Viral Load Workflow - CAP-CTM&CAP-CTM48 (Compatibility Mode)

IVD - Workflow
COBAS® AmpliPrep Instrument - COBAS® TaqMan® Analyzer

COBAS® AmpliPrep Instrument - COBAS® TaqMan® 48 Analyzer
Objectives
Upon completing this section, the trainee should be able to:
• Know the configuration and content of the Test Kits.
• Know and understand different workflow configurations using the COBAS®

AmpliPrep Instrument and the COBAS® TaqMan® / COBAS® TaqMan® Analyzers.
• Perform the complete workflow including the process of generating results.
Roche Molecular Diagnostics Version 2.0 Workflow COBAS® AmpliPrep Instrument with
November 2009 COBAS® TaqMan® Analyzers
Page 2
Generic IVD Kits
Contents
Sample Preparation Reagents

• Bead Reagent Cassette (CS1)
• Lysis Reagent Cassette (CS2)
• Multi Reagent Cassette (CS3)
• Test specific Cassette (CS4)
Control Reagents
• 4 or 6 Negative control (- Negative)
• 4 or 6 Positive controls (# High positive)
• 4 or 6 Positive controls (+ Low positive)
Control Barcode Clips
• 4 or 6 for each control
Documents
• Package Insert, Blue Card
Page 3
Generic IVD Kits
Storage and Working temperature
• Store at 2-8°C
• Insert immediately from

refrigerator into COBAS®
AmpliPrep Instrument and
equilibrate in the instrument for
30 min
Page 4
Generic IVD Kits
Cassettes contents (1)
BD
Cassette 1: Beads
– MGP in Isopropanol
Cassette 2: Lysis reagent

LYS
– Guanidine Thiocyanate
P Cassette 3: Multi-Reagent Cassette

– Pase: 8% Proteinase
– EB: Tris Buffer with 0.2% Methylparaben
EB
Page 5
Generic IVD Kits
Cassettes contents (2)
Cassette 4: Test specific Reagent Cassette

QS – QS
• Non-Infectious transcribed RNA (HCV, HIV),
armored with MS2-phage coat protein
• non-infectious DNA construct (HBV)
Mn
– Mn2+
• Mn-Acetate
– MMX
MMX
• Z05 DNA Polymerase
• Primers
• Fluorescent-labeled probes
• dNTPs
• AmpErase (Uracil-N-Glycosylase) enzyme
• Aptamer
Page 6
Easy begins here.
CAP/CTM System configuration
Software: control of the process
Samples Nucleic Acids + Master Mix Results
Integration : instruments, consumables, reagents, processes.
Page 7
Easy begins here.
CAP/CTM Docked System configuration
Software: control of
the process
Samples
Results
Page 8
Easy begins here.
CAP/CTM 48 System configuration
Software: control of the process
Samples Nucleic Acids + Master Mix Results
Page 9
1. Instrument Startup
Log On to Datastation and AMPLILINK Software
• It is recommended to shut down and restart the datastation weekly.
• Log on by entering your assigned AMPLILINK user ID and password.
Inspecting and maintenance of the COBAS® AmpliPrep and COBAS®

TaqMan® / COBAS® AmpliPrep and COBAS® TaqMan® 48 Instruments
• Perform daily maintenance (if necessary also periodic maintenance)
• Check for wash reagent supply on the COBAS® AmpliPrep Instrument
Page 10
2. Handle Reagents
• Remove reagents from storage

• Load immediately
(before condensation can occur Cassettes 2 – 4
and reagents need to equilibrate
for at least 30 minutes before
use)
Cassette 1: MGP
Page 11
2. Insertion of Reagents Racks
Reagents Rack 1 insert

Cassette 1: Beads
Reagents Rack 2 insert

Cassettes 2 – 4
Page 12
3. Sample handling
Remove Samples from Storage & prepare S-tubes
Storage recommendation:
• 1100 – 1200 µl-Aliquots of Plasma

(store according to the recommendation in the Package Insert)
• Minimal (maximal) S-tube Input Volumes:
HBV v1.0 HBV v2.0

HCV v1.0
HIV v1.0/v.20
Input 1000 (1050) µL 650 (1050) µL
Volume
Processing 850 µL 500 µL
Volume
Page 13
4. Load Consumables (I)
K-tips (full rack)

