Presentations on sample management including compound collections and biostorage
From LabAutopedia
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Presentations on sample management including compound collections and biostorage
Abstracts of presentations hosted on the web site of the Laboratory Robotics Interest Group (LRIG)
| 150th LabAutopedia article |
Considerations in Building a Compound Management Lab
Ted Peters; Compound Manager
Constellation Pharmaceuticals Inc.
The challenge of starting a compound management lab with the limited resources of a startup company has been a unique experience. Considerations of what is essential to the process including storage, automated pipetting needs, technician staffing and IT support. The focus of these consideration is to adopt new technologies and concepts for faster screening of assay ready plates. There is an ongoing effort to create a small scale lab with large scale expectations of HTS and hit to lead activities. The details at the one year mark of what has been accomplished and where we are striving to be.
Bringing a Compound Collection into the 21st Century: The Introduction of Automation and QC
Myra O'Leary; Research Technician, Compound Management
The Broad Institute
The Broad compound management team previously worked in a fully walk up mode. With our previous setup, throughput was limited and mistakes could go undetected. Collaborating with HiRes Biosolutions we established a fully automated screening center and compound management system. We also implemented quality control by LC/MS throughout our entire existing collection creating thresholds for compound quality. Details of our current compound management system include increased throughput, improved automation capabilities and compound quality, and novel informatics tools and a bright outlook for our future.
Progressive Compound Management: Strategies and Pitfalls
Rhett L. Affleck, Ph.D.; V.P. Technology
Nexus Biosystems
The cancer Biomedical Informatics Grid® (caBIG®): Resources to support translational research
Donna Messersmith, PhD; Integrative Cancer Research Product Representative
National Cancer Institute - Center for Bioinformatics and Information Technology
caBIG® is an NCI Initiative to establish a virtual network of organizations developing and adopting interoperable databases and analytical tools to facilitate translational cancer research. It is an open-source, open-access program, and all the tools and resources are freely available for the research community. Mature tools have been bundled into the Life Sciences Distribution and Clinical Trials Management Suite.
The Life Sciences Distribution includes tools that allow management and annotation of microarray data (caArray), biospecimens (caTissue), clinical information (CTODS), in vivo images (NCIA), genome-wide association studies (caGWAS), as well as integrated analysis and annotation of sequence and expression data (geWorkbench). All the LSD tools are connected to caGrid, which makes it possible for the databases at multiple institutions to be interconnected to support data sharing and integration.
The Clinical Trials Management Suite is a comprehensive set of modular and interoperable tools to support the management of study participant information through the clinical trial lifecycle. The Suite enables management of tasks such as: screening and registering patients for accrual to clinical trials; scheduling and tracking of patient encounters during the course of a study; integrating laboratory results with the patient record; tracking and managing adverse events; capturing, storing, analyzing and routing clinical data in a meaningful manner.
Biospecimen Research Database (BRD)
Andrew Breychak, PhD; Biospecimen Research Database (BRD) Representative
National Cancer Institute - Center for Bioinformatics and Information Technology
The Biospecimen Research Database (BRD) is designed to address the problem of no reliable means to find well vetted, sufficiently expressed experimental protocols for creating biospecimens. This affects researchers in terms of the time to search for and find a relevant protocol to utilize. If one is not found then additional time and effort is required to develop their protocol. The impact of a solution would be to expedite scientific research. The ideal solution would be to provide a searchable, well-documented means to prepare a repeatable and consistent biospecimen through a curated protocol.
The BRD addresses this need by promoting the idea that data about biospecimen protocols should be structured in a way to allow easy search and use. Papers and studies are curated to identify technology platform, analyte, and biospecimen location. As the curated quantities that represent best practices increases the BRD will become a preferred starting point to find well annotated protocols. This will give rise to Standard Operating Protocols (SOPs) built from the meta-analysis of biospecimen protocols. By posting published SOPs in the BRD and making them searchable entities with the characteristics of being digitally unique, versioned, able to be referenced, and portable the BRD will fulfill part of the mission of the Office of Biorepositories and Biospecimen Research (OBBR).
Mixed phase 21st century, world class biobanking story
Steve Arsenault, directeur de l’exploitation
Biobanque Génome Québec
Challenges of implementing a world class Biobank
Building a public resource: The Genome Quebec – Centre hospitalier affilié universitaire régional de Chicoutimi Biobank
Evaluating and choosing a cost-effective and sustainable infrastructure
Implementation Process and Timeline
Current Biobank Operations
DNA Extraction Technology Overview – Increasing Capacity 10X
Robert J.Corr
Pfizer Global Research & Development, DNA & BioFluids Center of Emphasis, Pfizer Inc., Kings Heights, Groton, CT
New protocols, extensive multiplexing, increased sensitivity of detection, and advances in miniaturization and automation have substantially reduced the amount of DNA required for downstream assays prompted the question: are we banking an appropriate amount of DNA?
The current DNA extraction platform at the DNA & BioFluids CoE was designed to extract large quantities of DNA from large volumes of human whole blood. After discussions with our colleagues in Exploratory Research, it was determined that decreasing banked DNA amounts while increasing throughput was preferable to the current model. This presentation describes the process of reviewing the current technology landscape with the intent of increasing daily DNA extraction capacity by ten fold while maintaining quality and reducing operating cost. The exploration of the technology landscape included the review of chemistry (solid-phase, precipitation, silica, and magnetic bead technologies) and various automation options. Additionally, in-house and outsourcing processing costs were compared.
Development of a Robotic Frozen Sample Aliquotting System
Dale Larson, Draper Laboratory (and Harvard Medical School), Cambridge, MA
John Slusarz, Harvard Medical School, Cambridge, MA
Steve Bellio, Draper Laboratory, Cambridge, MA
Vincent Chun, CryoXtract Instruments LLC, Quincy, MA
Helena Judge Ellis, Brown University, Providence, RI
Nader Rifai and Gary Bradwin, Children’s Hospital, Boston, MA
Freezing samples is a ubiquitous method of preserving the fidelity of biological specimens during long term storage. Some proteins and RNA are known to degrade if not frozen, small molecule compounds in DMSO absorb water vapor compromising the solubility of some of the compounds, and cell life is prolonged by freezing. All current methods of processing these frozen samples require thawing before aliquots can be prepared -- exposing them to freeze-thaw cycling that is detrimental to the quality of the specimens. Moreover, the thawing and mixing are time consuming. Freeze-thaw cycling is particularly problematic for biomarker research, both discovery and validation, where the troubling question is “Was a biomarker present but no longer there?” A robotic system is being developed that eliminates the need to thaw the samples before extracting aliquots; thus, maintaining biological stability and integrity of the remaining quantities, extending the usable life of biological specimens, decreasing operating costs, increasing throughput, and reducing lead times. Conceptually, the technology is a specialized core drilling system that uses a hollow Titanium tube with a cutting profile at its distal tip to cut a core from the frozen specimen under cryogenic conditions that will remain in the tube when the needle is withdrawn. The robotic system then positions the needle over an empty cryovial and deposits the core. The prototype will be deployed in the Rhode Island BioBank at Brown University in the spring of 2009. Commercialization is envisioned for both benchtop systems as well as integration with automated frozen storage systems. This talk will present the initial proof of principle data and describe the prototype design.
