(PDF) cobas system | Jonathan Bill Zambrano Perez - - Document Information
Any customer modification to the cobas x instrument or cobas z analyzer will render the warranty or service agreement null and void. Cobas z PCR analyzer is the latest generation of LightCycler® family. It was designed specifically for IVD and has high performance combined with. Specimens are processed using the cobas® DNA Sample Preparation Kit for manual sample preparation and the cobas z analyzer for automated amplification.
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- COBAS Z ANALYZER - Dialogue Diagnostics
A—6 Miscellaneous safety precautions A—7 Safety summary A—8 Warning messages A—8 Electrical safety A—8 Optical safety A—8 Biohazardous materials A—9 Waste A—10 Explosion and fire risk A—10 Caution messages A—11 Mechanical safety A—11 Reagents A—12 Insoluble contaminants in samples A—12 Evaporation of samples or reagents A—12 Cross contamination A—13 Hot surfaces A—13 Data security A—14 Notices A—15 Moving parts A—15 Circuit breakers and fuses A—15 Spillage A—15 Safety labels on the system A—16 Safety labels on cobas x instrument A—17 Safety labels on cobas z analyzer A—18 Disposal of the cobas x instrument and the cobas z analyzer Safety classifications This section explains how precautionary information is presented in this manual.
Familiarize yourself with the following meanings and icons: The safety alert symbol by itself without a signal word is used to promote awareness to hazards which are generic or to direct the reader to safety information provided elsewhere in the document.
Indicates a hazardous situation which, if not avoided, could result in death or serious injury. Indicates a hazardous situation which, if not avoided, could result in minor or moderate injury. Important information which is not safety relevant is indicated by the following symbol: Tip Indicates additional information on correct use of the system or useful tips. Safety precautions Particular attention must be paid to the following safety precautions.
If these safety precautions are ignored, the operator may suffer serious or fatal injury. Each precaution is important. Do not carry out operation and maintenance unless you have been trained by Roche Diagnostics. Follow standard laboratory practices, especially when working with biohazardous material. Safe and proper use of the instrument and analyzer Personal protective equipment.
Be sure to wear appropriate protective equipment, including, but not limited to, safety glasses with side shields, fluid resistant lab coat, and approved disposable gloves. Do not use reagents that have exceeded their expiration date, otherwise inaccurate data may be obtained. Each laboratory must verify that instrument, analyzer, and reagent performance meets the published specifications. Use the cobas x instrument only for preparing liquid samples with the provided reagents.
Operation outside of the specified ranges may lead to incorrect results or malfunction of the instrument or analyzer. Perform maintenance according to the specified intervals to maintain the operating conditions of the instrument and analyzer. This manual must be easily accessible at all times. Use of non-approved parts or devices may result in malfunction of the instrument or analyzer and may render the warranty null and void.
Only use parts and devices approved by Roche Diagnostics. Do not install any non-approved software. A power failure or momentary drop in voltage may damage the instrument or analyzer or lead to data loss. Perform regular backups of measurement results. Operation with an uninterruptible power supply UPS is recommended. Devices that emit electromagnetic waves may cause the instrument or analyzer to malfunction.
Do not operate the following devices in the same room where the instrument or analyzer are installed:. Do not attempt to relocate or transport the instrument or analyzer.
Leave relocation and transportation to personnel trained or authorized by Roche. Safety summary This safety summary contains the most important and general warning and caution messages. Additionally, you will find specific safety information at the beginning of Part Operation and Part Maintenance. Before operating the system, read the warning messages contained in this summary carefully.
Failure to observe them may result in death or serious injury. Do not touch any parts of the instrument or analyzer other than those specified. Especially do not touch any power supply parts. Never remove the middle grounding prong from the power cable or defeat its purpose by using an ungrounded adapter. Installation, service, and repair must only be performed by personnel authorized and qualified by Roche.
