Expanding the Compound  Management toolkit  Pierre Baillargeon   HTS/Lead Identification
About Scripps Florida  I.   Introduction to Lead Identification and Compound       Management at Scripps Florida  II. Revi...
The Lead Identification Laboratories at Scripps  Where robotics, chemistry and biology join forces to help discover new dr...
Issues With Compound Libraries I.   Introduction to Lead Identification and Compound      Management at Scripps Florida II...
Compound Management Challenges   What are your primary concerns in your current role or your department?                  ...
Compound Management Responsibilities & CustomersWhat role does CM play at                                                 ...
Compound Management Responsibilities & CustomersWhat operational challenges areencountered during these                   ...
Compound Management Responsibilities & CustomersWhat operational challenges are             How do we currently addressenc...
Opportunities For Error in Sample Distribution  COMPOUND SUBMISSION  • Has the correct sample been put into the labware?  ...
Introduction to Plate Auditor  I.   Introduction to Lead Identification and Compound       Management at Scripps Florida  ...
Why Do We Need Plate Auditor?                Are empty/partially filled                                              Do th...
Plate Auditor Applications & Features • Instant detection of errors from compound reformatting    • Detect missed/partiall...
What is Plate Auditor?• A custom HTS plate reader, incorporatingrecent advances in machine vision, imageanalysis, & the sp...
Plate Auditor Features: Instrument Design             The Scripps Research Institute © 2012 – All rights reserved
Plate Auditor Features: Color Recognition & Classification Before Processing                                              ...
Plate Auditor Features: Precipitate Detection    Compound plates contain precipitates which are masked by color: Plate Aud...
Plate Auditor Features: Low Volume Detection                                                                              ...
Plate Auditor Features: LIMS/Corporate Database Auditing                                            RESULTS OF COMPOUND PL...
Introduction to Plate Auditor  I.   Introduction to Lead Identification and Compound       Management at Scripps Florida  ...
Addressing Opportunities For Error in Sample Distribution  What new information do we obtain with Plate Auditor in the pro...
Practical Examples: HTS Library Analysis To date, Scripps has run over                        This includes Scripps Florid...
Practical Examples: HTS Library Analysis To date, Scripps has run over                          This includes Scripps Flor...
Plate Auditor data usage at Scripps Florida                                                                   1) Well data...
Identifying LIMS database errors in real timeWhen checking reformatted plates, Plate Auditor finds high # of LIMS disagree...
Identifying LIMS database errors in real time                          … CM team updates LIMS record and runs plate throug...
Using Sample color to track CM processes & sample quality    Plate Auditor data can be used to monitor consistency of samp...
Using Sample color to track CM processes & sample quality             Why should we care about sample color?            Th...
Using Sample color to track CM processes & sample quality Running color comparison reveals      color inconsistencies…    ...
Sample color is indicative of compound quality (MLSMR)                               2011 vs. 2009                        ...
Sample color is predictive of its performance in HTS             Why else should we care about sample color?          Typi...
Sample color is predictive of its performance in HTS                 Is there correlation between sample color and various...
Precipitate results measure effectiveness of solvation SOPs How can we monitor changes in precipitate? What impact does it...
Using precipitate detection to monitor library health         “Normal” screening plate                                  Pr...
Using precipitate detection to monitor library health  Plate Auditor helps to identify solubility issues when         anal...
Using precipitate detection to monitor library health freezer)BioFocus comparison: HTS copy 3 (in use) vs. HTS copy 4 (fro...
Interesting Observations: Labware QC          Why do we care if there are air bubbles in the polypropylene?       Air bubb...
Interesting Observations: Labware QC      Air bubbles can also exist in 1536 well polypropylene plates.In addition to plat...
Interesting Observations: Labware QC    Plate Auditor images can be used to document plate damage and                     ...
Interesting Observations: Labware QC                          Are all wells created equally?                     .28mm off...
Interesting Observations: Labware QC              What impact do offset wells have on experiments?         Plate with offs...
Impact Review             Review of Plate Auditor impact at Scripps Florida  1) Detect LIMS database errors in real time: ...
