The BeadXpress System: An Array of Applications for the Molecular Lab

Transcription

1 The BeadXpress System: An Array of Applications for the Molecular Lab Gianluca Roma Product Manager 29 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iselect, CSPro, GenomeStudio, Genetic Energy, and HiSeq are 1 registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

2 Illumina s First FDA Cleared In-Vitro Diagnostic Device The BeadXpress System is an FDA 51(k) cleared In-Vitro Diagnostic Device FDA Cleared BeadXpress System includes: BeadXpress Reader VeraScan Software The Intended Use Statement: The BeadXpress System is an In-Vitro Diagnostic Device intended for the simultaneous detection of multiple analytes in a DNA sample utilizing VeraCode holographic microbead technology. The BeadXpress System consists of the BeadXpress Reader and VeraScan software. It is cleared for use only with FDA cleared VeraCode tests. BeadXpress Reader and VeraScan Software 2

3 Illumina s Solution for Molecular Diagnostic Development VeraCode Technology Cylindrical glass microbeads 2 μm length x 28 μm diameter 3

4 VeraCode Technology CODE GENERATED BY CREATING EMBEDDED HOLOGRAPHIC DIFFRACTIVE ELEMENTS BEAD CODE IMAGE READING BEAM CONVENTIONAL CCD CAMERA BINARY CODE DECIMAL CODE = High Density Codes Easily Imprinted (24 bit) Virtually Unlimited Unique Bead Codes Available 626 unique codes used in launched products Glass Surface of Beads Ideal for Bioassays Specific panels created easily with addition or removal of specific bead types 4

5 BeadXpress Reader: Specifications SAMPLE DELIVERY FORMAT Standard 96-well plate & 8-well strip plates MULTIPLEXING PER SINGLE WELL 1 to 384 DETECTION Optional 1 or 2 color detection THROUGHPUT samples/hr at 1-plex samples/hr at 96-plex 5

6 6 BeadXpress Reader

7 VeraCode Bead Loading & Alignment CAPILLARY FORCE ATTRACTS BEADS INTO GROOVES GROOVE PLATE CROSS-SECTION BEADS FALL INTO GROOVE PLATE BEADS ALIGN TIGHTLY FOR OPTIMAL SCANNING EFFICIENCY 7

8 Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Pixel ADC Output Code Detection BEAD READING BEAM CCD LINE ARRAY

9 VeraScan 2. System Operation to Report Authentication Test selection & Setup Analysis & Report Scan Optional off-line analysis and review 9

10 Molecular Diagnostic Market Segments 1

11 Counts Log1(Net RFU) Intensity (B) Analyzer for Multiple Applications GENOTYPING FV GENE REGULATION - Intensity (A) PROTEIN EXPRESSION Analyte Fit 3-sigma LOD 5 4 IL-6 (6152) Conc (pm) Log1(Conc pg/ml) 11

12 VeraCode Product Portfolio (RUO) VeraCode Carboxyl Bead Sets VeraCode Universal Capture Bead Sets VeraCode ADME Core Panel Custom GoldenGate Genotyping, 48, 96, 144 & 384-plex DASL Custom Gene Expression, 32 to 384-plex Custom GoldenGate Methylation, 48 to 384-plex 12

13 VeraCode Product Portfolio (Regulated Products) VeraCode GPR Carboxyl Bead Sets VeraCode GPR Universal Capture Bead Sets VeraCode Pharamacogenetic Panel (in development) VeraCode Infectious Disease Panel (in development) 13

14 Available Products CARBOXYL BEAD SETS (PROTEIN BASED ASSAYS) PRODUCT GUIDELINES CUSTOMER DEVELOPED ASSAY + Unique Bead Code Types in Tubes Assay Design Guidelines (RUO) Customer controls level of multiplexing and number of samples For Research Use Only 14