Observe the system safety labels as illustrated in section Safety labels on the system on page A Optical safety Loss of sight due to staring into laser beam The barcode scanner on the autoloader of the cobas x instrument contains a class II laser diode. Do not stare into the laser transmitter beam as eyesight may be severely damaged. Biohazardous materials Infection by samples and associated materials Samples processed on the instrument and analyzer are provided in media that inactivate potentially biohazardous material.
However, as with all human-derived specimens, universal precautions should be taken when handling and processing samples. Contact with samples containing material of human origin may result in infection. All materials and mechanical components associated with samples of human origin are potentially biohazardous. Keep the main cover closed and in place while the cobas x instrument is operating.
When working with the main cover open while the cobas x instrument is powered on e. If any biohazardous material is spilled, wipe it up immediately and apply disinfectant. When any indication of potential sources of contamiriation is seen e.
Do not touch hot surfaces. Malfunction due to interfering electromagnetic fields Malfunction of system and incorrect results due to interfering electromagnetic fields Devices that emit electromagnetic waves may cause the analyzer to malfunction. The electromagnetic environment should be evaluated prior to operation of the device.
Do not operate this system in close proximity to sources of strong electromagnetic fields for example unshielded intentional RF sources , as they may interfere with proper operations.
Roche Diagnostics 22 System Manual Version 1. The system is not protected against malicious software and hacker attacks. The customers are responsible for IT security of their IT infrastructure and for protecting it against malicious software and hacker attacks. Failure to do so may result in data loss or render the system unusable. Roche recommends the following precautions: Allow connection to authorized external devices only Ensure that all external devices are protected by appropriate security software.
Ensure that access to all external devices is protected by appropriate security equipment. Do not copy or install any software on the software control unit unless it is part of the system software or you are nstructed to do so by a Roche Service representative.
It additional software is required, contact your Roche Service representative to ensure validation of the software in question. Do not use the USB ports to connect other storage devices unless you are instructed to do so by official user documentation or a Roche Service representative. Do not use them on public or home computers while connecting to the system.
Keep all external storage devices in a secure place and ensure that they can be accessed by authorized persons only Do not enter any confidential patient-relevant information into the work order file. There is the risk of unauthorized access to patient data. Notices NOTICE List of notices Before operating the system, read the notices contained in this summary carefully Failure to observe them may result in damage to equipment.
Moving parts Damage to the instrument due to contact with moving parts Contact with moving parts may damage some components. Keep all covers closed and in place while the instrument is operating. Do not touch any parts of the instrument other than those specified. Hoche Diagnostics System Manual Version 1. Spillage Malfunction due to spilled liquid Any liquid spilled on the instrument or analyzer may result in malfunction, or damage of the instrument or analyzer.
Do not place samples, reagents, or any other liquid on the surface of the instrument or analyzer other than in designated areas. Do not place the microweli plate on any part of analyzer other than the microweli plate loader. Roche Diagnostics 24 System Manual Version 1. The labels and their definitions are listed below according to their location. For replacement labels, contact your local Roche representative.
Instrument deck may contain biohazardous or chemically contaminated materials. Power connection Connect only to earth-grounded outlet. Connection to PC Use only the appropriate shielded cables.
USB connection Having a total cable distance of more than 5 m, signals can be interfered. E Moving parts Moving arm inside transparent cover. Aborts the run if cover is opened.
Biohazard warning Waste may contain biohazardous or chemically contaminated materials. Hot surface , Do not touch hot surfaces. These safety notes give more detailed information about potentially hazardous situations that may arise during daily operation or when carrying out maintenance procedures. During operation, be sure to observe both the safety labels and the safety notes in all relevant manuals.
Roche Diagnostics 26 System Manual Version 1. Decontamination ie. These items must be disposed of via designated collection facilities. For more information about disposal of your old product, please contact your city office, waste disposal service or your Roche representative. Constraint: It is left to the responsible laboratory organization to determine whether control unit components are contaminated or not. The system integrates fully automated total nucleic acid isolation directly from primary and secondary tubes, automated PCR setup, and real time PCR.