(GMMI#: 03287343 001)
• K-tubes
– CAP-CTM 48 on sample rack (performed
by operator)
– CAP-CTM via OT-Platform (full rack)
(GMMI#: 03137082 001)
• Flapless SPUs (loaded onto the SPU-rack)

(GMMI#: 03755525 001)
Page 14
4. Load Consumables (II)
SPU-loading
• Load SPUs correctly onto the SPU-

rack
• The SPU-rack can also be partially

filled
Instrument will count the SPUs via
S-tip Light-barrier
Page 15
4. Load Consumables (III)
K-carrier
COBAS® AmpliPrep/ COBAS® TaqMan® System COBAS® AmpliPrep/ COBAS® TaqMan® 48 System
K-carrier has to be loaded manually onto the COBAS®

AmpliPrep Instrument
K-carriers are loaded onto the COBAS® TaqMan®
Analyzer Necessary tools:
K-carrier-rack
Bar-coded K-carrier
K-carrier transporter
K-carrier holder
Page 16
Pre-preparation of K-carrier rack (I)
Ordering-Info – Taqman 48
• K-carrier rack and Labels have to be ordered

separately it’s not part of any Start-Up-Kit
– Order-Info: 2) Pins
• K-carrier rack (contains also the pins)
GMMI # 03286436 001
• K-carrier rack label
GMMI #:03287335 001
• The rack has to be prepared before the first

use as following: K-carrier Rack
1) Stick barcode label onto the rack 1) Labels
2) Add pins to the correct position
according to the label number (use the
binary-format)
Page 17
Pre-preparation of K-carrier rack (II)
Binary code of K-carrier rack
20 = 1 20 + 21 =
20 = 1 21 = 2 1+2=3
21 = 2
22 = 4
Rack No 1 Rack No 2 Rack No 3
23 = 8
24 = 16
25 = 32
22 = 4 20 + 22 = 21 + 22 =
26 = 64
1+4=5 2+4=6
27 = 128
Rack No 4 Rack No 5 Rack No 6
Page 18
5. Associate K-carrier with K-carrier rack (I)
Only COBAS® AmpliPrep/COBAS® TaqMan® 48 Analyzer
• Place a K-carrier on a K-carrier rack (1)

(nothing else !!!) (1) Pins
• Scan the barcode of K-carrier rack &

within 5 sec scan the barcode of K-
carrier using handheld barcode- K-carrier Rack
scanner Labels
• Note: the association (scanning) of the

K-carrier with the K-carrier rack can 2(2)
only be done under the instrument
system window (2)
Page 19
5. Associate K-carrier with K-carrier rack (II)
• After scanning the K-carrier rack

barcode a pop-up-window opens:
• Scan the barcode of the K-carrier

within 5 seconds.
Rack No
Binary code
of Rack No
Rack No
Page 20
5. Associate K-carrier with K-carrier rack (II)
• Load K-carrier rack onto the OT-platform

of the instrument
• The K-carrier rack occupies 2 slot positions

on Inserts M-P
Page 21
6. Creating Orders
Using the Sample rack Tab
1. Select „New“
2. Type in respective Sample Rack ID

2 1
3
3. Select desired Test Icon
(Check or uncheck „Docked“) 6
4
4. Assign Controls to desired position
1. HPC
2. LPC
3. NC 5
5. Assign/enter patient samples to

desired position
3
6. Save your order
Page 22
7. Sample & Control Handling
• Attach barcode clips for:

– controls (Kit specific)
– and samples (provided via Barcode clip
K-tube
the S-tube input box)
• Place S-tubes input in the S-tube

Sample Rack
• Vortex & pipette samples &

controls into the S-tubes input
• Place K-tubes on Sample rack

(only when using COBAS
AmpliPrep/COBAS® TaqMan® 48
analyzer configuration)
Controls are pipetted into S-tubes