15 Carboxyl Beads: Chemistry of Attachment PROTEIN ATTACHMENT: TWO-STEP PROCESS COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - COOH - Activate Surface EDC/Sulfo-NHS Covalently Bind NUCLEIC ACID ATTACHMENT: ONE-STEP PROCESS EDC/Sulfo-NHS plus NH 2+ Oligo Antibodies Antigens Peptides Streptavidin Nucleic Acids 15

16 Cytokine Sandwich Assay Overview Streptavidin Phycoerythrin PE PE PE Biotinylated Secondary Antibody Cytokine Antigens Antibodies immobilized via COOH surface and EDC linker chemistry For Research Use Only VeraCode Bead 16

17 Available Products UNIVERSAL CAPTURE BEAD SETS PRODUCT GUIDELINES CUSTOMER DEVELOPED ASSAY + Unique Bead Code Types in Tubes Assay Design Guidelines (RUO) VeraCode Assay Design Software Customer controls level of multiplexing and number of samples For Research Use Only 17

18 Allele-Specific Primer Extension (ASPE) G C G Match Mismatch G C Primer Extended Biotin-NTP s Incorporated G Primer Not Extended Wild-Type Variant For Research Use Only 18

19 Intensity (B) Intensity (B) Intensity (B) Intensity (B) Low Plex ASPE Genotyping Results FV FII Intensity (A) 2 3 Intensity (A) MTHFR667 MTHFR Intensity (A) Intensity (A) For Research Use Only 99.99% reproducibility % concordant genotypes 19

20 The VeraCode Assay Designer Software Access user-specific accounts Input SNP targets Choose workflow option Customize design parameters Select among possible assay designs Download detailed ordering information For Research Use Only 2

21 21 VeraCode ADME Core Panel

22 VeraCode ADME* Core Panel Investigate genetic associations to a drug Response Dosing Safety Pharmacogenetic studies can be: Completed Quickly More Efficiently More Precisely Bring Personalized Medicine closer to reality *Absorption, Distribution, Metabolism, and Excretion For Research Use Only 22

23 More Core Coverage Objective: Standardize content for pharmacogenetic drug studies PharmaADME working group contributed content Abbott, Bristol-Myers Squibb, GSK, Johnson & Johnson, Eli Lilly, Merck, Pfizer, Roche, Sanofi Aventis and Wyeth. Genome Quebec also participated VeraCode ADME include184 polymorphisms (34 genes) >95% Pharma ADME Core List ADME Core (34 genes, 184 markers) ABCB1 CYP2C9 NAT1 SULT1A1 ABCC2 CYP2D6 NAT2 TPMT ABCG2 CYP2E1 SLC15A2 UGT1A1 CYP1A1 CYP3A4 SLC22A1 UGT2B15 CYP1A2 CYP3A5 SLC22A2 UGT2B17 CYP2A6 DPYD SLC22A6 UGT2B7 CYP2B6 GSTM1 SLCO1B1 VKORC1 CYP2C19 GSTP1 SLCO1B3 CYP2C8 GSTT1 SLCO2B1 For Research Use Only 23

24 Validated Core Content that Matters Validated Biomarkers and the Drugs they Metabolize CYP2D6 Metabolizes codine to active drug morphine Metabolizes Stratera (atomoxetine), used for Attention Deficit Disorder Associated with tamoxifen metabolism CYP2C9 Referenced in the labeling for blood thinner warfarin CYP2C19 Referenced in label for anti-platelet Plavix (clopidogrel) Experimental Biomarkers and the Drugs they Metabolize CYP2A6 Associated with Nicotine metabolism For Research Use Only 24

25 Provides Highly Specific Assay For Research Use Only 25

26 Innovative Genotyping Approach [A/B] A B b b Make Target Add Oligos Cy Cy b Extend/Ligate PCR Make ssdna Cy c Hyb VBS For Research Use Only 26