Development of QC methods to monitor cross-contamination from fixed-tip automation used to extract DNA from clinical blood samples
Stephanie K. Hall, Jason Harraden and Diane L. Johnson
Pfizer Global Research & Development, Groton Laboratories, Pfizer Inc., Groton, CT 06340 DNA/Biofluids BioBank, Pfizer Inc., Kings Heights, Groton, CT
Clinical studies and gene-based target discovery require high quality DNA for genotyping, genetic association studies and resequencing efforts. Rigorous quality control (QC) procedures are required to assess the DNA extracted from our automated DNA extraction process to ensure high standards and sample integrity for the material used in our studies. Our DNA extraction process uses fixed-tip automation which could increase the potential of sample contamination. The QC procedures that have been developed to monitor cross-contamination will be discussed in our presentation.
Evaluating samples for cross contamination using water control samples is a critical step in our QC methodology. TaqMan genotyping assays were used initially to evaluate water samples from our DNA extraction process. Cross-contamination rates approaching 20% were detected in early development of the DNA extraction process. Enhanced tip washing procedures were implemented in addition to a tip bleaching step. These modifications significantly reduced observed cross-contamination levels to <2%. One limitation of the TaqMan assay is its inability to precisely quantitate the contamination that was detected. Copy number and plus/minus real-time PCR assays were developed and used with serially diluted DNA of known concentration to provide absolute quantitation of contamination levels. Using these assays, we have been able to detect contamination at levels of 1 pg/ul. A mixing experiment was performed to assess whether low level system contamination could alter the performance of extracted DNA samples in genotyping assays. A contaminated water sample from an individual homozygous for one SNP allele was combined in equal proportion with DNA from an individual homozygous for the other SNP allele. TaqMan genotyping assays were performed and no alteration in the genotype of the DNA sample was observed. The genotypes were always reflective of the DNA allele and were not affected by the presence of contamination from the combined water sample. Future enhancements are being developed to provide QC methods to evaluate clinical DNA samples extracted on our automated system.
ISBER, the International Society for Biological and Environmental Repositories
Dr. David Toke, Associate Managing Director
Rutgers University Cell & DNA Repository (RUCDR)
ISBER is the leading international forum that addresses the technical, legal, ethical, and managerial issues relevant to repositories of biological and environmental specimens. Dr. Toke will present a brief overview of ISBER; including advantages of membership, corporate sponsors, Best Practices 2nd Edition, and the annual meeting in May at Bethesda.
Development and validation of the UK Biobank sample handling, processing and archiving protocol
Tim Peakman, Executive Director
UK Biobank
UK Biobank is a large prospective study established in the United Kingdom to determine the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. Which biological samples are collected and how they are processed and stored will have a major impact on the future value of the UK Biobank resource. The UK Biobank sample handling and storage protocol has been carefully designed to future proof the study (i.e. to avoid, as far as can be predicted, processing or storage approaches that will preclude current or future assays) and to provide a resource that would give the maximum scientific value within the available budget. The protocol was developed through a thorough review of the literature on sample handling and processing as well as wide consultation within the academic community. This approach addressed issues such as which samples should be collected, how and when they should be processed, and how the processed samples should be stored to ensure their long term integrity. The factors involved in developing the final protocol will be discussed. The recommended protocol was also extensively tested in a series of pilot studies conducted by collaborating groups throughout the UK. Using a variety of technologies to assay the genome, transcriptome, proteome and metabolome, these studies examined the stability of a wide range of components of blood and urine maintained at either 4ºC or 18ºC for varying times prior to processing and cryopreservation. An overview of the results of these pilots will be presented. The sample processing and archiving protocol adopted by UK Biobank provides a feasible approach to quality and throughput that reflects the size and aims of the project within the available funding.
Implementation of the UK Biobank
Paul Downey, Director of Operations
UK Biobank
UK Biobank is a new organisation, set up to facilitate efficient medical and scientific research. The project will recruit 500,000 volunteer members of the public over a period of three years. The volunteers provide detailed information about the health and lifestyle and consent to access to their health care records. This will form a valuable resource that can be rapidly accessed by research organisations.
In order to deliver the project, a national network of recruitment clinics has been established to receive and process the volunteer participants. A biological specimen processing factory has been constructed and an automated biological specimen repository developed, having the capacity to process and store the 14,000,000 sample aliquots that will be created.
The use and delivered benefits of utilising modern manufacturing practices to design implement and operate a sample processing facility will be discussed. The use of appropriate techniques during the evolving phases of the project: the research and design phase, the operations development phase and the operational phase will be covered. Selection and implementing appropriate culture and quality systems at the phases of the project to support the organisational objectives will be discussed.
The Pfizer Liquid Store, DNA & BioFluids REMP Store
Craig Hines, Manager, Liquid Store Center of Emphasis
Diane Johnson, Head of DNA & BioFluids Center of Emphasis
Leonid Vodonos, Facility Manager
Pfizer - Kings Heights Technology Center
This presentation will discuss the Kings Heights Technology Center scientific business objectives in conjunction with the facility support infrastructure and operational service delivery model. The presenters will provide details of the unique relationship between the Kings Heights Scientific Lines and Global Operations that laid foundation for a dynamic and State-of-the-Art technological facility.
Recently Global Operations has collaboratively developed and implemented a wide variety of business specific services including Processing Labs humidity control, management of service contracts based on contractual partnership, scheduling and coordination of preventative maintenance, demand repair work, handling service related documentation, Facility Center asset management, 24/7 monitoring and equipment emergency response, production process consumable supply/tracking and lab support technical services. Global Operations has made a commitment to deliver cost-effective services and solutions that enhance scientific productivity.
The timelines for design, manufacture, and installation of the REMP Stores will be presented. As well as a number of functionalities that was developed for the Liquid Store, DNA & BioFluids REMP store & laboratories.
The Rutgers University Cell and DNA Repository
Dr. Andrew Brooks, Associate Director of Technology Development
Rutgers University Cell and DNA Repository (RUCDR)
The Rutgers University Cell and DNA Repository (RUCDR) is among the largest academic repositories in the world. The scope of the repository grows every year and includes service offerings that range from DNA extraction to cell line immortalization in addition to a considerable sample distribution program. Currently the RUCDR maintains several large federal respoitories for the following NIH institutes: NIAAA, NIDA, NIMH and NIDDK. Additionally, the RUCDR services several foundation projects that include and are not limited to the Simons Autism Foundation and the New Jersey Tourettes collection. In total the RUCDR currently manages over 60 different clinically based projects through these and other agencies which help geneticists around the world understand the genetic basis for over 25 different diseases. In order to coordinate the collection and processing of samples from over 400 collection sites worldwide and manage over 1 million cell line aliquots and 750,000 samples in mechanical storage the RUCDR has developed several sophisticated automation schemes to handle many aspects of the RUCDR workflow. The structure of the RUCDR, a description of its automation infrastructure and a detailed overview of the programs services will be discussed.