Page 23
8. Load Sample Racks
Page 24
8. Check Instrument Status (I)
for missing resources
Page 25
9. Check Instrument Status (II)
…Start the Run
Page 26
10. Finished Instrument Run
Transfer of the K-tubes
Docked system Undocked system COBAS® TaqMan® 48
•Transfer of K-carrier •Transfer Sample rack • Transfer K-carriers

via Docking-Station •Transfer must be done • Balance K-carriers
within 120 min (if needed)
• Transfer must be done
within 120 min
Page 27
Positioning scheme of K-carrier
For all 3 workflows
1 = 1st sample processed from the

sample rack
23 19 11 15 22
2 = 2nd sample processed from the
sample rack
13 5 3 8 18 3 = ……
9 1 2 10
17 7 4 6 14
21 16 12 20 24
Page 28
11. Results (I)
Where to find the results
Access the results using

the results icon/menu.
Page 29
11. Results (I)
Review and Accept/Reject Results
• Double click on one

sample to see the report
windows.
• Accept/reject the
results as batch or
individually (marked with
a black asterisk).
• Only accepted/rejected
results can be archived
and purged.
Page 30
12. Remove Instrument Waste…
From the COBAS® AmpliPrep Instrument
COBAS® AmpliPrep Instrument
• Remove reagent racks and store remaining reagents in refrigerator
• Remove used SPU racks
• Remove empty K-tip / K-tube racks
Page 31
12. Remove Instrument Waste…
From the COBAS® TaqMan® / TaqMan® 48 Analyzers
COBAS® TaqMan® Analyzer
• Remove Sample Racks
• Remove K-tubes from waste box & discard accordingly
COBAS® TaqMan® 48 Analyzer
• Remove K-carrier from COBAS® TaqMan® 48 Analyzer & discard K-tubes

accordingly
Page 32
Summary: COBAS® AmpliPrep Instrument loading configurations
Workflow
C1 C2, C3, C4
Docked Beads Reagents S tubes SPUs K tubes, K tips K carriers
CTM96 Beads Reagents S tubes SPUs K tubes1, K tips
CTM48 Beads Reagents S tubes SPUs K tips,

K tubes2 K carrier rack
introducing: K carriers
TNAI Beads Reagents S tubes SPUs Output S tubes, K tips
1 After sample processing, the used K tubes go to the sample racks and are ready for manual transfer
2 After sample processing, the K tubes are placed in the K carrier on the K carrier
Roche Molecularrack
Diagnostics Version 2.0 Workflow COBAS® AmpliPrep Instrument with
Page 33
Sampling COBAS TaqMan
Handling Area Analyzers AMPLILINK
COBAS AmpliPrep Software
Instrument
Daily Maintenance Daily Maintenance Start up Datastation
Load reagents (from fridge)
Remove samples from

storage
Load consumables
Sample handling Create order
Attach barcode clips Prepare/print worklist
Sample handling
•Vortex/pipet samples &
controls Associate K-carrier with K-
•Fill and place S-tubes in carrier-Rack
the sample rack
•Place K-tubes on Sample Transfer
rack Check instrument status and
start run.
Review and accept

results.
Remove instrument waste Remove instrument waste
Page 34
Features and Benefits of COBAS® AmpliPrep /
COBAS® TaqMan®
• Reduced Hands-On Time, Improved Lab Productivity
– The only fully automated system with sample-in, sample-out capability with no manual intervention required
during a run.
• Greater Flexibility and Rapid Turnaround Time

– Multiple test types can be run simultaneously and runs can be loaded continuously throughout a work shift.
• Simplified Workflow and Inventory Management

– Reagents are packaged in complete kits (stored at fridge temperature) consisting of multiple-use, bar-coded,
ready-to-use cassettes, requiring no preparation before use or manual assay calibration.
• Greater Confidence in Result Integrity

– Fully competitive quantitation standard, AmpErase (Uracil-N-Glycosylase) contamination control and closed-
tube format reduce the risk of contamination and ensure result integrity.
Page 35
Features and Benefits of COBAS® AmpliPrep /
COBAS® TaqMan®
• Constant Innovation in Assay Development
– Roche, through its Global Surveillance Program, is a global leader in monitoring viral genome sequence
changes. This allows for continual adaption of assays to the changing nature of viral genomes, ensuring assays
remain reliable and effective.
• Broad Test Portfolio

