Addressing Quality Control Issues  in Day-to-Day HTS Compound     Management Operations      Pierre Baillargeon        HTS...
About Scripps FloridaI. Introduction to Lead Identification and Compound   Management at Scripps FloridaII. Review of issu...
About Scripps Florida• Started activities in 2004• Located in Jupiter, FL• More than 450 employees• Screened 115 targets i...
Drug Discovery at Scripps Florida                                                       Discovery      Clinical Trials    ...
The Lead Identification Department at Scripps        Integrated Assay Development, uHTS and Compound Management    Assay D...
Compound Management Systems                                                               • “Working copies” of all HTS   ...
Issues With Compound LibrariesI. Introduction to Lead Identification and Compound   Management at Scripps FloridaII. Revie...
Compound Management Responsibilities & CustomersWhat role does CM play at                                                 ...
Compound Management Responsibilities & CustomersWhat operational challenges are                                           ...
Compound Management Responsibilities & CustomersWhat operational challenges are             How do we currently addressenc...
Opportunities For Error  COMPOUND SUBMISSION  • Has the correct sample been put into the labware?  • Is the volume and con...
Introduction to HIAPI-CMI. Introduction to Lead Identification and Compound   Management at Scripps FloridaII. Review of i...
Why Do We Need HIAPI-CM?                 Are empty/partially filled                                              Do these ...
HIAPI-CM Applications & Features• Instant detection of errors from compound reformatting    • Detect missed/partially fill...
What is HIAPI-CM?• A custom HTS plate reader, incorporatingrecent advances in machine vision, imageanalysis, & the spectro...
HIAPI-CM Features: Instrument Design• Completely automated& intuitive to operate• Classification Resultsshown in real-time...
HIAPI-CM Features: Plate Gallery    HIAPI-CM Plate Gallery provides an easy to navigate interface to                edit, ...
HIAPI-CM Features: Plate GalleryFrom the Plate Gallery, a user can click on a plate to load the Plate DetailView. The user...
HIAPI-CM Features: Color Recognition & Classification                                                         • HIAPI-CM d...
HIAPI-CM Features: Precipitate Detection Compound plates contain precipitates which are masked by colors in the           ...
HIAPI-CM Feature: Low Volume Detection                                                   What can cause a well            ...
HIAPI-CM Features: LIMS/Corporate Database Auditing                                             RESULTS OF COMPOUND PLATE ...
Opportunities For Error  What new information do we obtain with HIAPI-CM in the process?  • We know which wells have been ...
Why do we need HIAPI-CM?           The Scripps Research Institute © 2011 – All rights reserved
Why do we need HIAPI-CM?           The Scripps Research Institute © 2011 – All rights reserved
Practical Examples: HIAPI-CM 384 Well Plate TimingTo visually inspect three 384 well                      In the same amou...
Practical Examples: HTS Library Analysis To date, Scripps has run over                         This includes Scripps Flori...
Practical Examples: Color Analysis       HIAPI-CM data can be used to monitor consistency of sample color over time…      ...
Practical Examples: Color Analysis   Running color comparison reveals color inconsistencies…                              ...
Practical Examples: LIMS ComparisonFinds plates which have not been properly registered in corporate LIMS db…… in this cas...
Practical Examples: LIMS ComparisonWhen checking reformatted plates, CM team noticed high # of LIMS disagreement wells…   ...
Practical Examples: LIMS ComparisonWhen checking reformatted plates, CM team noticed high # of LIMS disagreement wells…… e...
Practical Examples: LIMS Comparison                        … CM team updates LIMS record and runs plate through HIAPI-    ...
Practical Examples: LIMS Comparison    HIAPI-CM Raw                 HIAPI-CM Raw Image                         LIMS Record...
Practical Examples: Precipitate Analysis       “Normal” screening plate                                Precipitate filled ...
Practical Examples: Precipitate Analysis       “Normal” screening plate                                Precipitate filled ...
Practical Examples: Precipitate Analysis                                                          A      HIAPI-CM helps to...
Compound Management Responsibilities & CustomersWhat operational challenges are                                           ...
Compound Management Responsibilities & CustomersWhat operational challenges areencountered during these                   ...
HIAPI-CM Summary                                                         •    CM staff is able to proactively capture     ...
One Final Thought…                                     “We now have the technical ability to get                          ...
Acknowledgements                                                                                      Scripps Florida     ...
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Addressing Quality Control Issues in Day-to-Day HTS Compound Management Operations

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This presentation looks at common issues encountered with DMSO-solvated compounds in HTS libraries and, current methods for identifying and tracking these issues. It also introduces applications of a novel high resolution and imaging processing instrument (HIAPI) for rapid assessment and quality control of HTS library compound library quality.