Shared Materials Repositories at the Harvard Institute of Proteomics
Stephanie Mohr, Ph.D.; Manager, PSI Materials Repository
Harvard Institute of Proteomics, Harvard Medical School
The Harvard Institute of Proteomics (HIP) hosts the DF/HCC DNA Resource Core plasmid repository, which has a collection of more than 30,000 plasmid clones that are stored, maintained and distributed at HIP. In addition, HIP was recently awarded a five-year, multimillion dollar grant from the NIGMS division of NIH to host a similar plasmid repository for the Protein Structure Initiative, a consortia group of researchers at several institutions who have generated more than 65,000 plasmid clones as part of their efforts to resolve the 3D structures of diverse proteins. At HIP, plasmid clone samples are transformed into phage-resistant bacterial host strains, single-colony selected and used to create glycerol stocks in a highly automated, highly quality-controlled manner. Plasmid clone samples are then stored at -80 degrees C in individually barcode-labeled tubes in a state-of-the-art automated freezer storage system, the BioBank (Thermo/Zmation) and back-up samples are stored in standard freezers. Plasmid clone information (vector info, insert info, growth conditions, etc.) is carefully curated and stored in our custom Plasmid Information Database (PlasmID; http://plasmid.hms.harvard.edu). Standard operating procedures for clone intake, sequence validation, storage, maintenance and distribution of plasmid clones will be discussed.
The Repository for the International HapMap Project
Donald L. Coppock, Ph.D.; Assistant Director
Coriell Cell Repositories, Coriell Institute for Medical Research
The International HapMap Project was established to create a resource for genetics research to make it possible to speed the identification of genes for diseases. The goal is to create a map of human variation by identifying single nucleotide polymorphisms (SNPs) in a number of populations from around the world. Coriell has provided the repository for these samples. In total there are 1,200 cell lines in the Repository. The Coriell approach to establishing this Repository will be described including interactions with the donor communities, establishment of cell lines, preparation of DNA, distribution of samples and handling the extensive data connected to the samples. Lastly, the possibility of automation of the Repository will be discussed in relation to the HapMap Repository.
NCI's Recent Initiatives in Biospecimen Research and Policy
Jim Vaught, Ph.D.; Special Assistant for Biorepository Science
Division of Cancer Epidemiology and Genetics, National Cancer Institute
Recognizing that biospecimen resources are crucial to the research community, the National Cancer Institute (NCI) established the Office of Biorepositories and Biospecimen Research (OBBR)in 2005. One of the goals of the OBBR is to unify policies and procedures for NCI-supported biospecimen resources. In early 2006 NCI released the First-Generation Guidelines for NCI-Supported Biospecimen Resources. The Guidelines include recommendations for biorepository technical and operational activities, informed consent, informatics, intellectual property and specimen custodianship. Future editions of the Guidelines will include revisions based on new NCI-OBBR initiatives in biospecimen research. Among other strategic initiatives the OBBR will also evaluate new technologies to improve the overall quality of biospecimens as well as to enhance the efficiency of collection, processing and storage of biospecimens for research.
Pfizer-REMP Biofluid BioBank Store
John Williams, Ph.D.; Director
Pfizer Global Research & Development
The need, capacity and design of a unique –20°C/-80°C combined automated REMP store for biofluid samples will be presented. The refrigeration design is novel and based on a system developed by Pfizer together with Environmental Specialties Inc. (ESI) for centralized –80°C long-term freezers. REMP has designed unique door access and robot access from a –20°C compartment into the –80°C freezers. A constraint of +/-5°C was imposed on all –80°C operations. The practical impact of this constraint on operational processes will be discussed. Several aspects of the most critical component, the Luwa Environmental Specialties (ESI) cascade freezer systems will be recounted with emphasis on redundancy specifications. Performance data for the operational systems will be discussed to illustrate the time constraints required to remain within the +/- 5°C specification. This aspect has required new REMP software incorporating a novel algorithm for optimal access to the multiple freezers to fulfill a single order across multiple storage racks. Furthermore a specific loading algorithm has been added to ensure all samples are loaded from the bottom of freezers to maximize sample cooling in partial freezers.
DNA samples are stored in the –20°C compartment that is a standard REMP store. DNA samples are thawed and refrozen after each access and are in the proprietary REMP 96-well 900ul tubes. Individual samples are replaced in their original locations to prevent store fragmentation. In contrast biofluid samples are in the same tubes but heat-sealed and used as single use samples to minimize freeze/thaw cycles.
The timelines for design, manufacture, and installation, will be presented. A number of functionalities that were developed for the earlier REMP stores and their reuse will be discussed, together with the rationale for a partial FAT at Oberdiessbach will be presented with respect to reduced time and cost versus potential issues.
Rutgers University Cell and DNA Repository
Dr. David Toke; Associate Managing Director
Rutgers University Cell & DNA Repository (RUCDR)
Dr. Toke will share his professional expertise on:
* managing large volumes of specimens and data generated from research
* enabling public and private organizations to share data to enhance the research process
* addressing the short and long term storage and logistics needs of biorepositories
* meeting HIPAA and IRB compliance requirements and patient consent restrictions
Rutgers University Cell and DNA Repository is a nationally renowned facility and has combined partnerships with the National Institutes of Health (NIH), including the National Institute of Diabetes, Digestive, and Kidney Disease(NIDDKD), the National Institute of Mental Health (NIMH), the National Institute on Drug Abuse (NIDA), as well as, private organizations, such as the Cure Autism Now/Autism Genetic Resource Exchange.
Micro and Nano-Fabrication: Using Asymmetric Structures to sort biological objects
Prof. Robert Austin
Princeton University
Samples in DMSO: What an end user needs to know
Christopher Lipinski, Ph.D.; Adjunct Senior Research Fellow
Pfizer Global Research and Development, Pfizer, Inc., retired
The end user of samples in DMSO is someone who uses and stores samples for a relatively short period of time. The body of existing literature suggests storing samples in dry DMSO at room temperature for no more than three months and then discarding them. DMSO and water exhibit very non-ideal behavior when mixed together. This behavior is responsible for a range of property changes when the two solvents interact. These include; the hygroscopicity of DMSO; the viscosity increase when DMSO is wet and most importantly for this discussion: the marked solubility decrease of compounds in wet DMSO. When compounds precipitate from wet DMSO about half the time they can be resolubilized by sonication. The trend in chemistry to make amorphous compounds is an advantage in that initial solubilization in DMSO is easy. The downside is that the DMSO solutions have to be kept absolutely dry and freeze thaw cycles need to be minimized. Trifluoroacetic (TFA) contamination of samples in DMSO is a serious problem. TFA as low as 10 nM is cytotoxic in 24-hour cell cultures. This is not much of a problem in the typical short incubation HTS but it could be a problem as longer time interval safety assays get pushed into discovery. When TFA contaminated samples in DMSO become wet, acid hydrolysis becomes a serious concern. Many heterocycles made by a dehydration step are perfectly stable under neutral conditions but are hydrolyzed by TFA in wet DMSO.
