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COBAS AMPLICOR™ System Laboratory

 

CONTENTS

 

Laboratory Setup

Sample Laboratory Design -- Because the COBAS AMPLICOR™ Analyser reduces operator intervention and manual steps in PCR procedures, a simplified laboratory design is possible.  The sample laboratory design outlined below depicts the entire PCR process.

  1. Dead-air Box.
  2. Reagent Refrigerator.
  3. Biological Safety Hood.
  4. Standard Clinical Centrifuge and/or Microfuge.
  5. Dry-heat Temperature Block.
  6. Specimen Refrigerator.

 

  1. Post-PCR Refrigerator.
  2. Computer.
  3. Printer.
  4. COBAS AMPLICOR™ Analyser.

 

Pre-PCR Reagent Preparation Supplies

These supplies and equipment should be dedicated to each pre-PCR activity.   Some items are not necessary for all COBAS AMPLICOR™ Analyser Automated PCR tests.

Reagent Preparation

  1. If using one room, a dead air box with an optional ultraviolet (UV) light or, if using two rooms, a clean, dedicated area should be used for reagent preparation.
  2. Dedicated pipettors with plugged (aerosol-barrier) tips, dedicated positive-displacement pipettors and tips or a repeat pipettor.  RNase-free plugged tips are necessary for RNA tests such as AMPLICOR HIV-1 MONITOR™ and AMPLICOR® HCV tests.
     
  3. COBAS AMPLICOR™ Analyser consumables/parts (A-rings, A-ring Holder).
  4. Vortex Mixer.
  5. Screw-cap tube racks (to hold Master Mix tubes).
  6. Refrigerator.
  7. Laboratory coat.
  8. Gloves (protective, latex, powder-free).
  9. Safety glasses.
  10. Biohazard container.
  11. 0.5% sodium hypochlorite*, for decontamination, prepared fresh daily.

    12. 70% ethanol, for decontamination.

* Commercial liquid household bleach typically contains a concentration of 5.25% sodium hypochlorite.  A 1:10 dilution of bleach will produce 0.5% sodium hypocholorite solution.

 

Pre-PCR Specimen Preparation Supplies

These supplies and equipment should be dedicated to Pre-PCR.

Specimen Preparation

  1. Biological Safety hood.
  2. Standard clinical tabletop centrifuge and/or microcentrifuge (min. RCF 12,500 x g), refrigerated high-speed centrifuge (min. RCF 24,000 x g).
  3. Dedicated pipettors with plugged RNase-free (aerosol-barrier) tips or dedicated positive-displacement pipettors and tips. RNase-free plugged tips are necessary for RNA tests such as AMPLICOR HIV-1 MONITOR™ and AMPLICOR® HCV tests.
  4. Sterile fine-tipped transfer pipets.
  5. Serological pipets.
  6. Vortex mixer.
  7. Sterile screw cap tubes and rack(s).
  8. Refrigerator/freezer.
  9. Dry-heat temperature block(s).
  10. Timing device.
  11. COBAS AMPLICOR™ Analyser parts (A-ring holder).
  12. Laboratory coat.
  13. Gloves (protective, latex, powder-free).
  14. Safety glasses.
  15. Biohazard container.
  16. 0.5% sodium hypochlorite*, for decontamination, prepared fresh daily.

    17. 70% ethanol, for decontamination.

  17. Isopropanol, for specimen preparation.
    70% ethanol, for specimen preparation.

* Commercial liquid household bleach typically contains a concentration of 5.25% sodium hypochlorite. A 1:10 dilution of bleach will produce 0.5% sodium hypochlorite solution.

 

Post-PCR Amplification and Detection Supplies

These supplies and equipment should be dedicated to Post-PCR.

Amplification and Detection

  1. COBAS AMPLICOR™ Analyser.
  2. Optional AMPLILINK™ Software or Laboratory Information System (LIS).
  3. Printer and paper.
  4. COBAS AMPLICOR™ Analyser consumables/reagents/parts (D-cups, wash buffer, generic and specific reagents, reagent racks and maintenance supplies).
  5. Vortex mixer.
  6. Refrigerator.
  7. Serological pipets (5 or 10 mL).
  8. Graduated cylinder (or other suitable container for preparing working wash buffer).
  9. Laboratory coat (different from the one worn in Pre-PCR).
  10. Gloves (protective, latex, powder-free).
  11. Safety glasses.
  12. Biohazard container.
  13. 0.5% sodium hypochlorite*, for decontamination, prepared fresh daily.
    70% ethanol, for decontamination.

* Commercial liquid household bleach typically contains a concentration of 5.25% sodium hypochlorite. A 1:10 dilution of bleach will produce 0.5% sodium hypochlorite solution.

 

Tips for Optimising Laboratory Workflow

These suggestions will help maximize efficiency in the COBAS AMPLICOR™ ANALYSER AUTOMATED PCR TEST laboratory.

 

  1. To minimize Analyser programming, use preprogrammed profiles and racks.
  2. Enter A-ring worklists as far in advance as possible.
  3. Use barcode scanner for easy entry of A-ring ID, specimen ID, reagent rack ID, cassette ID, QS and control values.
  4. To automate creation of A-ring orders and results collection, consider connecting the AMPILINK™ Software to the COBAS AMPLICOR™ Analyser.
  5. Aliquot Master Mix into A-rings and store refrigerated in resealable plastic bags for the time specified in the Method Manual for the COBAS AMPLICOR™ Analyser.
  6. Prepare specimens for the first run of the day during the prior afternoon or evening.   Samples for additional runs should be prepared while the COBAS AMPLICOR™ Analyser is in the amplification process.
  7. Prepare working wash buffer in bulk and store in a container for use within two weeks (store at room temperature).
  8. Add working wash buffer to the wash buffer reservoir and empty the waste container at the end of the day.
  9. Use the basic run mode for overnight runs, especially for tests with longer amplification times.
  10. Identify specific laboratory needs and constraints and use the tips above to improve workflow. 

 

Laboratory Needs

 

Laboratory Considerations