Instrument The instrument prepares the samples. The instrument is loaded with samples, consumables and reagents. After sample preparation, the microweli plate with the PCR-ready samples is unloaded, sealed, and transferred to the analyzer for amplification and detection using real time PCR. The procedure for sample preparation is as follows; 1. Specimen-specific processing 2. Generic binding, washing, and elution 3.
Version 1. Sealing, loading, and unloading the microweli plate are the only manual interventions. The software guides the user through the entire process from sample preparation to amplification and detection and result interpretation. A hand-held barcode reader is connected to the control unit. It is used to scan reagent and reagent reservoir barcodes during loading of reagents as well as sample barcodes to set up the ivork order file.
For details about the control unit and the hand-held barcode reader, see Control unit p. Orders are downloaded automatically from the LIS after samples are loaded onto the instrument.
After reviewing of the final results, results have to be manually uploaded to the LIS using the export function in the Results work area. The System overview tab displays the status of the LIS connection. Roche Diagnostics 34 System Manual Version 1. The administrator can define whether only accepted resuits or all results can be uploaded to the [IS. Use the sample editor to create the work orders for a PCR Only run. The procedure for sample preparation is as follows: 1. Working master mix preparation and PCR-setup Depending on the test, the instrument is able to process up to 96 samples 94 patient specimens plus two controls in a single run.
The main parts of the instrument are shown in Figure A Left side cover B Front cover Figure C Right side cover Covers of the instrument The front cover protects you from moving parts inside the instrument.
The front cover can be opened for user intervention during maintenance. Always close the front cover when you have finished maintenance work. During a run, the front cover must be closed. While t is possible to force the front cover open during a run, doing so will cause an emergency stop. The run will be aborted and all on board reagents and in-process samples will be lost. Do not attempt to start the run with cover open. Roche Diagnostics 40 System Manual Version 1.
The status LEDs inform you where to place the carriers on the autoload tray and which tracks on the instrument deck are occupied by a carrier.
No action necessary. Indicates the track positions in which the carrier must be loaded. Place the carrier at the indicated positions on the autoload tray and insert the carrier until the stop hooks. The stationary carrier is not removable and hoids heater and shaker unit, magnet plate, and the plate holders for the deepweil plate and the microweil plate. The tracks are numbered so that you can readily identify the location where a carrier must be loaded.
The track positions are stamped on the surface of the autoload tray. Track assignment is test-specific. The instrument deck layout below shows you an example of the areas for each carrier type. A Plate carrier for deepweli plate and microwell plate E Tip carrier right B Tip carrier left F Stationary carrier used for sample processing C Sample loading area G D Depending on the test, sample loading area or tip carrier middle Reagent area for reagent reservoir carriers mL and 50 mL and reagent carrier Figure 3—4 Example of the instrument deck layout Track positions The following table summarizes the track positions on the instrument deck.
For additional details about sample carriers, see Sample carriers p. The autoloader detects waiting carriers with their tubes and containers and scans the barcodes. The carriers are inserted by the operator into their designated position on the autoload tray. During loading, the barcode reader on the autoloader scans the carrier barcode and the barcodes of the supplies on the carrier samples, reagents, and disposables.
Inserted carrierwaiting to be loaded D Autoloaderwith barcode reader B Slide block E Autoload tray C Track position stamped on the autoload tray A Figure 3—5 Autoload unit with autoload tray and autoloader Inserting carriers on autoload tray The autoload tray contains slide bio cks that engage tracks in the carriers to guide the carriers when they are loaded.
When inserting a carrier onto the autoload tray, be sure that the tracks on the carrier properly engage the slide blocks. Insert the carriers into their designated position on the autoboad tray until they touch the stop hooks on the far side of the tray. Insert the carriers into the tracks between the front and rear slide blocks of the Autoboad tray until they touch the stop hooks on the far side of the tray.