Poor Aqueous Solubility and Compound Aggregation: Detection, Differences, and impact on In-Vitro Screens
Joseph Goodwin
BD Biosciences
Poor aqueous solubility and compound aggregation are two persistent problems that interfere with both high throughput and secondary screens. Poor solubility and compound aggregation both directly impact the effective compound concentration and the accuracy of the in-vitro assay results. In addition, the formation of compound aggregates can cause false positives by interacting non-specifically with the enzyme ligand interaction. The negative effects that particle formation has on in-vitro screens will be discussed. In addition, new methods that can be used to distinguish aggregation from precipitation will be presented using the BD GentestTM Solubility Scanner, a flow cytometry instrument specifically optimized for rapid and highly sensitive detection of insoluble and aggregate particles. The primary distinction of this technology verses other light scatter methods, is the ability to generate distinct light scatter signals for each particle as it passes through the excitation beam. This unique capability enables the analysis of a wide variety of sample types (from traditional assay buffers to more complex samples containing excipients and serum).
Automation of compound management at Schering-Plough Research Institute (SPRI)
Marybeth Burton; Associate Director, Chemical Technologies
Schering-Plough Research Institute
Proprietary research sample collections are one of the most valuable assets for large pharmaceuticals companies. Investment in technology to store, retrieve, prepare, and analyze this key resource is critical for the support of current and future drug discovery screening efforts. This presentation describes the project undertaken by Schering-Plough Research Institute (SPRI) to automate compound management processes and highlights improvements in request processing cycle time resulting from this initiative.
Practical Considerations for Enlightened Compound Management
Rhett Affleck, Ph.D.; V.P. Technology
Nexus Biosystems
Beyond the choices of storage systems, container types, and compound selection, many questions remain regarding how to best achieve a compound management facility’s goal: delivering the proper amount of each requested compound – at the required throughput and at a reasonable cost. Precipitation and degradation of compounds in DMSO stocks is a known problem. Should compounds be stored dry, in DMSO, or both? If in DMSO, at what concentration? Should multiple copies of each compound be aliquotted and stored? These and other decisions will ultimately influence screening results and should be considered by compound managers and screeners before processes are put in place that needlessly waste or don’t actually deliver a large fraction of the library.
Compound Management, One Size Fits All? and Other Pitfalls
Paul Gosnell; Group Leader, Compound Management
Bristol-Myers Squibb
The past ten years of compound management has been an extremely dynamic period of development and growth. During this period all of the major pharmaceutical companies and many of the larger biotechnology companies have invested heavily in their compound management capabilities. Much success has been achieved and through a partnering with technology vendors, compound management has become an inherent part of successful drug discovery. However, the past ten years has been a time of rapid change and a myriad of paths have been pursued in drug discovery, as a result many of the compound management solutions delivered have been the victims of planning, design and implementation pitfalls. This presentation will expose several common pitfalls of compound management and discuss options for avoiding the same pitfalls in future compound management endeavors.
GenVault: Dry-state DNA storage: Enabling Pharmacogenomics through Smart Biosample Management
Dr. David Wellis, PhD; Senior Vice President Sales and Marketing
GenVault
The management of biosamples has become increasingly important for pharmaceutical companies and contract research organizations in light of access, traceability and cost requirements. Biosamples must be easily shipped, repeatedly accessed and conveniently distributed. Biosamples must also be stored in cost-effective, long term storage conditions that are secure and traceable. GenVault exceeds these demands with a fully integrated sample management system designed for optimizing storage and retrieval and quick accessibility of collected biological samples. The core of the platform, the GenPlate, enables long-term storage, high throughput access, standard shipment and recovery of high quality DNA all at room temperature. GenVault’s state of the art system is automated and offers clinical informatics to meet the needs of both small and large repositories.
When Robots Are Good...Fully Automated Thermo/CRS Robotic Assay System with Dual FLIPR-Tetra and TAP SelecT Robotic Tissue Culture System
Veronica Soloveva, James LaRocque, Edward McKillip
Wyeth, Collegeville, PA
GPCRs and ion channels are very popular targets in research for new drug candidates. Measurement of rapid biological responses in cells using fluorescent dyes requires fluorescent plate readers equipped with liquid handling automation. The FLIPR (Molecular devices Co) has become one of the most popular and useful kinetic readers, because it enables both simultaneous addition of liquid and simultaneous monitoring for changes in fluorescence in every well of a plate. The new generation FLIPR TETRA offers improved quality and reliability. The fully automated Thermo/CRS robotic system integrates several different automated elements such as a BioTek ELX washer unit, a PE Evolution pipettor and PE FlexDrop dispensers that can perform complex, multi-step processes, unattended. The sophisticated Thermo/CRS robotic control software, POLARA, ensures that each and every plate of sensitive cells in a large batch experiences the same procedure as an individual plate assayed in the gentle hands of a scientist. Such robotic systems can process hundreds of plates a day and require large-scale automated support for cell preparation. The TAP SelecT is an automated robotic system that can plate 100-300 plates of cells per day with inhuman accuracy and precision. In addition to plating cells the SelecT can also pass and expand cell lines. We will present a case study of a GPCR mediated Ca-flux assay, where the exceptional quality of the continuously cultured cells provided by the TAP SelecT was an enabling factor in reducing this screen to practice. Working together, this robotic team can enable high throughput logistics for even very sensitive cell based assays.
Leveraging Compound Management Capabilities in Support of Drug Discovery: From Sample Archive to Sample Distribution - Driving Efficiency and Improving Productivity
Michael J. Sofia, Ph.D.; Group Director New Leads Chemistry
Bristol-Myers Squibb Pharmaceutical Research Institute; Wallingford, CT
The physical compounds within a pharmaceutical company’s compound collection are the embodiment of many years of creativity and innovation, and through the screening process, these compound assets are the genesis of new leads and future drugs. Therefore, for the future success of the business, it is essential that these assets be effectively managed and leveraged to support all drug discovery needs from lead discovery through lead optimization. Pharmaceutical compound management organizations have evolved to manage these critical compound assets and to service the vast array of compound needs for global discovery operations. Technology advances and process optimization have broadened the scope of compound management’s impact on the drug discovery environment and have lead to significant productivity and efficiency gains. The expanded role of compound management within the BMS drug discovery environment and the impact of technology and process development on functional and organizational productivity and efficiency will be described.
Impact of Acoustic Non-Contact Transfer of Compounds upon Compound Management and Ultra High Throughput Screening
Timothy Spicer; Research Scientist
Bristol-Myers Squibb Company; Wallingford, CT
Research and development organizations are under constant pressure to streamline processes, remove bottlenecks and reduce costs in order to be successful in new drug development. The demand to move from 384-well based screening to rapid and miniaturized screening in 1536-well density formats, from a pharmaceutical development perspective, has been a priority for many years and until recently, largely unsatisfied. Recently, we have overcome a significant hurdle towards that goal by implementing acoustic non contact droplet ejection (ADE) to enable the reformatting of compounds from 384-well source plates into 1536-well assay plates. This has been coupled to fully automated flexible screening platforms to allow us to screen 100K compounds per day. While we have realized the power of this new technology in terms of enabling ultra high throughput screening, there are multiple changes that must be properly understood and implemented within our current compound collection supply line. However, the benefit with regards to reagent costs, consumables costs, the environment, the potential for closed loop screening, the potential for compound conservation and the ability to acoustically audit each source well justify these changes and will be discussed.