Impact of Plate Auditor at Scripps What operational challenges are encountered during these interactions? • Verifying qual...
Plate Auditor Summary & More Information Scripps has licensed the Plate Auditor technology to Brooks Life Science Systems ...
Acknowledgements                                                                                      Scripps Florida     ...
Upcoming SlideShare
Loading in …5
×

Expanding the Compound Management toolkit: leveraging technology to streamline sample QA/QC in high throughput environments

728 views
648 views

Published on

The continual evolution of compound management labs in terms of sample capacity and capabilities provides opportunities to improve the associated QA and QC operations. As new technologies enable support of greater plate densities and library sizes, new approaches to QA and QC must follow suit.

• Review of potential for error in compound management labs and impact of new technology on QA/QC efficiency

• Leveraging sample color to quickly identify problems

• Novel methods for monitoring the health of large sample libraries over time
• Correlating visual properties of solubilized samples to experimental results and calculated properties

Published in: Technology, Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
728
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
5
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • Like a game of battleship…
  • Accumulation of error causes failure:Liquid handler slightly off + plate slightly off = errorWells are 10% off spec (2.25mm distance center to center = 40 pixels, wells are off by 4 pixels in both cases)
  • Expanding the Compound Management toolkit: leveraging technology to streamline sample QA/QC in high throughput environments

    1. 1. Expanding the Compound Management toolkit Pierre Baillargeon HTS/Lead Identification
    2. 2. About Scripps Florida I. Introduction to Lead Identification and Compound Management at Scripps Florida II. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issues III. An introduction to the Plate Auditor IV. Impact of Plate Auditor results on our CM & HTS operations The Scripps Research Institute © 2012 – All rights reserved
    3. 3. The Lead Identification Laboratories at Scripps Where robotics, chemistry and biology join forces to help discover new drugs Integrated Assay Development, uHTS and Compound Management • Located in Jupiter, FL • >982K Compound Screening Collection • >175 targets screened in over 185 primary campaigns to • >622K Proprietary (largest in generate more than 60 million data points for academic & academia, ~30k unique compounds, focused industrial collaborators sub-libraries, professionally curated) • S1P1 drug candidate entered phase 1 clinical trials in • >360K Public Domain (NIH) January 2011 • Integrated Compound QC (LC-MS, Plate Auditor) The Scripps Research Institute © 2012 – All rights reserved
    4. 4. Issues With Compound Libraries I. Introduction to Lead Identification and Compound Management at Scripps Florida II. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issues III. An introduction to the Plate Auditor IV. Practical applications of Plate Auditor The Scripps Research Institute © 2012 – All rights reserved
    5. 5. Compound Management Challenges What are your primary concerns in your current role or your department? Sample quality 66.70% New automation technology 33.30% Integration of automation technology 33.30% Sample data management 66.70% Building a library to meet new research requirements 66.70% Budget cuts limiting technology investment 16.70% Job cuts 16.70% % of respondents 0% 20% 40% 60% 80% 100% Graph reproduced from the 2012 IQPC „Setting up Compound Management Globally‟ Compound Management report http://www.compoundmanager.com/uploadedFiles/EventRedesign/UK/2012/May/11314006/Assets/IQPC---Compound-management-060112.pdf The Scripps Research Institute © 2012 – All rights reserved
    6. 6. Compound Management Responsibilities & CustomersWhat role does CM play at HTSScripps?• HTS Library Procurement• HTS Library Stewardship Medicinal DMPK & Chemistry Pharm• HTS Library QC (via LC-MS)• Cherry pick for HTS Core• Compound re-synthesis & Compound Management restock• Receive & reformat samples from external collaborators Compound External Vendors Collaborator• Ship samples to external collaborators• Medicinal Chemistry support Therapeutic Areas The Scripps Research Institute © 2012 – All rights reserved