NOTICE Instrument damage due to improper carrier handling Make sure the carriers are inserted completely until they touch the stop hooks on the autoload tray Exercise care when inserting the carriers do not push carriers against the stop hooks with excessive force. Extend the safety guards to avoid bumping into the carriers on the autoload tray. This barcode type is not enabled by default. For details about barcode specifications, see Barcode reader p.
This allows you to further process or store the samples without having to wait for the run to finish. You can also define that the sample carriers be left in the instrument and manually unloaded when the run is finished. Roche tiiagnostics 44 System Manual Version 1. During operation, the pipetting arm moves left-and-right x direction , picks up the required number of disposable pipetting tips, aspirates, dispenses, and mixes the liquids, and then ejects the used tips into the tip solid waste bag.
Each air-displacement pipetting channel can move forward-and-back y-direction and up-and-down z-direction during the pipetting operation. A disposable pipetting tip is picked up by each pipetting channel at the beginning of a pipetting cycle. The pipetting tip is ejected into the tip solid waste bag at the completion of pipetting for that cycle. A Pipetting channel B Pipette stop disc Figure C Pipetting arm Pipetting arm of instrument Each pipetting channel contains a pipette stop disc which aligns the disposable pipetting tip when it is picked up by the pipetting channel at the beginning of a pipetting cycle.
Aspiration and dispensing is achieved by air displacement. The pipette stop disc does not contact the liquid that is being aspirated into and dispensed from the disposable pipetting tip. The pipette stop discs must be cleaned on a weekly basis.
For additional details, see Weekly niaintenance p. A iSWAP Figure ISWAP Teaciting needies The instrument uses eight teaching needies to automatically check and adjust if necessary z-positioning and over- and under-pressure of each pipetting channel at the appropriate time. The teaching needies are stored near the waste station, next to the tip waste.
The teaching needies are cleaned during the preventive maintenance visit. The following safety messages in particular are relevant: Warning messages: Infection by biohazardous waste p. The instrument can be installed on either a bench top or on a trolley that accommodates a larger solid waste bag. This solid waste bag has a capacity for tips of at most one full run. Exchange the small solid waste bag each time before starting a new run to avoid overfilling of the tip waste.
For details about replacing the small solid waste bag, see Daily niaintenance p. The large solid waste bag holds tips of at most three full runs. The level of the liquid waste is monitored by the system and a warning is issued when it is not possible to do a full run. In this case, it is not possible to start the run.
The liquid vaste is emptied during daily or weekly maintenance. The liquid waste container is reusable. For details about emptying the liquid waste container, see Daily maintenance p. For additional details, see Seconday tubes p.
For additional details, see Secondary tubes p. Depending on the test, up to 94 patient specimens can be loaded onto the instrument per run. The sample barcodes must face to the right of the carrier. Roche Diagnostics 50 System Manual Version 1. Controls are loaded together with the reagents onto the reagent carrier.
NOTICE Instrument damage due to the use of inappropriate or closed tubes Using the incorrect tube types or closed tubes en sample carriers can damage the instrument Use only specified tube types for sample carriers.
Do not use closed tubes en sample carriers. Always open tubes on all sample carriers. Barcode dirnensions c c B EL1 U. A A B Label length: max. For additional details about barcode types and specifications, see Barcode reader p. The position sample carrier uses one track on the instrument deck. EJ3 For details about the types of tubes you can use on the sample carrier, refer to the test specific package insert.
Infection by samples and associated materials CAUTION 1-track carriers such as a sample carrier can fall over and cause injury or contamination. Handle 1 -track carriers with particular care, position them on the autoload tray or place several carriers together to minimize this risk. Carrier barcode Primary or secondary tubes Figure position sample carrier position sample carrier The position sample carrier is optionally available and hoids up to 32 primary or test-spec fic secondary tubes.
An aliquot can be manually transferred from the primary tube to the secondary tube if necessary. For details about the types of tubes you can use on the sample carrier, refer to the test specific package insert. Collection medium carrier The collection medium carrier is optionally available and hoids up to 12 Collection test-specfic medium primary tubes.