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Addressing Quality Control Issues in Day-to-Day HTS Compound Management Operations

  1. 1. Addressing Quality Control Issues in Day-to-Day HTS Compound Management Operations Pierre Baillargeon HTS/Lead Identification
  2. 2. About Scripps FloridaI. Introduction to Lead Identification and Compound Management at Scripps FloridaII. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issuesIII. An introduction to the High-resolution Image Acquisition and Processing Instrument for Compound Management applications (HIAPI-CM) The Scripps Research Institute © 2011 – All rights reserved
  3. 3. About Scripps Florida• Started activities in 2004• Located in Jupiter, FL• More than 450 employees• Screened 115 targets in over 145primary campaigns to generate more than35 million data points for academic &industrial collaborators• First drug candidate entered phase 1clinical trials in January 2011 Phase I & II (Feb 2005-Sep 2006): 75,000 sq ft lab space Phase III (early 2009): 350,000 sq ft lab space The Scripps Research Institute © 2011 – All rights reserved
  4. 4. Drug Discovery at Scripps Florida Discovery Clinical Trials Biology Identify “target” for drug discovery In Vivo Lead ID Studies Identify drug-like Prepare leads for clinical studies “leads” for target Translational through High Throughput Research Screening Institute Determine ifleads have drug- Improve like properties pharmacologic Medicinal properties of DMPK leads Chemistry The Scripps Research Institute © 2011 – All rights reserved
  5. 5. The Lead Identification Department at Scripps Integrated Assay Development, uHTS and Compound Management Assay Development HTS Compound Management• Tissue culture suite • >250,000 tests per day • >982K Screening File• 96/384/1536 well format • 1536 well format • >622K Proprietary (largest insupported • 1 of 6 worldwide GNF/Kalypsys academia, ~30k unique• “From test tube to plate” platforms compounds, focused sub-• Protein expression/purification • All major HTS screening formats libraries, professionally curated) supported • >360K Public Domain (NIH) • Integrated Compound QC (LC-MS, HIAPI-CM) >$20MM Investment by Scripps Florida The Scripps Research Institute © 2011 – All rights reserved
  6. 6. Compound Management Systems • “Working copies” of all HTS screening samples are available for quick cherry picking and reformatting. • CM Automation integrates proven hardware solutions with customized software to improve process efficiency. • Equipment and procedures optimized for rapid response. Automation is closely integrated with software, ensuring timely delivery of samples and minimizing waste. Photo by Tom Arban The Scripps Research Institute © 2011 – All rights reserved
  7. 7. Issues With Compound LibrariesI. Introduction to Lead Identification and Compound Management at Scripps FloridaII. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issuesIII. An introduction to the High-resolution Image Acquisition and Processing Instrument for Compound Management applications (HIAPI-CM) The Scripps Research Institute © 2011 – All rights reserved
  8. 8. Compound Management Responsibilities & CustomersWhat role does CM play at HTSScripps?• HTS Library Procurement• HTS Library Stewardship• HTS Library QC (via LC-MS) Medicinal Chemistry DMPK & Pharm• Cherry pick for HTS Core• Compound re-synthesis & restock Compound• Receive & reformat samples Management from external collaborators• Ship samples to external collaborators Compound External• Medicinal Chemistry support Vendors Collaborator Therapeutic Areas The Scripps Research Institute © 2011 – All rights reserved
  9. 9. Compound Management Responsibilities & CustomersWhat operational challenges are HTSencountered during theseinteractions?• Quality of external samples & sample data Medicinal DMPK & Chemistry Pharm• Degradation of samples over time• Enforcing internal QA/QC standards Compound 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 becoming Therapeutic Areas depleted, new acquisitions, etc.) The Scripps Research Institute © 2011 – All rights reserved
  10. 10. Compound Management Responsibilities & CustomersWhat operational challenges are How do we currently addressencountered during these these issues and what are theinteractions? limitations?• Quality of external samples & sample data • LC-MS (time consuming)• Degradation of samples over time• Enforcing internal QA/QC • Acoustic auditing (time standards consuming, labware• Tracking sample properties & dependent) genealogy in a way that can be easily audited in the • Manual visual inspection (time future consuming, subjective)• Managing large sample libraries which are constantly in flux (multiple copies, samples becoming depleted, new acquisitions, etc.) The Scripps Research Institute © 2011 – All rights reserved
  11. 11. Opportunities For Error 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? COMPOUND DELIVERY • Do we have a record of what we are delivering? The Scripps Research Institute © 2011 – All rights reserved
  12. 12. Introduction to HIAPI-CMI. Introduction to Lead Identification and Compound Management at Scripps FloridaII. Review of issues with DMSO solvated compounds in HTS libraries and methods for addressing these issuesIII. An introduction to the High-resolution Image Acquisition and Processing Instrument for Compound Management applications (HIAPI-CM) The Scripps Research Institute © 2011 – All rights reserved