27 Faster and Simplified Assay Workflow For Research Use Only Assay 32 samples per shift, < 2.5 hours hands on time 27

28 ADME Core: Convenient Visualization Tools 28

29 Reports with Automatic Translation 29

30 Quality Performance Specifications Parameter Performance Specification ILMN Verification (465 samples, 3 users, 3 systems) Beta Data (3 sites, 4 users, 24 in house samples and more than 143 beta site samples ) Locus Success 95% 95.7% 95.7% Assay Time, 32 samples DNA to data Hands on time 8 hr 2.5 hr 7 hr 38 min 1 hr 37 min Sample Throughput 1 user, 1 run, 1 plate: 32 1 user, 1 run, 2 plates: 64 8 hr 2.5 hr Average Call Rate 98% 99.5% 99.2% Concordance with Reference Infinium, GA, Sanger sequencing, DMET 99.5% 99.8% 99.8% Reproducibility 99.5% 99.8% 99.7% For Research Use Only 3

31 VeraCode ADME Core Panel More of What s Important 34 genes, 184 polymorphisms Covers >95% core content Quality Counts >99.5% Concordance >99.5% Reproducibility >98% Call Rate Speed Matters Single day sample processing <2.5 hrs hands-on Simplified workflow Useful reports For Research Use Only 31 Highest quality data. Simplest fastest workflow. More core.

32 Follow-on VeraCode Pharmacogenetic Test (In Development) CYP2C19 *2,*3,*4,*5,*6,*7,*8,*17 CYP2C9 *2,*3, VKORC1-1639G>A Amp Label Hybe Scan 32

33 Enabling Clinical Early Adopter FDA cleared BeadXpress System Regulated device ensures quality and performance meet the standards for a clinical laboratories General Purpose Reagent Beads Enables customers to develop their own assays using royaltyfree beads Path to FDA Submissions BeadXpress clearance and GMP reagents create a platform for follow-on diagnostic development 33

34 Enabling Diagnostic Partners Signed agreements with EraGen: Expanded Menu EraGen can port content to BeadXpress EraGen potential transfer menu includes: CFTR, Factor II/V, MTHFR Respiratory Viral Panel Improved Workflow Faster chemistry on BeadXpress Reduced labor costs Faster turnaround Enables further menu expansion in infectious disease BeadXpress 51(k) Clearance Removes a Significant Hurdle for development of diagnostic tests by Partners 34

35 EraGen Workflow on BeadXpress 35

36 Multiplex Assay Workflow Comparison EraGen Workflow Analysis Automation Friendly Sample* to Answer Step Description Time ILMN (EraGen) 2:35 Prep Transfers = Washes = Filtration = Labor (hrs) =.25 RXN Setup PCR 2 µl Master Mix 1 µl Sample Amplify and Label :5 1:3 Third Wave Luminex (TmBio) 5:3 6:3 Prep Transfers = 1 Washes = 1 Filtration = Labor (hrs) = 2 Prep Transfers = 1 Washes = 1 Filtration = 1 Labor (hrs) = 3 Hyb Setup Hybridization BeadXpress 5 µl Hybridization Buffer 3 µl Reaction Room 85 RPM Read Full Plate (96 Samples) :5 :15 : 7: 96 Clinical Specimens Total Assay Time: 2:35 *Workflows start from extracted DNA 36 36

37 37 The BeadXpress: For Infectious Disease Testing

38 Advantages of Multiplexed Panels Increase Productivity More results in less time Decrease Costs Lower Reagent costs per analyte detected RT- PCR Singleplex VeraCode Multiplex 38

39 An Array of Applications for the Molecular Laboratory Research Use Only Regulated Products VeraCode Universal Capture & Carboxyl Beads VeraCode GPR Carboxyl Beads VeraCode ADME Core Panel VeraCode GPR Universal Capture Beads Custom GoldenGate Genotyping, 48, 96, 144, 192 & 384-plex VeraCode PGx Panel (in development) DASL Custom Gene Expression, 32 to 384-plex VeraCode IDx Panel (in development) Custom GoldenGate Methylation, 48 to 384-plex 39