Fully Automated Compound Distribution Center
Collette DeChard; Manager Basic Biological Support; Compound Management Group
Merck & Co. Inc.; Rahway, NJ
Four years ago Merck's Compound Management Group started a journey to design, develop and implement a Fully Automated Compound Distribution Center. Come see how our vision became a reality!
Compound precipitation from DMSO and the synergy between water uptake and freeze / thaw cycles
Christopher Lipinski, Ph.D.; Adjunct Senior Research Fellow
Pfizer Global Research and Development, Pfizer, Inc., retired
Freeze / thaw cycles have been recognized as deleterious to compound storage in DMSO stock solutions but largely for the wrong reasons. Historically, freeze thaw cycles have been viewed mostly as harmful with respect to compound stability, i.e. chemical degradation. This is probably incorrect. Freeze / thaw cycles in synergy with water uptake into DMSO are primarily harmful with respect to compound precipitation. The synergy aspect is very important. It may be difficult to experimentally show an adverse effect of freeze thaw cycles if the DMSO is bone dry or if materials initially dissolved in DMSO are crystalline as opposed to amorphous. It is the uncontrolled water uptake into DMSO stocks in synergy with cooling that is the problem and that is solved by single freeze thaw tube storage systems. The bottom line is to treat DMSO in compound storage as if it were a water sensitive reagent.
Can anything be done about precipitated samples? Rather remarkably the answer is yes. In the majority of cases precipitated samples can be re-dissolved by sonication. This behavior is beneficially unexpected, is without literature precedent and is counter to simplistic thermodynamic considerations. In a minority of cases sonication induces precipitation from super saturated solutions. This behavior does have limited literature precedent.
Overcoming the Problems Associated with Long-Term Storage of Compounds in DMSO
Timothy J. Waybright and Thomas G. McCloud
Natural Products Support Group, SAIC-Frederick, Inc.; National Cancer Institute at Frederick, Frederick, MD
Lessons Learned in Liquid Dispensers Validation
Jonathan Peterson, PhD.; Instrument Validation Manager
Molecular Devices Corp.
Getting a liquid handler “dialed in” for precise, reliable operation can consume many hours (and many cases of microplates). Having been through this discovery process on a number of instruments, Molecular Devices has developed some expertise in validating its liquid handlers. We will present some of the lessons we’ve learned during the development and validation of fluidics instrumentation. Some topics covered in this presentation will include: How do you select an appropriate detection method (absorbance vs fluorescence)? How do you select an appropriate dye and concentration? What can you do to minimize detection artifacts? What can you do to minimize meniscus effects? Special considerations for air displacement dispensers. How to characterize carryover and tip washing effectiveness.
Note: John has published a related paper. The citation info is: Petersen J., Nguyen, J. Comparison of Absorbance and Fluorescence Methods for Determining Liquid Dispensing Precison. JALA (2005) Vol. 10, No. 2, pp. 82-87.
Stability of Compounds Stored in TekCel Plate Management System: Application of New Approaches for Ultra-High-Throughput Analysis of Compound Stability
James A. Connelly Ph.D.; Director of Library Production and QC
Aventis Combinatorial Technologies Center
Biological and Environmental Repositories - Current and Future Directions
Robert Hanner, Ph.D., President
International Society for Biological and Environmental Repositories (ISBER)
Repository based specimen collections are an essential part of the infrastructure underpinning life sciences and biotechnology. They can contain environmental samples, culturable organisms (e.g. micro-organisms, plant, animal and human cells), replicable parts of these (e.g. genomes, plasmids, viruses, cDNAs), viable but not yet culturable organisms, tissues and organs, as well as databases containing geographical, molecular, physiological and structural information relevant to these collections. Such repositories contain valuable (often irreplaceable) samples that might have been collected for one purpose, but because of the unique population they represent, might be useful to many future investigators for many other purposes. The International Society for Biological and Environmental Repositories (www.ISBER.org) serves as a forum to share knowledge and experience among repositories, so that collectively, they can operate more efficiently to build and maintain collections while giving consideration to emerging new technologies. Because repositories tend to expand with time and the emergence of new research techniques, a pressing need exists to facilitate the automation of many repository activities, which involve both specimens and associated data. To illustrate this phenomenon several new initiatives are discussed, including the National Dialogue on Cancer, the National Childrens Study, and DNA barcoding.
Septa Applications for Compound Preparation
Sam Abdelhamid and Paul Blake
Purdue Pharma, Cranbury, NJ, USA
Controlling the amount of water in chemical samples has become a priority among compound preparation departments. It is well known that DMSO can quickly absorb water from the surrounding air. This can compromise screening samples by lowering the concentration of dissolved material, and or causing sample precipitation. The introduction of septa based applications cannot only save time, by eliminating de-capping steps; they can also reduce the amount of water absorbed by solvents. By using vented tips that are filled with nitrogen, it is now possible to aspirate and dispense solutions from vials and deep well plates, without allowing the sample to come in contact with air. The use of liquid handling systems that incorporate septa and vented tips can also be used for combinatorial chemistry methods that use water sensitive reactants (i.e. acid chlorides). Septa caps ensure that moisture does not come into contact with air sensitive reagents. Various customs racks, holders, and vented tips were integrated with our current liquid handling procedures to yield liquid transfers under an inert atmosphere. The equipment and supplies used to implement these procedures, along with results, will be discussed in detail.
Integration of Sample Management & HTS at Wyeth
Michael Longden, M.S., Supervisor of Screening Resources Group, Screening Sciences; John Morin, Ph.D., Director HTS, Screening Sciences; Dominick Mobilio, Ph.D., Director of Cheminformatics and Compound Resources, Screening Sciences
Wyeth Research, Pearl River, NY, USA
Two years ago, Wyeth Research presented at MipTec 2001 their plans for a hybrid sample storage and retrieval system composed of modular units provided by 2 different vendors. (TekCel and The Technology Partnership) Although the price of innovation included some unplanned but not unexpected delays, this system is now complete. The installation will be described in detail, including the metrics of operation. The chemical integrity and quantitative recovery of compounds from this system will also be evaluated. The workflow enabled by this system and the IT infrastructure that supports it have bridged the gap between compounds and HTS at Wyeth.
