cobas 4800 CT/NG and HPV Workflow Overview

cobas ® 4800 CT/NG and HPV Workflow Overview

Upon completing this section, you will be able to:

• Perform the required maintenance activities prior to the start of a run

• Understand the assay workflow using the cobas® 4800 System

Objective

Full Workflow

Recovery Workflow

Workflow Overview: Full Run I

System Introduction SW 2.2 System Workflow Design

Daily Maintenance takes app. 10-20 minutes to complete Daily Maintenance

Results are shown and can be printed out Result Reporting

CT/NG ~ 90 minutes

HPV ~ 120 minutes

Real-Time Amplification

&

Detection

CT/NG ~ 120 minutes for 96 samples

HPV ~ 160 minutes for 96 samples

Sample Preparation

& PCR Set Up

Up to 30 minutes to load samples, reagents and consumables for up to 96 samples/controls Instrument Set Up

1. Start up cobas® 4800 System

Start up cobas® 4800 instruments

1. Switch on the cobas® z480 analyzer

2. Switch on heater/shaker unit

3. Switch on the cobas® x480 instrument

Start up and log on to cobas® 4800 software:

1. Switch on the monitor and control unit

• The Windows 7 operating system starts automatically

• Double click the cobas® 4800 software icon on the desktop and log in

• The cobas® 4800 software displays the System tab

2. Click to log on and enter your assigned user ID and password

3. Click OK

2. cobas® x480 Instrument Maintenance

• Select Overview tab and check maintenance status of cobas® x480 instrument

– If weekly maintenance is due, click Run Weekly Maintenance

– If daily maintenance is due, click Run Daily Maintenance

• Follow the software wizard guidance

2. cobas® x480 Instrument Daily Maintenance

The following tasks are part of the daily maintenance:

1. Shutdown and restart the cobas® 4800 system

2. Check if instrument deck is clean

3. Empty the tip waste and the liquid waste container, clean the tip eject plate

4. The cobas® x480 instrument automatically checks the tightness of the pipetting channels and verifies the functioning of the liquid level detection

3. Remove Samples and Reagents from Storage

• Remove HPV or CT/NG samples & HPV or CT/NG reagents from storage

• The run size is either 24 or 96 batch for Sample Preparation kits

Note: MMx and Mn2+ can be loaded directly from the fridge onto cobas® x480

instrument

4. Start New Run

Start a new run

1. Click

2. Select Workflow Type:

– Full

– Recovery (Only for CT/NG and HPV)

3. Select test

4. Type run name (optional)

5. Click OK The default as shown

5. Load Specimens (1)

Load specimens

1. Uncap specimens

2. Place specimens in corresponding carrier

3. Insert sample carriers on autoload tray

4. Click Load Specimens

A) Specimen barcodes facing to the right

B) Sample carrier

C) Tracks 17 - 34 are reserved for sample carriers

B

A

C

5. Load Specimens (2)

Unloading Samples/Sample Carriers Option

Default is checked—unloading of sample carriers:

6. Define Work Order (without LIS)

Define work order

1. Specimen IDs are scanned by

the autoloader

2. Select Specimen

3. Select Specimen type:

CT/NG – PC, Swab, Urine

HPV – PC, SP

4. Select Requested Result

• CT/NG:

a. CT

b. NG

c. CT and NG

• HPV:

a. HPV High Risk Panel

b. HPV High Risk Panel

+ Genotyping

5. Select Next

7. Load Consumables

1. Place listed consumables on appropriate

carriers

2. Insert carriers on autoload tray

3. Click Load Consumables:

Use the following tracks:

• Plate carrier: tracks 1 through 6

• Left tip carrier: tracks 11 through 16

• Right tip carrier: tracks 35 through 40

8. Load Reagents (1)

To minimize handling errors the reagent reservoirs are filled and placed using

the scan-scan-pour principle:

1. Scan the barcode of the required reagent

2. Scan the barcode of an unused reagent reservoir

3. Pour the reagent in the scanned reagent reservoir

4. Place the filled reagent reservoir onto the required position of the reagent

reservoir carrier as indicated in the software

• The reagent reservoirs are available in the two sizes: 200 mL and 50 mL

• The reagent reservoir barcodes must align with the barcode of the carrier (face to

the right of the carrier)


Continued

• All reagents except MGPs are homogeneous and do not require

vortexing/shaking

• Each reagent has a specific location assigned to it on the carriers

• All reagents except MMX and Mg/Mn must be at ambient

temperature prior to loading on the instrument

• The MMXs and Co-factors may be taken directly from 2-8 ºC storage


Continued

• The reagent inventory marks a reagent as used as soon as it is assigned to

a reservoir. From this time point on, the reagent is dedicated to this run and

cannot be used later on another run even if the reagent is not used due to aborting

the run

• The cobas® 4800 System has an internal timer to monitor reagent on-board

stability

• Once the wash buffer is scanned, 1 hour (60 minutes) is allowed to

complete the loading process and to start the sample preparation run

• A countdown timer is displayed on the Workplace tab


Wash Buffer

200 mL reagent reservoir carrier

1. Load a 200 mL reagent reservoir

on the carrier:

Scan – Scan – Pour - Place

2. Insert carrier on the autoload tray:

200 mL reagent reservoir

carrier: tracks 48 through 49

3. Click Load Reagents


SDS, Lysis, MGP & Elution Buffer

50 mL reagent reservoir carrier

1. Load reagents on 50 mL reagent

reservoir carrier as indicated in

the wizard

2. Insert the carrier onto the

autoload tray:

50 mL reagent reservoir

carrier is placed on track 50

3. Select Load Reagents


Controls, MMX & Metal(s)

Reagent carrier

1. Uncap reagent vials and load them

on reagent carrier as indicated in

the wizard

2. Insert carrier on autoload tray:

CT/NG:

Reagent carrier: track 51

IC, Control Dil, RMECs,

MMx and Co-factor

HPV:

Reagent carrier: track 51

PK, RMECs, MMx and

Co-factor

3. Click Load Reagents

9. Start Sample Preparation Run

Select “Start run”

10. Unload & Seal Microwell Plate

Sample Preparation Run Complete (1)

• Amplification and detection should be started as soon as possible but no

later than 90 minutes (1 h 30 min) after the end of the cobas® x480

instrument run

• A countdown timer is displayed on the Workplace tab

To see flags

• Click Sample Prep

Results to review the

results of the sample

preparation

• The Sample Preparation

Results window pops up

• Samples that had clots or

pipetting errors will have

“failed” and will show

flags


Sample Preparation Run Complete (2)

Sample Workflow Overview: Full Run Part II


1. Click Unload

2. Seal the microwell plate:

• Remove the protection layer from

the sealing film

• Cover the microwell plate with the

adhesive side of the sealing film

• Firmly press the sealing film to the

plate surface using the sealing

film applicator

• Remove both ends of the sealing

film alongside the perforation

3. Click Next

11. Load Microwell Plate

1. Press Load button on cobas® z480 analyzer

2. Place the sealed microwell plate into the extended loader

3. Press load button again. The amplification and detection run starts automatically

12. Review and Accept Results

Review and accept results:

1. Click Show Results

2. Review and accept results in

Results tab

3. Select results and click to

print the results report

13. With LIS, send the results to LIS

Consider that depending on the

configuration, all results are

transferred to LIS or only accepted

results are transferred to LIS.

• Control results are always

uploaded to LIS

• Select a result or group of

results and choose the Send

results to LIS button

14. Unload cobas® z480 analyzer

Unload cobas® z480 analyzer:

• After the run has finished, unload the microwell plate from the cobas®

z480 analyzer as soon as practical

• The sealing film adhesiveness may degrade with time and without

pressure. Removing the microwell plate promptly minimizes any possible

contamination of the cobas® z480 analyzer

Full Workflow

Recovery Workflow

Recovery Run

Overview

• The recovery workflow allows the user to recover failed runs where the sample

has been successfully prepared

• A run can only be recovered once

Note: Recovery Workflow is available only for CT/NG and HPV (all

specimen types)

Not available for C. diff, HSV 1/2 and MRSA/SA or Virology assays

Recovery Run

Overview

• User can perform the recovery workflow anytime a full run fails, under the

following conditions:

– DWP preparation stage is completed during sample preparation

– Recovery workflow is started within 24 hours of the start of the full run

• Possible recovery scenarios

– If run was aborted during sample preparation (after DWP prep is completed)

– If run was aborted during plate transfer

– If run was aborted during amplification and detection

A full run has been aborted by a user (M2 flag) or the analyzer (Z1 flag)

Recovery Run

Overview

• The recovery workflow is intended for repeat amplification from the remaining

eluate in the deepwell plate

• For the recovery workflow, the microwell plate is manually prepared with working

master mix reagent, Mn reagent and residual eluate from the deepwell plate

Sample Workflow Overview: Recovery Run

1. Start a recovery run

1. Choose (New run)

2. Select the Recovery option

3. Select the appropriate test check

box

4. Optionally, type a run name

5. Choose the OK button

2. Select the run to recover and add new IDs

1. Choose the run to recover

2. In the Microwell plate ID field,

scan the microwell plate barcode

3. In the Master Mix ID field, scan

the master mix reagent barcode

4. In the Mn Reagent ID field, scan

the Mn reagent barcode

3. Print the microwell plate layout

1. To print the work order file for

microwell plate setup, choose

(Print) from the global navigation bar

2. In the software, choose the Next

button

4. Retrieve the deepwell plate

Do one of the following:

– If the deepwell plate has been unloaded by the

instrument, remove it from the plate carrier, or

– If the deepwell plate has been stored, retrieve it from

storage, or

– If the deepwell plate has not been unloaded by the

instrument, unload the deepwell plate manually

5. Set up the new microwell plate

Set up the microwell plate for the recovery run in the following way:

1. Perform manual PCR setup according to the test-specific package insert

2. Seal microwell plate

3. Centrifuge microwell plate

4. In the software, choose the Next button

6. Load microwell plate into the analyzer

1. Press the load button on the

analyzer

2. Place the sealed microwell plate

into the microwell plate loader

3. Press the load button again to

close the drawer

The amplification and detection run

starts automatically

4. Check the timer in the wizard

7. Review and accept results

1. Choose the Show result button

2. Review and accept results in

Results work area

3. Select results and choose

(Print) to print the results report, if

required

8. With LIS, send the results to LIS

Consider that depending on the

configuration, all results are

transferred to LIS or only accepted

results are transferred to LIS

• Control results are always

uploaded to LIS

• Select a result or group of results

and choose the Send results to

LIS button

9. Unload the microwell plate from the cobas®

z480 analyzer

Unload cobas® z480 analyzer:

• After the run has finished, unload the microwell plate from the cobas® z

480 analyzer as soon as practical

• The sealing film adhesiveness may degrade with time and without

pressure. Removing the microwell plate promptly minimizes any possible

contamination of the cobas® z480 analyzer

Doing now what patients need next

Documents

cobas 4800 CT/NG and HPV Workflow Overview