    7. 7. Compound Management Responsibilities & CustomersWhat operational challenges areencountered during these HTSinteractions?• Verifying quality of external samples & sample data Medicinal DMPK & Chemistry Pharm• Degradation or precipitation of samples over time• Enforcing internal QA/QC Compound standards Management• Tracking sample properties & genealogy in a way that can be easily audited in the future Compound External Vendors Collaborator• Managing large sample libraries which are constantly in flux (multiple copies, samples Therapeutic becoming depleted, new Areas acquisitions, etc.) The Scripps Research Institute © 2012 – All rights reserved
    8. 8. Compound Management Responsibilities & CustomersWhat operational challenges are How do we currently addressencountered during these these issues and what are theinteractions? limitations?• Verifying quality of external samples & sample data • LC-MS (time consuming)• Degradation or precipitation of samples over time • Acoustic auditing (time• Enforcing internal QA/QC consuming, labware standards dependent)• Tracking sample properties & genealogy in a way that can be • Manual visual inspection (time easily audited in the future consuming, subjective)• Managing large sample libraries which are constantly in flux (multiple copies, samples • Suspension of solids or becoming depleted, new precipitated samples acquisitions, etc.) (sonicating, heating, solvent change, etc.) The Scripps Research Institute © 2012 – All rights reserved
    9. 9. Opportunities For Error in Sample Distribution COMPOUND SUBMISSION • Has the correct sample been put into the labware? • Is the volume and concentration of the sample accurately recorded? COMPOUND PROCESSING • Has the sample store delivered the correct samples? • Has the liquid handling automation pipetted the samples properly? • Has the plate been registered correctly? • Is the sample itself of high quality? COMPOUND DELIVERY • Do we have a record of what we are delivering? Room for improvement! How can we QC samples more efficiently? The Scripps Research Institute © 2012 – All rights reserved
    10. 10. Introduction to Plate Auditor I. Introduction to Lead Identification and Compound Management at Scripps Florida II. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issues III. An introduction to the Plate Auditor IV. Practical applications of Plate Auditor The Scripps Research Institute © 2012 – All rights reserved
    11. 11. Why Do We Need Plate Auditor? Are empty/partially filled Do these wells wells in Quadrant 1? contain precipitate? My db says this well isempty. Does it actuallyhave sample in it? My HTS detection format is sensitive to Are these wells partially purple compounds. Where are they? filled? The Scripps Research Institute © 2012 – All rights reserved
    12. 12. Plate Auditor Applications & Features • Instant detection of errors from compound reformatting • Detect missed/partially filled wells, quadrant effects • “Pre-screen” compound plates for HTS assay interferents • Detect colored compounds, suspended materials • Identify database entry errors in corporate LIMS db • Determine which full/empty wells in plate differ from the full/empty well assignments in corporate db • Periodic check-ups on the “health” of stored compounds • Detect ppt. formation, evaporation • Detection of compound solubility • Identify HTS library samples that have “crashed out” of solution The Scripps Research Institute © 2012 – All rights reserved
    13. 13. What is Plate Auditor?• A custom HTS plate reader, incorporatingrecent advances in machine vision, imageanalysis, & the spectroscopy sciences• It saves labor by automatically identifying& annotating issues specific to compoundlibraries: • Colored compounds • Precipitate / Crystallization • Low volume / Full wells• It can be used in “stand-alone” mode, orintegrated with automation• Works with microtiter plates• Fast: reads a 384 well plate in <1 minute• All measurements are non-contact• User-friendly, intuitive analysis software The Scripps Research Institute © 2012 – All rights reserved
    14. 14. Plate Auditor Features: Instrument Design The Scripps Research Institute © 2012 – All rights reserved
    15. 15. Plate Auditor Features: Color Recognition & Classification Before Processing Limit of Color Dye Used Detection Detected (uM) Red Allura Red 35.1 Green Brilliant Green 9.0 Blue Euroglaucine 0.6 Yellow Tartrazine 12.7 Violet Gentian violet 1.3 After Processing The Scripps Research Institute © 2012 – All rights reserved