Compound Solubility and HTS Screening
Christopher Lipinski, Ph.D., Adjunct Senior Research Fellow
Pfizer Global Research and Development, Pfizer, Inc., retired
Sessions on reproducibility in HTS screening appear in the 2003 and 2004 annual meetings of the Society for Biomolecular Screening. The focus has largely been on the biological aspect, i.e. how large is the overlap in screening results when the same library of compounds is tested against the same target but using different assay methods. What is only slowly being realized is that there is another dimension to the HTS screening quality issue. HTS assay quality is very much better if you really know the concentration of compound in DMSO stocks and if you really know the compound concentration when the DMSO stocks are diluted into aqueous assay medium. Relevant to this issue are the following sub-topics: 1) from the 1880’s Oswalds “rules of stages” and why it explains many DMSO solubility issues; 2) the dependence of DMSO freezing point on water content; 3) what exactly is there about freeze thaw cycles that causes solubility problems; 4) why is there such erratic behavior in terms of precipitation from DMSO and 5) what is the evidence that globally about 20% of compounds might ultimately have a DMSO solubility problem. Additionally, what has changed in the last year in terms of software and hardware that could help with the compound in DMSO solubility problem will be discussed.
Drug-Likeness and Lead-Likeness: An Overview of Recent Studies
Zhengming (Jimmy) Chen
Purdue Pharma L.P., Cranbury, NJ
The distinction between drug-like and non drug-like molecules has been a hot research topic in recent years. The most well known early study in this field is the “Lipinski’s rule of five” which was derived empirically from the analysis of the World Drug Index on the properties that maximize an oral drug candidate’s probability of surviving clinical development: molecular weight (MW) < 500, number of hydrogen bond donors < 5, number of hydrogen bond acceptors < 10, and ClogP < 5. The rule of five is now widely used to filter out compounds likely to have poor pharmacokinetic properties early on in drug discovery. Lead-likeness (compounds’ likelihood to be good lead candidates), as distinct from drug-likeness, is a new concept that is gaining acceptance in recent years. Lead-like molecules are generally smaller to allow for structural additions to enhance effectiveness during lead optimization, and is being incorporated into the library design and lead optimization processes. In this presentation, I am going to present an overview of recent studies on the topic of drug-likeness and lead-likeness. The presentation will provide a few intriguing insights into the influence of molecular properties on the likelihood of progression through the drug development process and trends in modern drug discovery.
SHOW, Sample Handling Operation Wizard
Ping Du, Livingston, NJ
Sample Handling Operation Wizard (SHOW) is a system developed to guide manual sample handling in the research laboratory. It comprises a sample tray mounted on a flat-panel computer monitor. Up to four transparent micro titer plates and up to 8 reagent vials may be placed on the sample tray. Images of the wells of the plates and vials are generated on the monitor and controlled by computer software. These images are directly aligned with the positions of the physical wells. By highlighting the wells or vials involved in a sample handling step of a pre-defined protocol, manual operation can be performed with precise guidance from the system. As a result, the risk of locating a wrong sample or placing a sample at a wrong location can be minimized, and sample handling operations become more efficient and less stressful.
Automation in Pharmaceutical Profiling
Edward H. Kerns, Li Di, Susan Petusky, Susan Li and Donna Huryn
Wyeth Research, Chemical and Screening Sciences, Princeton, NJ
Selection and optimization of candidates for activity and selectivity have traditionally played a dominant role in drug discovery. However, in recent years the complimentary nature of pharmaceutical properties in candidate success has been recognized. This has led to the implementation of pharmaceutical profiling as part of the discovery process. Several objectives of drug discovery pharmaceutical profiling can be met through strategies and tactics that involve automation: 1) The need for more information on in vivo delivery of the candidate to the therapeutic target has led to the implementation of assays that model key in vivo ADME barriers; 2) The need to improve discovery efficiency has led to accelerated analysis and early collection of data to avert ADMET problems that cause failure at later stages; 3) The need to perform discovery research more effectively has led to the application of pharmaceutical property information to better plan and interpret discovery activity assays. These applications require high capacity because of the large number of discovery compounds and speed because discovery moves quickly. This presentation describes the automation of pharmaceutical profiling assays for the properties: integrity, lipophilicity, solubility, permeability, metabolic stability, and CYP450 inhibition. The management of the resulting data and its delivery to discovery teams are also key elements of the pharmaceutical profiling workflow.
Quality Perspectives for Compound Storage
Dania Yaskanin, Ph.D.; Manager
Johnson and Johnson Pharmaceutical Research and Development Corporate Compound Logistics Center
The Corporate Compound Logistics Center (CCLC) is actively investigating compound quality and storage issues. Several approaches are being used, including studies of production materials, process verifications, and storage environment.
Production material changes over the past year have included compound storage vials, microplate seals, and DMSO vendors. The compound vials were replaced with a different vial type to improve compound handling and data quality. At J&J PRD, solubilized compounds in DMSO are stored in microplates in a controlled environment. To optimize compound storage in this environment, seven different microplate seals were evaluated for seal integrity with physical stress tests and detection of materials leached into DMSO. A portion of the solubilized compound inventory is also being moved into sealed polypropylene tubes that will allow comparison of compound quality when stored in plates versus tubes.
Process verifications have shown that solvent handling during compound solubilization and dilution influences the quality of compounds in solution. Qualitative analysis of a representative portion of the compound library is underway, with the goal of repeating the analysis over several years to record compound deterioration over time. Additional procedures for evaluating compound quality are currently being added to department capabilities, such as quantitative analysis of compound concentration, percentage of water content, and detection of contaminating materials extracted by DMSO.
A Summary of Compound Stability Experiments Performed at GlaxoSmithKline
Zoe Heaton, GlaxoSmithKline
Ensuring Compound Integrity With Modular, Scalable, Automated Solutions
Stuart Naylor, European Sales Manager, TekCel Inc.
Managing the ‘Crown Jewels’
Krystyna Holden, Millennium Pharmaceuticals
Purification for Quality
Biotage, Inc.
Automation Without Robotics, a Comparison of Common Approaches to Low Temperature Compound Storage
Ian Whitehall, TTP LabTech
Introduction of the Personal Digital Assistant into the Analytical Laboratory
Dan Brooke, GlaxoSmithKline
Evaluation of Technologies for Potassium Channel Targets Compound Screening
Dr. Weimin Tang, Principal Scientist, Johnson and Johnson/Pharmaceutical Research Institute
We have seen a surge of research in development of fast and reliable HTS methods for ion channel targets. This is driven by the fact that hundreds of ion channel genes from the human genome project and their functional association with human diseases. Some of the channels have been proved to be important in the drug discovery process such as HERG and various calcium channels. Traditional potassium channel functional study has relied on Patch-Clamp electrophysiology and Rb86 efflux assay. However, those methods were not easily deployed for drug screening because of the concern for cost and speed. Pharmaceutical companies have relied on dye based ion channel readers such as FLIPR and VIPR for many years and the results are controversial. This talk will focus on the development of non-radioactive Rb+ efflux assay using ICR8000, a system designed for medium throughput functional HERG channel screening. The development of HTS ICR12000 will also be discussed.
Issues in Compound Storage in DMSO
Christopher A. Lipinski, Adjunct Senior Research Fellow, Pfizer Global R&D, Groton Labs
Through-Hole Microarrays: A High Throughput Platform for Synthesis, Storage and Screening
Tanya Kanigan, BioTrove Inc.