  13. 13. Why Do We Need HIAPI-CM? Are empty/partially filled Do these wells wells in Quadrant 1? contain precipitate?The contentsof a plate area fingerprintfor all of the potentialproblems youencounter in a CM operation! 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 © 2011 – All rights reserved
  14. 14. HIAPI-CM 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• Quantitative detection of compound solubility • Useful for medicinal chemistry synthesis operations, DMPK experiments The Scripps Research Institute © 2011 – All rights reserved
  15. 15. What is HIAPI-CM?• 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 © 2011 – All rights reserved
  16. 16. HIAPI-CM Features: Instrument Design• Completely automated& intuitive to operate• Classification Resultsshown in real-time• Simple interface onlyrequires user to selectplate type to performanalysis• Analysis resultsexported as text file orcompared to existingrecords in corporateLIMS database The Scripps Research Institute © 2011 – All rights reserved
  17. 17. HIAPI-CM Features: Plate Gallery HIAPI-CM Plate Gallery provides an easy to navigate interface to edit, export or browse analysis results The Scripps Research Institute © 2011 – All rights reserved
  18. 18. HIAPI-CM Features: Plate GalleryFrom the Plate Gallery, a user can click on a plate to load the Plate DetailView. The user can inspect different artifact analysis results or overwrite classifications made by HIAPI-CM. The Scripps Research Institute © 2011 – All rights reserved
  19. 19. HIAPI-CM Features: Color Recognition & Classification • HIAPI-CM detects and classifies colored Before Processing compounds • HIAPI-CM currently recognizes and classifies the “standard” colors listed below: Limit of Color Dye Used Detection Detected (uM) Red Allura Red 35.1 Green Brilliant Green 9.0 Blue Euroglaucine 0.6 After Processing Yellow Tartrazine 12.7 Violet Gentian violet 1.3 The Scripps Research Institute © 2011 – All rights reserved
  20. 20. HIAPI-CM Features: Precipitate Detection Compound plates contain precipitates which are masked by colors in the wells: HIAPI-CM Precipitate analysis is: • Insensitive to color • Able to detect ppt. beyond “naked eye” inspection The Scripps Research Institute © 2011 – All rights reserved
  21. 21. HIAPI-CM Feature: 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 40uL 20uL 10uL 8uL 4uL 2uL 1uL incorrect wells/quadrants, etc .) HIAPI-CM distinguishes normal wells (“full”) from empty/partially filled wells (“low volume”) - low volume designation dependent on plate type The Scripps Research Institute © 2011 – All rights reserved
  22. 22. HIAPI-CM Features: LIMS/Corporate Database Auditing RESULTS OF COMPOUND PLATE QUERY IN CORPORATE DATABASE: • Scripps database (MDL Symyx/Plate Manager) displays several wells as empty (white rectangles in figure on left) RESULTS OF THE SAME COMPOUND PLATE QUERY IN HIAPI-CM DATABASE: • HIAPI-CM compares instrument results to corporate db records • HIAPI-CM identifies discrepancies with corporate db (red “x’s” in figure on left): • Colored compounds (upper left) • Full wells that corporate db assigns as “empty” HIAPI-CM CAN BE USED TO AUDIT/UPDATE CORPORATE DB RECORDS The Scripps Research Institute © 2011 – All rights reserved
  23. 23. Opportunities For Error What new information do we obtain with HIAPI-CM 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 have precipitated What can 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 © 2011 – All rights reserved
  24. 24. Why do we need HIAPI-CM? The Scripps Research Institute © 2011 – All rights reserved
  25. 25. Why do we need HIAPI-CM? The Scripps Research Institute © 2011 – All rights reserved
  26. 26. Practical Examples: HIAPI-CM 384 Well Plate TimingTo visually inspect three 384 well In the same amount ofplates: time, HIAPI-CM can automaticallyPlate #1 – 3 minutes 12 seconds inspect fifteen 384 well plates!Plate #2 – 1 minute 46 secondsPlate #3 – 1 minute 40 seconds The Scripps Research Institute © 2011 – All rights reserved
  27. 27. Practical Examples: HTS Library Analysis To date, Scripps has run over This includes Scripps Florida‟s 1,000 plates through HIAPI-CM internal 622k Drug Discovery resulting in over 1,000,000 wells library and the NIH‟s Molecular which have been analyzed for Libraries-Small Molecule color, precipitate and low volume Repository (MLSMR) 362k library. artifacts. How can we leverage all of this new data to improve our workflow? The Scripps Research Institute © 2011 – All rights reserved
  28. 28. Practical Examples: Color Analysis HIAPI-CM data can be used to monitor consistency of sample color over time… A sample provided by an external source in 2009 vs. the same sample provided by the same source in 2011. With HIAPI-CM, we can automatically query and identify inconsistencies across entire compound collections. Is this the same sample? Is the concentration recorded correctly? The Scripps Research Institute © 2011 – All rights reserved
