Somatic cancer applications of NGS in in vitro Diagnostics. Nitin Udar PhD In Vitro Diagnsotics Division Illumina, Inc. 2013 Illumina, Inc. All rights reserved. Illumina, IlluminaDx, BaseSpace, BeadArray, BeadXpress, cbot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium, iselect, MiSeq, Nextera, NuPCR, SeqMonitor, Solexa, TruSeq, TruSight, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registered trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
Disclaimer Employee of Illumina Comments in this presentation are my personal opinions and not the expressed opinion of Illumina 2
Vision Illumina is improving human health by unlocking the power of the genome Overview Headquartered in San Diego, CA > 3,100 Employees > 850,000 square ft. in 8 countries > 135 issued patents; > 168 pending History 1998 - Company was founded 2000 - Initial public offering 2006 - Acquired Solexa 2007 - Forbes #1 Fastest Growing Technology 2008 - Added to the NASDAQ-100 listing 2014 MIT Technology Review - Smartest Company Facts Recognized leader in NGS > 90% of the world s sequencing data generated using Illumina platforms ~80% market share in DNA array genotyping > 3,800 peer reviewed publications 3
Next Generation Sequencing Markets Served Molecular Dx Life Sciences Applied Markets Consumer 4
US Lifetime Healthcare Expenses = $400,000 per person Health Care Costs $400K Preconception IVF PGD/PGS Early Life Cardiovascular Cancer 5
6 Copyright 2008 American Cancer Society We are losing the war on cancer Death Rates* for Cancer and Heart Disease for Ages Younger than 1975 to 2004 From Jemal, A. et al. CA Cancer J Clin 2008;58:71-96.
7 Mean=28
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Breadth of Coverage Molecular Characterization by Next Generation Sequencing Targeted Panel Whole Exome Sequencing Whole Genome Sequencing Small Content High Sequencing Depth Shorter TAT Large Content High Sequencing Depth Medium TAT Large Content Lower Sequencing Depth Longer TAT Sensitivity, Throughput 9
10 DNA is present in two location within a cell
Variations introduced during cell division Mitosis Meiosis M G2 G 1 S Recombinatio n Meiosis I Meiosis II 11
Genetic Diseases Duchene Muscular Dystrophy Turners Sickle Cell Anemia Hurler Deficiency of alpha- L-iduronidase Downs Color Blindness Cystic Fibrosis MELAS Retinoblastoma Achondroplasia FGFR3 12
Variations introduced during cell division Mitosis Meiosis M G2 G 1 S Recombinatio n Meiosis I Meiosis II 13
Molecular Testing for Oncology Risk Prediction Screening Early Detection Diagnosis Prognosis Response to Therapy (Companion Diagnostics) Recurrence 14
Somatic Cancer Solid Tumors Lung Cancer, Colorectal, Melanoma, Gastric, Breast, Thyroid Ovarian, Hepatic, Kidney, Pancreatic, Prostate, Bladder, Testicular, Brain Hematology/Oncology. AML Leukemias and Lymphomas 15
Content with Clinical Utility Only Mutations Single nucleotide KRAS G12D (c.35g>a) Multiple nucleotide KRAS G12F (c.34_35 GG>TT) Insertions/Deletions EGFR exon 16 del (LREA) Fusions EML4/ALK Amplification ERBB2 Deletion/Loss Of Heterozygoxity, TP53 Not included are polymorphism and variants of unknown significance 16
Companion Diagnostics and Therapeutics BLA or sbla PMA 17
2014 Illumina Oncology focus NGS Companion Diagnostics Partnership Actionable Genome Consortium Define content Illumina Dana-Farber Cancer Institute Fred Hutchinson Cancer Research Center MD Anderson Memorial Sloan Kettering Cancer Center 18
Regulatory Submissions BeadXpress instrument and Factor II & V assay Cleared 2010 iscan instrument and Cyto SNP12 assay Submitted 2/2013 Received comments from FDA 4/2013 MiSeq Open Platform Submitted 12/2012 EU Launched Q2 2013 MiSeqDx and CFTR Diagnostics assay and CFTR carrier screening assay Submitted 12/2012 EU Launched Q2 2013 Verifi IVD Pre-submission pack sent 3/2013 Pre-Submission meeting 5/2013 19
PMA for Companion Diagnostics Design Sample type, DNA/RNA extraction, QC test, Assay, Reporting Analytical QC test, Sensitivity, Specificity, DNA input, Cross contamination, Exogenous/interfering substance etc Software User Interface locked down in Dx mode, Setup, Assay Run, Analysis, Reporting Clinical Accuracy, Reproducibility Manufacturing Process Qualification, Batch records, Builds, Batch Size, QC acceptance criteria, mandatory FDA inspection Regulatory Presub, Modular/NonModular Submission Quality Established Quality System, project DHF, Design Input Document Support and Marketing 20
Example of Product Specifications Parameter Details Impact Panel Size 21kb Sequence more of the regions that matter for solid tumors. Content 175 amplicons Amplicons tiled over exons for a broader view of variation. Amplicon Size 165-195 bp Optimized for FFPE DNA Input 21 20ul eluent based on DNA QC (typical range: 30-300ng based on DNA quality) Minimize DNA input based on sample quality. >99% of passing samples yield successful libraries. Assay Time <7 hrs, 2.5 hrs hands-on Streamlined workflow Sequence Run Time 22 hrs Walkaway sequencing Sequence Run 2x 121bp Optimized for inclusion of relevant in-dels like EGFR LREA. Limit of Detection Coverage 5% Minor Allele Frequency Reporting Limit = 3% 1,000x coverage of every amplicon; 7,000x mean coverage Throughput 4 samples per MiSeqv2 300 cycle run Scalable workflow Breadth of sequencing with sensitivity of PCR. CAP guidelines recommend 5% LOD for resistance. 5% LOD across every amplicon = no dropouts. Reporting Only reports mutants with clinical utility Only verified targets
DNA Extracted from FFPE is Damaged and Degraded Degraded DNA Fragments QC Assay Determine quality of DNA Nucleotide Damage 22
High Precision - Differentiate True Variation from Artifacts Non-modified bases Modified base Pool 1 Pool 2 Pool 1 Pool 2 sequencing primer 1 5 P Extension ligation 3 C G G 3 sequencing primer 2 5 5 3 C C G P 3 5 Forward Strand Reverse Strand 5 3 P *C G A 3 5 5 3 C C P G 3 5 universal primer 1 index G C Extension/ligation product A C universal primer 2 PCR amplification G C G C PCR product A T G C Combine and Sequencing Demultiplex, Alignment and Analysis Combine and Sequencing Demultiplex, Alignment and Analysis 23
Variant Frequency F Reverse Variation Confirmed Below 10% Minor Allele Frequency Dual Stranded Calls Variant Frequency Forward 24
Thank You the sequence of the human DNA is the reality of the species, and everything that happens in the world depends upon those sequences. Renato Dulbecco, Nobel Laureate 25 25 2