Illumina s Cancer Research Portfolio and Dedicated Workflows
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1 Illumina s Cancer Research Portfolio and Dedicated Workflows Michael Sohn Clinical Sales Specialist Spain&Italy Illumina, Inc. All rights reserved. Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cbot, CSPro, CytoChip, DesignStudio, Epicentre, ForenSeq, Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iscan, iselect, MiniSeq, MiSeq, MiSeqDx, MiSeq FGx, NeoPrep, NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome, TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the US and/or other countries. All other names, logos, and other trademarks are the property of their respective owners. For Research Use Only. Not for use in diagnostic procedures.
2 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? 2 Image from Chen et al., J Thorac Dis Jun;5(3):E93-7. doi: /j.issn Figure 2
3 A potential future: Broad panel adoption ensures coverage of future relevant biomarkers Genomes and Exomes A portion of translational biomarkers may become clinically relevant Broad Panels Relevant Biomarkers Translational Biomarkers Targeted Panels 3
4 Further along Genome/exome adoption may become necessary to cover ever expanding number of relevant biomarkers Biomarkers across the genome may become relevant Genomes and Exomes Broad Panels Relevant Biomarkers Translational Biomarkers Targeted Panels 4
5 TruSight Tumor 170 Content Gene List and Variant Classification CEBPA CREBBP CD79A CTNNB1 CD79B DDR2 CDH1 BARD1 DNMT3A CDK12 BCL6 EP300 CDKN2A BRIP1 BTK AKT1 CARD11 NRG1 APC CCND2 FLT3 ROS1 ARID1A KDR ATR KMT2A (MLL) BAP1 AKT3 MDM2 BCL2 MYCL1 CCNE1 MYCN CSF1R MLLT3 ERG MSH2 FLT1 NOTCH1 NOTCH2 ABL1 NOTCH3 AXL ETV4 EML4 ETV5 NTRK2 ETS1 EWSR1 NTRK3 ETV1 FLI1 PAX3 KIF5B PAX7 NTRK1 PPARG TMPRSS2 5 ALK AR BRAF BRCA1 BRCA2 CDK4 EGFR ERBB2 ESR1 ERBB4 GNA11 EZH2 GNAQ FAM175A GNAS FANCI HNF1A FANCL HRAS FBXW7 IDH1 FOXL2 IDH2 GEN1 FGFR1 FGFR2 FGFR3 FGFR4 JAK2 KIT MET MYC PDGFRA PDGFRB PIK3CA RET RPS6KB1 RAF1 CCDN3 FGF19 INPP4B MPL JAK3 MRE11A MAP2K1 MSH3 NF1 MAP2K2 MSH6 NPM1 MCL1 MTOR PALB2 MLH1 MUTYH PIK3CD MYD88 PIK3CG NBN PIK3R1 AKT2 PMS2 ATM PPP2R2A CCND1 FGF7 PTCH1 CDK6 FGF8 PTPN11 CHEK1 FGF9 RAD51 CHEK2 FGF10 RAD51B ERBB3 FGF14 RAD51C ERCC1 FGF23 RAD51D ERCC2 KRAS RAD54L FGF1 MDM4 RB1 FGF2 NRAS SLX4 FGF3 PIK3CB FGF4 PTEN FGF5 RICTOR FGF6 LAMP1 TFRC For Research Use Only. Not for use in diagnostic procedures. SMAD4 SMARCB1 SMO SRC STK11 TERT TET2 TP53 TSC1 TSC2 VHL XRCC2 Amplifications Small Variants Fusions & Splice Variants
6 TruSight Tumor 170 Multi-Biomarker Cancer Panel Single assay: Detection of currently relevant DNA & RNA variants for multiple types of cancer 6 Lung * AKT1 ALK BRAF DDR2 EGFR ERBB2 FGFR1 FGFR3 KRAS MAP2K1 MET NRAS PIK3CA PTEN RET TP53 Melanoma BRAF CTNNB1 GNA11 GNAQ KIT MAP2K1 NF1 NRAS PDGFRA PI3KCA PTEN TP53 Colon AKT1 BRAF HRAS KRAS MET MLH1 MSH2 MSH6 NRAS PIK3CA PMS2 PTEN SMAD4 TP53 Variant detection from both DNA and RNA targets *NCCN Clinical Practice Guidelines in Oncology for NSCLC v5 March 16, 2017 recommend broad molecular profiling. Ovary BRAF BRCA1 BRCA2 KRAS PDGFRA FOXL2 TP53 Gastric BRAF KIT KRAS MET MLH1 PDGFRA TP53 For Research Use Only. Not for use in diagnostic procedures. Breast AKT1 AR BRCA1 BRCA2 ERBB2 FGFR1 FGFR2 PIK3CA PTEN Bladder MSH6 PMS2 TSC1 Prostate AR ERG TMPRSS2
