omation mbers - Society for Laboratory Automation and Screening
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omation mbers - Society for Laboratory Automation and Screening

omation mbers - Society for Laboratory Automation and Screening omation mbers - Society for Laboratory Automation and Screening

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11:00 am Thursday, February 5 Genomics – Advanced Topics Room A1 Sheri Olson Applied Biosystems 850 Lincoln Center Drive Foster City, California 94404 olsonsj@appliedbiosystems.com Co-Author(s) Lewis T. F. Wogan, Warren Tom, Charles Hsieh, Kyle Leinen Applied Biosystems 106 Gerri Shaw, Jim Shaw Bernard Shaw International Evaluation of High Throughput SNP Genotyping Lab Data Using FOCUS Statistical Software FOCUS statistical software (version 4.0) was used to evaluate daily processing efficiency and instrument functionality in a High Throughput Genotyping lab using the fluorogenic 5´ nuclease (TaqMan ® ) assay at Applied Biosystems. Laboratory processing data related to a specific customer project generated over thirty-five different processing days were recorded by an internally developed Laboratory Information Management System (LIMS). The LIMS captured reagent, consumable, instrument and operator information. The LIMS data was merged with corresponding data from internally developed Genotyping analysis software to create Daily Query Results files (DQRs). The DQRs were uploaded into the FOCUS software and the FOCUS Pre-Processor tool was used to isolate specific factor sets to assess processing efficiency and instrument performance. In the High Throughput Genotyping lab at Applied Biosystems, automated liquid handling instrumentation is used to prepare the Polymerase Chain Reaction (PCR) based TaqMan ® assay to evaluate Single Nucleotide Polymorphisms (SNPs) in a 384-well format. Consequently, the performance of the liquid handling automation has a significant impact on the genotyping results and on the efficiency of the overall genotyping process. Therefore, FOCUS statistical software was used to evaluate the liquid handling performance for each reaction plate processed as part of the customer project. Additionally, acceptance specifications incorporated in the Genotyping analysis software categorized the resulting genotype data with either a “passing” or “REDO” status. The FOCUS software also evaluated the results associated with a “REDO” status to calculate daily processing efficiencies.

11:30 am Thursday, February 5 Genomics – Advanced Topics Room A1 Ralf Muckenhirn Fraunhofer IPA Nobel Strasse 12 Stuttgart, 70569 Germany rhm@ipa.fhg.de 107 Co-Author(s) Philipp Dreiss Johann Dorner Akhauri P. Kumar Future Clinical Analysis: Component Based Framework for Modular Hardware and Software Integration of Different Clinical Equipment The Component Based Framework provides the mechanism to define the existing clinical equipment in form of hardware modules, which can be a combination of different analysis equipment performing specific operations or it can be, containers which carry the incoming and outgoing samples or it can be, manufacturing islands such as clinical equipments not integrated in the current Laboratory Information Management Systems (LIMS). Thus defined hardware modules can be clustered together with central handling system (cluster) responsible for transporting the samples to the individual modules (analysis equipments) These modules can be connected/ disconnected to/from the clusters dynamically, even in an ongoing analysis process. This allows the system wide scheduling to optimize and configure the analysis area based on the actual needs. In addition to this the Component Based Framework provides dedicated services such as: • centralized database to store sample information and its current position • centralized access rights management to establish equipment specific access rights configuration, • recipe management system to provide recipes on demand, • equipment management component to administrate the analysis equipment, • analysis planning unit providing connectivity to LIMS and translating incoming sample information to analysis area internal sample information, • scheduler component to interpret the internal information and to generate a schedule, • process management component to execute the analysis specific process recipes The presentation will show the hardware mapping of these modules by the software and the corresponding required software components as discussed above to show the easy and rapid deployment of such frameworks allowing a very high degree of flexibility in sense of adaptation to new analysis steps. PODIUM ABSTRACTS

11:00 am Thursday, February 5 Genomics – Advanced Topics Room A1<br />

Sheri Olson<br />

Applied Biosystems<br />

850 Lincoln Center Drive<br />

Foster City, Cali<strong>for</strong>nia 94404<br />

olsonsj@appliedbiosystems.com<br />

Co-Author(s)<br />

Lewis T. F. Wogan, Warren Tom, Charles Hsieh, Kyle Leinen<br />

Applied Biosystems<br />

106<br />

Gerri Shaw, Jim Shaw<br />

Bernard Shaw International<br />

Evaluation of High Throughput SNP Genotyping Lab Data Using FOCUS Statistical Software<br />

FOCUS statistical software (version 4.0) was used to evaluate daily processing efficiency <strong>and</strong> instrument<br />

functionality in a High Throughput Genotyping lab using the fluorogenic 5´ nuclease (TaqMan ® ) assay at Applied<br />

Biosystems. <strong>Laboratory</strong> processing data related to a specific customer project generated over thirty-five different<br />

processing days were recorded by an internally developed <strong>Laboratory</strong> In<strong>for</strong>mation Management System (LIMS).<br />

The LIMS captured reagent, consumable, instrument <strong>and</strong> operator in<strong>for</strong>mation. The LIMS data was merged with<br />

corresponding data from internally developed Genotyping analysis software to create Daily Query Results files<br />

(DQRs). The DQRs were uploaded into the FOCUS software <strong>and</strong> the FOCUS Pre-Processor tool was used to<br />

isolate specific factor sets to assess processing efficiency <strong>and</strong> instrument per<strong>for</strong>mance. In the High Throughput<br />

Genotyping lab at Applied Biosystems, automated liquid h<strong>and</strong>ling instrumentation is used to prepare the<br />

Polymerase Chain Reaction (PCR) based TaqMan ® assay to evaluate Single Nucleotide Polymorphisms (SNPs) in a<br />

384-well <strong>for</strong>mat. Consequently, the per<strong>for</strong>mance of the liquid h<strong>and</strong>ling aut<strong>omation</strong> has a significant impact on the<br />

genotyping results <strong>and</strong> on the efficiency of the overall genotyping process. There<strong>for</strong>e, FOCUS statistical software<br />

was used to evaluate the liquid h<strong>and</strong>ling per<strong>for</strong>mance <strong>for</strong> each reaction plate processed as part of the customer<br />

project. Additionally, acceptance specifications incorporated in the Genotyping analysis software categorized the<br />

resulting genotype data with either a “passing” or “REDO” status. The FOCUS software also evaluated the results<br />

associated with a “REDO” status to calculate daily processing efficiencies.

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