Design of a Laboratory for Cell-based High Throughput Screening
Jessica Rivers, Research Associate, Maxim Pharmaceuticals, San Diego, CA
Low Volume Liquid Handling By A Dispensing Well Plate™
Roland Zengerle, IMTEK Institute for Micro System Technology, University of Freiburg, Germany
High-Throughput Protein Crystallography with the Corning Protein Crystallography Plate on the Beckman Coulter Multimek 96 Automated 96- Channel Pipettor
Phillip Bradford, Dr. Rongbao Li, Jennifer Fiedler and Dr. Thomas Fletcher III (Southern Research Institute), Edwin Dario and Tom Harrison (Beckman Coulter), Dr. Ma Sha and Gerald Campbell, Jr. (Corning)
An Automated Platform for Miniaturized Protein Crystallization
Holger Eickhoff, Patrick Umbach, Lajos Nyarsik , Martin Horn, Thomas Przewieslik , Wolfram Saenger , Hans Lehrach , Günther Knebel , Peter Opfermann
The Protein Structure Factory, Free University of Berlin, Institute for Crystallographie, Max-Planck-Institute for Molecular Genetics, Greiner Bio-One GmbH
Minimizing Compound Exposure
W. Steven Fillers, Ph.D., TekCel, Inc., Hopkinton, MA
Automated Microplate Sealing and Unsealing with SealTite
W. Steven Fillers, Ph.D., TekCel, Inc., Hopkinton, MA
Modular Strategies for Automated Storage and Retrieval
John Morin, Ph.D.; Biological Chemistry Section, Wyeth-Ayerst Research, Pearl River, NY, USA
The Wyeth-Ayerst Research (WAR) High Throughput Screening (HTS) group is responsible for supporting project teams from 6 different therapeutic areas and maintains HTS laboratories at 2 separate sites. In addition to providing assay development and HTS services, we are responsible for dissolving compounds in DMSO and formatting them into micro-titer plates for distribution inside and outside the company. The WAR corporate library has swollen over the past 10 years through merger activities and the acquisition of combinatorial chemistry collections. By mid-1999 we estimated that sample preparation, storage and retrieval were consuming more than half of our personnel and equipment resources, so we began a project to improve our sample management functions. We achieved greater efficiency almost immediately simply by consolidating responsibility for sample management to a small group of volunteer specialists. Further gains came from collapsing our old 96-well sample plate library into 384-well plates, but the manual storage and retrieval of sample plates in over 70 upright freezers was still a bottleneck. We therefore circulated a Request for Proposals to several leading vendors of automated storage and retrieval systems. After many presentations and extensive deliberation, we ultimately chose to avoid the standard approach of a large, complex, integrated system with multiple overlapping and interdependent functions and to invest instead in a novel hybrid system composed of modular units provided by 3 different vendors: (TekCel, The Technology Partnership and Packard/CCS) I will describe what we’re building and why we chose this path. I will also update our progress as elements of the system have begun to arrive.
SmartPlate integrates library management and assay platforms to increase throughput and preserve compound library
Jeffrey A. Karg, PE; Boston Innovation Inc.; Cambridge, MA
Assay miniaturization has pushed the limits of fluid handling. 384 and 1536 well screening requires accurate and reliable compound dispensing during the reformatting procedure. This time-consuming and wasteful step is eliminated with the SmartPlate™ shipping, storing, and dispensing technology that includes integral dilution. A new concept assigns a DMSO dissolved compound to an individually addressable sealed tap. The taps are the storage, metering, dispensing, and diluting elements and formatted in a 384-well plate-based array. Compound dispense volumes range from 5-200nl. Reformatting, disposable tips, and wash cycles are eliminated. This presentation will highlight how SmartPlate10 works, implementation examples, and current performance data.
The Effect Of Sealing Versus Lidding Plates On Degradation And Water Uptake Of Compounds Held In DMSO At 4ºC
Zoe Heaton, César Ramírez-Molina - Analytical Sciences, Dr Sue Holland, Rob Hughes, Dr Rob Lifely, Compound Management, Linda Robb, Statistical Sciences; GlaxoSmithKline, Stevenage, UK
The Effect Of Freeze Thawing And Storage Time On Degradation Of Compounds At 4ºC Under Humidity Control Using Experimental Design
Zoe Heaton, Analytical Sciences, Dr Sue Holland, Rob Hughes, Dr Rob Lifely, Compound Management, Linda Robb, Statistical Sciences; GlaxoSmithKline, Stevenage, UK
The Importance Of Karl Fischer In Quality Control For The Support Of Automated Liquid Stores
Zoe Heaton, Mark Connell, Analytical Sciences, Dr Sue Holland, Rob Hughes, Dr Rob Lifely, Compound Management; GlaxoSmithKline, Stevenage, UK
The Effect of Freeze/Thaw Cycles on the Stability of Compounds in DMSO
B. A. Kozikowski, L. E. Williams, D. Tirey, B. Kuzmak and K. L. Morand
Procter & Gamble Pharmaceuticals
High Throughput Screening Degradation Study: Determination Of Storage Options And Retention Limits
L.E. Williams, B.A. Kozikowski, T. Burt, B. Kuzmak, K. L. Morand Williams, B.A. Kozikowski, T. Burt, B. Kuzmak, K. L. Morand
Procter & Gamble Pharmaceuticals
DNA microarray fabrication and processing – Automation in the laboratory
Gary Hardiman Ph.D., Director BIOGEM (BioMedical Genomics Microarray Facility), Division of Biology, University of California, San Diego, CA
An Automated Approach to the Supply of Samples for Screening
Terry Wood, Pfizer Global Research & Development, Sandwich, UK
Liquid handling in Chemical Synthesis- The Celltech approach
Nick Ray - Celltech R&D, Granta Park, Cambridge UK
A cost-effective way to pipet 384 samples simultaneously
John Herich, Manager- HTS, Maxim Pharmaceuticals
How Exposed Are Your Compounds?
W. Steven Fillers, Ph.D., Andrée Proulx and Marsha Paul, TekCel, Inc., Hopkinton, MA
Compound Management Automation at AstraZeneca
Ian Yates, Head, Compound Management & Automation, AstraZeneca HTS Centre Sweden
The AstraZeneca HTS Centre based in Mölndal, Sweden is one in a network of four HTS centres that support the AstraZeneca drug discovery process. Integrated within the department is the Compound Management Team. This team, in partnership with compound management groups across the organisation, is responsible for managing the compound collection and ensure it’s accessibility to both the local HTS group and scientists globally. In common with many other companies in the pharmaceutical industry Astrazeneca has experienced a dramatic increase in both the size of it’s compound collection and it’s screening capacity. This has resulted in tremendous pressure being placed on compound management groups to manage and supply more compounds, and to do so quicker. This presentation will look at the automated systems that have been, are currently being, and will be, used at the HTS Centre in Sweden to enable us to meet this high demand. It will start with an overview of the systems that were implemented when the Centre was founded five years ago. It will then cover the systems in use today and conclude with a preview of a new automated compound management facility planned for the Centre. This facility forms part of AstraZeneca’s strategy for a more efficient and truly global compound collection.