7 Building A Standard Solution for Tumor Profiling TruSight Oncology Library Prep and Enrichment TruSight Oncology Workflow TruSight Tumor 170 TruSight ImmunoOncology ctdna Solutions DNA Library Prep DNA Library Prep DNA Library Prep DNA Library Prep RNA Library Prep RNA Library Prep RNA Library Prep UMI Adapters Enrichment TST170 Enrichment Exome Enrichment Enrichment Sequencing Sequencing Sequencing Sequencing Post Analytic Variant Calling: SNV Indels Fusions Splice Variants Copy Number Expression UMIs 7
8 The Neoantigen Story: Assessing the Immunogenicity of Tumors 8 Schumacher and Schreiber, Science, 2015; 348(6230): 69-74
9 Exome and RNA Sequencing To Understand Response To Checkpoint Blockade Rizvi et al, Science, 2015; 348(6230): ; Snyder et al, N Engl J Med, 2014; 371: ; McGranahan et al, Science, 2016; 351(6280): ; Le et al, N Engl J Med, 2015; 372(26): ; Tumeh et al, Nature, 2014; 515: ; Van Allen et al, Science, 2015; 350 (6257): For Research Use Only. Not for use in diagnostic procedures.
10 Multi-Omics Approach A holistic view Whole-genome Sequencing (WGS) Targeted sequencing Methylation analysis RNA sequencing 10
11 Liquid Biopsy Potential applications Vigilance Diagnosis Therapy Selection, Response to Treatment, Resistance Monitoring Asymptomatic screening, risk assessment, high-risk screening Includes prognostic testing Identify biomarkers predictive of treatment, response to targeted therapy, and the emergence of resistance Assess response, progression, and recurrence 11
12 Liquid Biopsy Illumina UMI Toolkit Unique Molecular Identifiers (UMI) enable error correction Introducing the lllumina UMI Toolkit Raw reads A G G G Collapsed, error corrected reads and G Adapters and indices required for the generation of UMIcontaining libraries Error-correction software Shipping Q For Research Use Only. Not for use in diagnostic procedures. 12
13 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. 13
14 Liquid Biopsy ctdna sequencing on NovaSeq Series 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) % 0.4% 100% (36/36) % 0.6% 100% (36/36) % 0.8% Observed Allele Frequency 0.6% 0.4% 0.2% 0.0% 0.2% 0.4% 0.6% High concordance between detected and expected allele frequency Expected Allele Frequency * Data calculations on file. Illumina, Inc For Research Use Only. Not for use in diagnostic procedures. 14
15 Thank You 15
Jennifer Hauenstein Oncology Cytogenetics Emory University Hospital Atlanta, GA
Comparison of Genomic Coverage using Affymetrix OncoScan Array and Illumina TruSight Tumor 170 NGS Panel for Detection of Copy Number Abnormalities in Clinical GBM Specimens Jennifer Hauenstein Oncology
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