    16. 16. Plate Auditor Features: Precipitate Detection Compound plates contain precipitates which are masked by color: Plate Auditor precipitate analysis is: • Insensitive to color • Able to detect ppt. beyond “naked eye” inspection The Scripps Research Institute © 2012 – All rights reserved
    17. 17. Plate Auditor Features: Low Volume Detection What can cause a well to have a low volume? • Incorrectly reported volume in LIMS • Oversampled by cherry picking operations • Evaporation • Liquid handling errors (clogged tips, samples transferred to incorrect wells/quadrants, etc.) 40uL 20uL 10uL 8uL 4uL 2uL 1uLPlate Auditor distinguishes normal wells (“full”) from empty/partially filled wells (“low volume”) The Scripps Research Institute © 2012 – All rights reserved
    18. 18. Plate Auditor Features: LIMS/Corporate Database Auditing RESULTS OF COMPOUND PLATE QUERY IN CORPORATE DATABASE: • Scripps database displays several wells as empty (white rectangles in figure on left) RESULTS OF THE SAME COMPOUND PLATE QUERY IN Plate Auditor DATABASE: • Plate Auditor compares instrument results to records archived in corporate db • Plate Auditor identifies discrepancies with corporate db records(red “x’s” in figure on left): • Colored compounds (upper left) • Full wells that corporate db assigns as “empty” PLATE AUDITOR AUDITS CORPORATE DB RECORDS The Scripps Research Institute © 2012 – All rights reserved
    19. 19. Introduction to Plate Auditor I. Introduction to Lead Identification and Compound Management at Scripps Florida II. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issues III. An introduction to the Plate Auditor IV. Practical applications of Plate Auditor The Scripps Research Institute © 2012 – All rights reserved
    20. 20. Addressing Opportunities For Error in Sample Distribution What new information do we obtain with Plate Auditor in the process? • We know which wells have been filled and which have low volume • We know which wells contain colored samples • We know which wells contain compounds that have precipitated What do we do with this information? • Compare filled & low volume wells against LIMS to verify proper liquid handling & plate registration • Compare „color fingerprint‟ of samples against database of known samples to identify issues with incorrect concentration & samples • Take measures to put precipitated samples back into solution (sonication, heating, etc.) • Keep a historical record of the health of the plate at the point when it was delivered (a receipt of transaction) The Scripps Research Institute © 2012 – All rights reserved
    21. 21. Practical Examples: HTS Library Analysis To date, Scripps has run over This includes Scripps Florida‟s 1,000 plates through Plate internal 622k Drug Discovery Auditor resulting in over library and the NIH‟s Molecular 1,000,000 wells which have been Libraries-Small Molecule analyzed for color, precipitate Repository (MLSMR) 362k library. and low volume artifacts. How can we leverage all of this new data to improve our workflow? The Scripps Research Institute © 2012 – All rights reserved
    22. 22. Practical Examples: HTS Library Analysis To date, Scripps has run over This includes Scripps Florida‟s 1,000 plates through Plate internal 622k Drug Discovery Auditor resulting in over library and the NIH‟s Molecular 1,000,000 wells which have been Libraries-Small Molecule analyzed for color, precipitate Repository (MLSMR) 362k library. and low volume artifacts. How can we leverage all of this new data to improve our workflow? 1) Identify LIMS database errors in real time 2) Use sample color to track fidelity of CM processes & sample quality 3) Use sample color as a predictor of sample performance in HTS 4) Precipitate results measure effectiveness of solvation SOPs 5) Using precipitate detection to monitor library health 6) Other interesting observations: Labware QC The Scripps Research Institute © 2012 – All rights reserved
    23. 23. Plate Auditor data usage at Scripps Florida 1) Well data classified via Plate Auditor GUI 2) Well data merged with sample information from Corporate Plate DB and stored in Plate Auditor DB 3) Resulting data set exported from Plate Auditor DB and merged with HTS, Cheminformatics and LC- MS results By making Plate Auditor data available in the same web- based informatics portal as other HTS data, project biologists & chemists can easily examine HTS library samples for volume, color and precipitate issues The Scripps Research Institute © 2012 – All rights reserved
