Dr Dale Charlton

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DNA Profiling and LIMS Integration Booth 6518

• Dr Dale Charlton
• CSols Inc,
• Pittcon 2002 New Orleans
• March 2002

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Agenda for Pittcon 2002

• Introduction to CSols
• DNA profiling background
• DNA profiling - Results interpretation
• Summary

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CSols Business

• Advanced Instrument Integration Specialists
• Solution Providers (products, services, and
  custom solutions)
• Specialize in automation of laboratory processes
• Flagship product Links for LIMS

Pharmaceutical QA and RD Biotechnology Chemical
Petrochemical Food Beverage
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What is Instrument Integration?
is automation of what is currently done
manually

• It is much more than just linking instruments

• It should
• Be automation of the laboratory process
• Ideally give the end result the customer wants !
• Do above with minimum user intervention gt
  AUTOMATION!
• Audit Trace
• Archive all information

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Advanced Application
DNA Profiling

• Forensic DNA profiling
• Legal Paternity Cases
• Genomic RD in Pharmaceuticals/Biotechnology

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DNA Profiling - Sample Analysis

• Buccal scrapes/swabs
• DNA extraction (magnetic bead separation)
• DNA Quantification (fluorescence dye - microplate
  reader)
• Dilution (robotic sample processor)
• Digestion into fragments site specific
• Polymerase Chain Reaction (PCR) amplification
• DNA sequencing (Gel Sequencer)
• Interpretation of results based on rules
• Category (allele) identification and comparison
  (DNA profiling)

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Instrument Output
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DNA Profiling Linking Architecture
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Rules Engine The Interpretation Process
The Rules engine must be able to confirm..

• If the Run is okay?
• Check Standards - PCR pos/neg standards
• The Run Standards (13 of them) peak height,
  peak area, peak position etc.
• Is this Sample okay?
• Are Internal Standard Peaks as expected/sample
• Deal with known PCR Technique Artifacts
• Pullup Peaks, N- Peaks, Stutter Peaks
• Assign categories (true allele peaks) to the
  results
• number of repeats in each category
• gt LIMS or db

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The Results

• Put results for each run (gel) in a database
• Apply Rules (Rules Engine)
• Display samples and their interpretation in
  Windows Explorer view
• Allow manual override, acceptance

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Show Detail

• Categories for each sample (12)

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Manual Override

• Limit to automation
• Allow user to override

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DNA Profiling Similar to Traditional Techniques
of Linking

• Link to instrument and collect Results
• See if Run was okay (Rules engine)
• Decide which samples were okay (Rules Engine)
• Assign (allele) category (Rules Engine)
• Show details to analyst
• Allow manual override of failed samples (audit
  trace)
• Archive run/user changes
• Send to LIMS

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Where different is db Rules Engine!
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Summary

• Biotech links essentially similar to traditional
  linking
• but not the same (apply db Rules Engine)
• Effective instrument integration and Link
  software is
• much more than reading and moving data
• general solution is/can be as complex as LIMS
• major benefits are here

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Currently building application knowledge in
Biotechnology

• Genomics/Proteomics
• DNA profiling - (paternal testing, forensics)
• MALDI-TOF protein chip analysis
• High Throughput Screening (HTS)
• Microplate readers e.g. DNA Quantification,
  immunoassays ELISA
• Scintillation Counters e.g. SPA screening
  technologies
• Microbiology
• Colony counters
• Minimum Inhibitory Concentration - Automated
  Assay antibiotic sensitivity testing
• Robotic and Automation System LIMS integration
• Sample processors e.g. Zymark, Beeline, Skalar,
  Peerless
• Bespoke robotics, stand-alone instrumentation e.g
  RTS Thurnall, CRS

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Working Together Booth 6518
Win a Palm! Pick the best name for our Oracle
based Version 5 product!
Americas Sandy Ahmed Newark, DE T.
302-731-5290 Sandya_at_csols.com
United Kingdom Asia Dr. Dale Charlton Runcorn,
UK T. 44 (0)1928 513535 Dalec_at_csols.com
Europe Mathieu Schoeber Roermond, NE T. 31 (0)475
375170 Mathieus_at_csols.com