– HIV-1 qualitative, HIV-1 viral load, HBV viral load, HCV viral load, CMV viral load.
• Easy-to-Use Software
– AMPLILINK software provides a simple and efficient user interface to the custom-built, Windows®- based PC
supplied with the system. The system has the capability for bidirectional interfacing to laboratory information
systems (LIS).
Page 36
IVD Workflow
Version History
Version Date Modifications
1.0 March 2005 Original File
1.1 March 2006 • P15: new slide, Contains information on K-carrier, K-carrier Holder
and K-carrier Transporter
• P17: new slide, Contains information that K-carrier rack and labels
have to be ordered separately
1.2 May 2006 • P4: changed from weekly shutdown to shut down and restart the
datastation daily
1.3 December 2007 •Replaced AMPLILINK 3.1 with AMPLILINK 3.2 Series printscreens
(added slide 22)
• P3: Restricted area for loading reagents on CAP
• P3: Added “Print worklist” to point E
•Include MMix components and description
•daily maintenance: removed the statement using the Service Wizard
Page 37
IVD Workflow
Version History
Version Date Modifications

•Combined from two previous workflow presentations (versions Workflow_CAP-
CTM48_DRAFT V1.4_Dec_2008.ppt and Workflow_CAP-CTM_DRAFT V1.3_Dec_2008.ppt
2.0 November 2009 •Combined information of COBAS TaqMan and COBAS TaqMan 48 into one presentation.
•Updated content to reflect the AMPLILINK 3.3 software (print-screens)
•Restart of datastation weekly instead of daily
Page 38
We Innovate Healthcare
Page 39

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IVD - Workflow

COBAS® AmpliPrep Instrument - COBAS® TaqMan® Analyzer

Upon completing this section, the trainee should be able to:

• Know the configuration and content of the Test Kits.

• Know and understand different workflow configurations using the COBAS®

• Perform the complete workflow including the process of generating results.

Sample Preparation Reagents

• Insert immediately from

Cassette 2: Lysis reagent

P Cassette 3: Multi-Reagent Cassette

Cassette 4: Test specific Reagent Cassette

Software: control of the process

Samples Nucleic Acids + Master Mix Results

Integration : instruments, consumables, reagents, processes.

Integration : instruments, consumables, reagents, processes.

Software: control of the process

Samples Nucleic Acids + Master Mix Results

Integration : instruments, consumables, reagents, processes.

Log On to Datastation and AMPLILINK Software

• It is recommended to shut down and restart the datastation weekly.

• Log on by entering your assigned AMPLILINK user ID and password.

Inspecting and maintenance of the COBAS® AmpliPrep and COBAS®

• Perform daily maintenance (if necessary also periodic maintenance)

• Check for wash reagent supply on the COBAS® AmpliPrep Instrument

• Remove reagents from storage

Reagents Rack 1 insert

Reagents Rack 2 insert

• 1100 – 1200 µl-Aliquots of Plasma

• Minimal (maximal) S-tube Input Volumes:

HBV v1.0 HBV v2.0

K-tips (full rack)

(GMMI#: 03137082 001)

• Flapless SPUs (loaded onto the SPU-rack)

• Load SPUs correctly onto the SPU-

• The SPU-rack can also be partially

K-carrier has to be loaded manually onto the COBAS®

• K-carrier rack and Labels have to be ordered

• The rack has to be prepared before the first

• Place a K-carrier on a K-carrier rack (1)

• Scan the barcode of K-carrier rack &

• Note: the association (scanning) of the

• After scanning the K-carrier rack

• Scan the barcode of the K-carrier

• Load K-carrier rack onto the OT-platform

• The K-carrier rack occupies 2 slot positions

2. Type in respective Sample Rack ID

5. Assign/enter patient samples to

• Attach barcode clips for:

• Place S-tubes input in the S-tube

• Vortex & pipette samples &

• Place K-tubes on Sample rack

Controls are pipetted into S-tubes

Docked system Undocked system COBAS® TaqMan® 48

•Transfer of K-carrier •Transfer Sample rack • Transfer K-carriers

1 = 1st sample processed from the

Access the results using

• Double click on one

COBAS® AmpliPrep Instrument

• Remove reagent racks and store remaining reagents in refrigerator

• Remove used SPU racks

• Remove empty K-tip / K-tube racks

COBAS® TaqMan® Analyzer

• Remove Sample Racks