    24. 24. Identifying LIMS database errors in real timeWhen checking reformatted plates, Plate Auditor finds high # of LIMS disagreement wells…… examining the plate detail view reveals a pattern in quadrant 1…… checking the LIMS record reveals samples in quadrant 1 are not registered … The Scripps Research Institute © 2012 – All rights reserved
    25. 25. Identifying LIMS database errors in real time … CM team updates LIMS record and runs plate through Plate Auditor to confirm the corrected LIMS record matches the physical locations of samples within the plate. Real time detection of registration errors saves CM time and resources LIMS Comparison feature also used to detect formatting errors The Scripps Research Institute © 2012 – All rights reserved
    26. 26. Using Sample color to track CM processes & sample quality Plate Auditor data can be used to monitor consistency of sample color over time…We now can query and identify color inconsistencies across entire compound collections or the same sample distributed across multiple working copies of the library. The Scripps Research Institute © 2012 – All rights reserved
    27. 27. Using Sample color to track CM processes & sample quality Why should we care about sample color? The Scripps Research Institute © 2012 – All rights reserved
    28. 28. Using Sample color to track CM processes & sample quality Running color comparison reveals color inconsistencies… Sample 1 Sample 2 Two copies of plate prepared by external vendor reveal inconsistencies Sample 3 Sample 4 Sample 5 Color data identifies problematic samples earlier in CM processes The Scripps Research Institute © 2012 – All rights reserved
    29. 29. Sample color is indicative of compound quality (MLSMR) 2011 vs. 2009 Degraded sample (left) vs. expected sample (right), both verified via LC-MS 2011 vs. 2011 Expected sample (left) copy 2 vs. failed sample (right, precipitated) from copy 1, both verified via LC-MS Cherrypicked samples vs. screening deck Expected cherrypicked samples (left, middle) vs. failed screening deck sample (right), all verified via LC-MS Plate Auditor results predict LC-MS results The Scripps Research Institute © 2012 – All rights reserved
    30. 30. Sample color is predictive of its performance in HTS Why else should we care about sample color? Typical primary screen plate Typical confirmation screen plate With the Plate Auditor, can we show a true correlation between sample color and its hit activity? The Scripps Research Institute © 2012 – All rights reserved
    31. 31. Sample color is predictive of its performance in HTS Is there correlation between sample color and various assay properties? % Colored samples % of hits containing color vs. HTS readout technology 12/2007-12/2011 N=90 assays18% 80%16% 70%14% 60%12% 50%10% 40% Readout Technology 8% 30% Average % hits 6% 20% Overall average % hits 4% 2% 10% 0% 0% MLPCN HTS compound HTS hits collection Sample color data has impacted HTS assay development (biologists) & follow up of HTS hits by Project Chemists The Scripps Research Institute © 2012 – All rights reserved
    32. 32. Precipitate results measure effectiveness of solvation SOPs How can we monitor changes in precipitate? What impact does it have on CM operations? Heat, mixing solvent change, sonicat ion, etc… Tubes containing DMSO Tubes containing DMSO solvated samples (pre- solvated samples (post- sonication) sonication) Quantitative precipitate monitoring improved compound solvation SOPs The Scripps Research Institute © 2012 – All rights reserved
    33. 33. Using precipitate detection to monitor library health “Normal” screening plate Precipitate filled screening plate Plate Auditor automatically identifies plates with high levels of precipitate The Scripps Research Institute © 2012 – All rights reserved
    34. 34. Using precipitate detection to monitor library health Plate Auditor helps to identify solubility issues when analyzing samples from sublibraries … A % of library Library containing precipitate Sublibrary A 0.1% B Sublibrary B 2.5% Sublibrary C 0.8% … providing a useful dataset when communicating problems with suppliers, collaborators and CM staff C internally. The Scripps Research Institute © 2012 – All rights reserved
    35. 35. Using precipitate detection to monitor library health freezer)BioFocus comparison: HTS copy 3 (in use) vs. HTS copy 4 (from Baseline precipitate levels can be established with Plate Auditor data Representative plate from copy 3 of sublibrary B Representative plate from copy 4 of sublibrary B Plate # Copy 3 Copy 4 2 10 34 3 17 60 4 34 97 5 65 128 6 24 39 TOTAL 150 358 % increase 139% Helps identify existing samples that need re-solvation...or remediation The Scripps Research Institute © 2012 – All rights reserved