  29. 29. Practical Examples: Color Analysis Running color comparison reveals color inconsistencies… Two copies of plate prepared by external vendor reveal inconsistencies The Scripps Research Institute © 2011 – All rights reserved
  30. 30. Practical Examples: LIMS ComparisonFinds plates which have not been properly registered in corporate LIMS db…… in this case, LIMS record had odd barcode for plate instead of even barcode. The Scripps Research Institute © 2011 – All rights reserved
  31. 31. Practical Examples: LIMS ComparisonWhen checking reformatted plates, CM team noticed high # of LIMS disagreement wells… The Scripps Research Institute © 2011 – All rights reserved
  32. 32. Practical Examples: LIMS ComparisonWhen checking reformatted plates, CM team noticed 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 © 2011 – All rights reserved
  33. 33. Practical Examples: LIMS Comparison … CM team updates LIMS record and runs plate through HIAPI- CM to confirm the corrected LIMS record matches the physical locations of samples within the plate. The Scripps Research Institute © 2011 – All rights reserved
  34. 34. Practical Examples: LIMS Comparison HIAPI-CM Raw HIAPI-CM Raw Image LIMS Record Image vs. LIMS Record Comparison Plate arrived from external vendor with empty wells backfilled with DMSO, but accompanying data file showed them as empty. HIAPI-CM was able to identify this discrepancy. The Scripps Research Institute © 2011 – All rights reserved
  35. 35. Practical Examples: Precipitate Analysis “Normal” screening plate Precipitate filled screening plate HIAPI-CM automatically identifies plates with high levels of precipitate The Scripps Research Institute © 2011 – All rights reserved
  36. 36. Practical Examples: Precipitate Analysis “Normal” screening plate Precipitate filled screening plate HIAPI-CM automatically identifies plates with high levels of precipitate The Scripps Research Institute © 2011 – All rights reserved
  37. 37. Practical Examples: Precipitate Analysis A HIAPI-CM helps to identify solubility issues when analyzing samples from sublibraries … % of library Library containing precipitate B Sublibrary A 0.1% Sublibrary B 2.5% Sublibrary C 0.8% … providing a useful dataset when communicating problems with suppliers, collaborators and CM staff internally. C The Scripps Research Institute © 2011 – All rights reserved
  38. 38. Compound Management Responsibilities & CustomersWhat operational challenges are HTSencountered during theseinteractions?• Quality of external samples & sample data Medicinal DMPK & Chemistry Pharm• Degradation of samples over time• Enforcing internal QA/QC standards Compound 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 becoming Therapeutic Areas depleted, new acquisitions, etc.) The Scripps Research Institute © 2011 – All rights reserved
  39. 39. Compound Management Responsibilities & CustomersWhat operational challenges areencountered during these • HIAPI-CM enables externalinteractions? samples to be quickly QC‟d• Quality of external samples & and compared against sample sample data data upon arrival• Degradation of samples over • HIAPI-CM enables monitoring time of compound library health• Enforcing internal QA/QC over time standards • HIAPI-CM allows CM staff to• Tracking sample properties & enforce QA/QC business rules genealogy in a way that can by alerting them to problems be easily audited in the • HIAPI-CM creates a snapshot future of a plate in time and allows• Managing large sample users to track samples over libraries which are constantly time in flux (multiple • HIAPI-CM makes QC of large copies, samples becoming libraries more manageable by depleted, new automating time intensive acquisitions, etc.) visual inspections The Scripps Research Institute © 2011 – All rights reserved
  40. 40. HIAPI-CM Summary • CM staff is able to proactively capture and address problems early on and prevent them from propagating downstream. HIAPI-CM allows CM staff to capture errors in real-time. • Time saved from not having to visually inspect plates allows CM staff to spend more time on other important tasks. • Color detection helps better understand source of HTS data artifacts and allows us to track compound plating fidelity over time. • Analysis of HIAPI-CM data can reveal interesting trends. Do plates from one vendor have more artifacts (precipitate?) than another?Additional information, including HIAPI-CM Pilot Screen results, can be found in “Monitoring ofHTS 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 © 2011 – All rights reserved
  41. 41. One Final Thought… “We now have the technical ability to get the wrong answers with unprecedented speed. If you put the wrong stuff into the front end of our analytical pipeline, we will not only lose the war on cancer, we’ll pollute the scientific literature with incorrect data that will take us a long time to sort out. This is a crisis that requires disruptive innovation.” Carolyn Compton – Director, Office of Biorepositories and Biospecimen Research at National Cancer Institute Wired Magazine article on Biobanking, May 2010 The Scripps Research Institute © 2011 – All rights reserved
  42. 42. 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 Christine Pinello Louis Scampavia Timothy Spicer The Scripps Research Institute © 2011 – All rights reserved

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