biopsy
ctDNA sequencing on NovaSeq Series
* Data calculations on file. Illumina, Inc. 2017
For Research Use Only. Not for use in diagnostic procedures.
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