Conversion of manual access of 384 lidded plates to an automated storage and retrieval system
Pavel Rychetsky, Martha Ackerman, Patti Willson; Biology Automation
Selectide, a subsidiary of Aventis Pharmaceuticals Inc., Tucson, Arizona, USA
Compound management and logistic support is an integral part of high-throughput screening activities. Usually, intermediate microtiter plates with diluted compounds have to be prepared in advance of a screening run. We eliminated this step by implementing a procedure for compound transfer directly from 384-well compound storage plates into assay plates during a screening run using a pin tool. After the screening run the storage plates are stored in freezers and reused later in the next screen. As loading and unloading compound plates for routine HTS runs became the most time-consuming step in our lab operation, we felt that further efficiency could be achieved by integrating an automated storage and retrieval system by TekCel Corp. into the HTS robot. The storage system is capable of presentation of storage plates to the screening robot without human intervention. Two major areas of application for the refrigerated storage and retrieval system are HTS and "cherry-picking". The advantages of this storage system concept, with its unique plate sealing capability, compactness, and expandability, will be presented.
Mass Storage / Retrieval of Chemical and Biological Libraries
Dr. Terry V. Iorns, Iorns Consulting, Inc., 6334 E. Viewmont Drive, Mesa, AZ 85215 USA
Storage, retrieval, and distribution of chemical and biological libraries is a critical activity in drug discovery. Successful high throughput screening requires careful coordination and interaction of screening technology with assay / reagent preparation and availability of screening libraries. Failure of any of these to come together leads to a problem in the discovery program.
What is a library? Consider a library as a collection of chemical compounds or biological substances that should be handled or screened together. Examples include:
· Compound Collection – all the compounds/substances a pharmaceutical company can put their hands on.
· Related compounds by activity in a class of assay – such as a kinase or protease library.
· Related by structure or synthesis – combinatorial libraries
· Purchased collections
How are libraries received, stored and exchanged? There are four major ways to handle libraries:
· Solubilized in plates
· Solubilized in tubes or microtubes
· Neat substances in vials
· Neat substances in tubes or plates
Neat substances are generally quite stable and are generally stored at room temperature. Sometimes neat substances must be stored cold, in an inert atmosphere, or protected from light. Solubilized substances are generally stored in 100% DMSO. Most organizations store these solutions cold, near the freezing point of DMSO. Source plates or tubes generally contain a fairly high concentration, usually in the range of 3 to 20 mM. Collections are generally distributed to screening laboratories at much lower concentrations, usually less than 1 mM and often in the mM range.
Handling issues to consider:
· Automation of processes to prepare and distribute libraries
· Vendor and equipment reliability
· Sealing tubes and plates to protect solutions from evaporation or water absorption
· Unsealing or piercing plate seals to allow sampling by screening robots
· Stability of substances in solution over long periods of time and conditions
This paper will conclude with a survey of equipment and techniques to make the handling of libraries easier and more reliable. Products from several vendors in the following categories will be mentioned:
· Storage and retrieval systems
· Sealing and piercing devices
· Replication systems
· Robotic systems
Comparison of Microplate Sealing Tapes Using Standardized Test Protocols
Terry W. Lewis, PhD, Maurice H. Kuypers, Mialena M. Walker Medical Specialties Department - 3M Health Care - St. Paul, Minnesota
Adhesive tapes have become an attractive option to cover microplates in bioanalytical, genomic, and pharmaceutical research. Primary performance criteria for microplate adhesive tape seals include: prevention of evaporation from the individual wells; low contamination of well contents by the tape adhesive; prevention of cross-contamination between individual wells, and clean tape removal for access to well contents. Depending on the particular research objective, other criteria for adhesive tape seals may be important. These include pierce-ability for access to individual wells without entire tape removal, good optical properties, for monitoring well contents through the tape, and temperature resistance over wide ranges to include compound storage and PCR. This poster will describe results of a wide variety of adhesive tape performance testing designed to mimic actual industry use conditions. The tests include evaporation data with water, DMSO, and aqueous mixtures of isopropanol, methanol, and acetonitrile. Microplate composition and manufacturer were also varied. Temperature conditions ranging from -70° C up to room temperature and actual PCR cycling were evaluated. Other testing results on adhesive extractables, tape optical properties, and tape application and removal will be presented.
Micro-volume liquid dispensing. Analysis and examples
Ilya Feygin, Manager Research Engineering
Pharmacopeia, Inc
Precise dispensing of micro volumes of reagents in liquid form becomes more and more important with continuing miniaturization of the High Throughput and High Content Research process. Applicable to all platforms, from medium and high density plates to "micro-chips", fast and repeatable liquid dispensing can often become the key to a successful experiment. Various methods of existing dispensing technologies will be analyzed and Pharmacopiea's experience in implementing high speed dispensing will be presented.
A Complete Solution for Drug Discovery
Steve Fillers, Ph.D.; Chief Scientific Officer; TekCel, Inc.
Comparison of Robot Arms for the Laboratory Environment
Douglas Gurevitch, P.E., Director of Microarray Automation
Biocept, Inc.
The TekCel TekBench: An Innovative Tool for High Throughput Screening
Ben Knight
Millennium Pharmaceuticals
A Novel Process for Completely Automating Microplate Sealing, Unsealing and Storage
Julian Warhurst, Chief Technical Officer
TekCel Corporation, Hopkinton, MA
Over the past decade, the application of automation techniques to High Throughput Screening has made great strides. Automation has enabled HTS to increase productivity by ten-fold or more. Labs are now processing hundreds of plates per day. "A plate a minute with some automation strategies". Surprisingly enough, these advancements paid little attention to the way plates are handled before and after the actual screening process. Questions still remain about where and how to store these increased compound plates without compromising integrity.
Central to the concept of plate handling up and downstream is an effective way to automatically seal and unseal a microplate. Conventional approaches such as adhesive or thermal systems have been used with various levels of success in automated systems. However, neither of these technologies can be reused, once they have been removed from the plate or pierced by awaiting pipettors. The SealTite* microplate cover is the cornerstone of a unique system that provides a reusable, fully automated sealing and unsealing technique that guarantees sample integrity under an inert gas tight seal. Used with the totally automated PlateServer Workstation, plates are retrieved from the PlateStore storage module, thawed, unsealed, logged through the barcode and delivered to any vendor's automated platform at rates up to 240 plates per hour.
TekCel's new model for plate handling, storage and sealing is destined to change how microplates are automatically delivered and retrieved to various screening platforms as well as moved to long term storage. This novel approach can draw and analogy to the migration path the computer industry took in moving away from the core main frame to the client server distributed architecture. In this model data is stored and work is performed in multiple places as opposed to one large, inflexible system.
Assay Translation: Some guidelines for turning a manual laboratory process into an automated laboratory process
Douglas Gurevitch
Axys Pharmaceuticals
96 to 384 - Challenges and Solutions
Seth P. Cohen Ph.D.; Associate Director, HTS; Millennium Pharmaceuticals, Inc.
Automation Architectures for HTS and Their Impact on Productivity
Julian Warhurst; Vice President, Research and Development; TekCel Corporation, Hopkinton, MA
Automation Architectures for HTS and Their Impact on Productivity
Bob Trinka; Robocon Inc.
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