    36. 36. Interesting Observations: Labware QC Why do we care if there are air bubbles in the polypropylene? Air bubbles cause plates to be warped & unusable with automation. When creating new compound plates, Scripps discards plates with air bubbles as precautionary measure. The Scripps Research Institute © 2012 – All rights reserved
    37. 37. Interesting Observations: Labware QC Air bubbles can also exist in 1536 well polypropylene plates.In addition to plate warping, bubble artifact in 1536 well poses additional problems for machine vision QA/QC. The Scripps Research Institute © 2012 – All rights reserved
    38. 38. Interesting Observations: Labware QC Plate Auditor images can be used to document plate damage and deformities The Scripps Research Institute © 2012 – All rights reserved
    39. 39. Interesting Observations: Labware QC Are all wells created equally? .28mm offset 2.25mm 2.25mm.28mm offset The Scripps Research Institute © 2012 – All rights reserved
    40. 40. Interesting Observations: Labware QC What impact do offset wells have on experiments? Plate with offset wells Plate with no offset wells Plate from different vendor Plate Auditor provides data to communicate problems with third parties The Scripps Research Institute © 2012 – All rights reserved
    41. 41. Impact Review Review of Plate Auditor impact at Scripps Florida 1) Detect LIMS database errors in real time: • LIMS DB errors are detected & corrected immediately upon plate creation 2) Using Sample color to track CM processes and sample quality: • Color data identifies problematic samples earlier in CM processes • Plate Auditor results predict LC-MS results 3) Use sample color as a predictor of sample performance in HTS: • Susceptibility of a HTS assay to color interference is considered during assay development (biologists) and hit-follow up (chemists) • Correlation between color and hit performance helps determine HTS false negative/positive rate 4) Use precipitate as a measure of solvation effectiveness: • Quantitative precipitate monitoring improved compound solvation SOPs 5) Use precipitate as an indicator of library health: • Helps identify existing samples that need re-solvation...or remediation 6) Other interesting observations: • Images can be used to document plate damage and deformations • Images can be used to communicate problems with third parties The Scripps Research Institute © 2012 – All rights reserved
    42. 42. Impact of Plate Auditor at Scripps What operational challenges are encountered during these interactions? • Verifying quality of external • Received samples are quickly QC‟d samples & sample data upon arrival; Plate Auditor results are then compared to the vendor‟s plate • Degradation of samples over map. time • Plate Auditor periodically audits • Enforcing internal QA/QC compound library over its lifecycle standards • Automated QA/QC of samples removes subjective analysis and prevents CM • Tracking sample properties & staff burnout genealogy in a way that can be easily audited in the future • Plate Auditor plate “snapshots” allow us to easily & visually track sample • Managing large sample libraries genealogy which are constantly in flux • Routine QC of large libraries now (multiple copies, samples possible by automating labor becoming depleted, new intensive visual inspections acquisitions, etc.) The Scripps Research Institute © 2012 – All rights reserved
    43. 43. Plate Auditor Summary & More Information Scripps has licensed the Plate Auditor technology to Brooks Life Science Systems for commercialization & sale. The Brooks Plate Auditor will be part of the Brooks sample analysis line of instrumentation.Additional information, including Plate Auditor Pilot Screen results, can be found in “Monitoringof HTS compound library quality via a high-resolution image acquisition and processinginstrument”. Baillargeon P, Scampavia L, Einsteder R, Hodder P. ; J. Lab Automation, June 2011 The Scripps Research Institute © 2012 – All rights reserved
    44. 44. Acknowledgements Scripps Florida Funding Corporation http://hts.florida.scripps.edu bpierre@scripps.edu Lead Identification: Peter Hodder Pierre Baillargeon Peter Chase Joseph Datsko Christina Eberhart Imarhia Enogieru Ross Einsteder Katharine Emery Virneliz Fernandez-Vega Lina DeLuca Franck Madoux Becky Mercer Laura Pedro-Rosa Christine Pinello Louis Scampavia Timothy Spicer The Scripps Research Institute © 2012 – All rights reserved

    ×