This carrier uses two tracks on the instrument deck. Open the collection medium containers before inserting the carrier on the autoload tray. Roche Diagnostics 52 System Manual Version 1. The reagent reservoir barcodes must face to the right of the carrier. The required reagents are decapped and then placed onto their dedicated positions on the reagent carrier.
The reagent barcodes must face to the right of the carrier. The reagent carrier is the same carrier as the position sample carrier. NOTICE Instrument damage due to the use of closed reagent vials Using closed reagent vials on reagent carriers can damage the instrument. Do not use closed reagent vials on reagent carriers. Always open reagent vials on reagent carriers.
The deepweil plate is used to process the samples. The microweli plate is used to hold the final prepared samples that are ready for PCR. Place the deepweil plate on position 1 and the microweli plate on position 3 of the plate carrier. The other positions on the carrier are not used. The deepweli plate barcode must face to the right of the carrier. The deepweil plate barcode is read during loading of the plate carrier.
The microweil barcode is read after loading being brought in front of the barcode reader on the autoloader by the iSWAP. At the end of the run, the plates are placed back on the plate carrier. Unload the plate carrier, seal the microweil plate and dispose of the deepweil plate according to the local regulations unless further off-the-system use is intended.
A B Deepweli plate on position 1 Microweli plate on position 3 Figure Plate carrier Tip rack carriers The tip rack carriers hold the tip racks with the disposable pipetting tips. Depending on the test, up to three tip rack carriers can be loaded for a single run holding a total of 15 tip racks.
The tip rack barcodes must face to the right of the carrier. The total number of pipetting tips per run varies and depends on several criteria test type, sample media, run size, and so on The instrument tracks tip usage from run to run. The instrument checks if enough pipetting tips have been loaded to perform the run. To avoid this message, fully bad all the required tip rack carriers for each run.
Partially used racks can be used in next run. To perform a run, all the required tip rack carriers must be loaded into the instrument. Each tip rack holds 96 tips. Figure Tip rack carrier Stationary carrier The stationary carrier is the area where the samples are processed. It is mounted on the instrument deck and is not removable. Roche Diagnostics 56 System Manual Version 1. Be aware, that the magnets are not affixed to the plate so any metal can remove the magnets from its holder.
A Magnet on magnet plate Figure Magnet plate Holders for deepweil plate and The holders for the deepweli plate and the microweli plate are where the washing and microweliplate PCR setup occurs during sample processing.
Use only Roche consumables designed for use on the system. Do not reuse consumables. All consumables are designed for one time use only. Inspect consumables before use. Do not use damaged consumables. Do not use consumables that have exceeded their expiry date. Replace expired consumables with unexpired consumables before sample processing. Pipetting tips Disposable pipetting tips with filters are used for pipetting of all liquids during sample processing.
The pipetting tips are available in tip racks of 96 tips each. Tip racks are placed into tip rack carriers. For details about tip rack carriers, see Tip rack carriers p.
Use only disposable tips that are specified by Roche. Figure 3—28 Tip rack with 96 disposable pipetting tips Reagent reservoirs The reagent reservoirs hold the reagents used for sample preparation. The reagent reservoirs are barcoded and are filled manually by the operator scan-scan-pour place principle for each run. Scan-scan-pour-placeprinciple To minimize handling errors the reagent reservoirs are filled and placed using the scan-scan-pour-place principle: 1.
Scan the barcode of the required reagent using the hand-held barcode reader. Scan the barcode of an unused reagent reservoir using the hand-held barcode reader. Pour the reagent in the scanned reagent reservoir. Place the filled reagent reservoir onto the required position of the reagent reservoir carrier as indicated in the wizard.
Roche Diagnostics 58 System Manual Version 1. For details about reagent reservoir carriers, see Reagent reservoir carriers p.
The software tracks the use of the reservoirs and rejects previously used reagent reservoirs. A sign within the reagent reservoir indicates the maximal fili height. Always follow the scan-scan-pour-place principle. A mL reagent reservoir Figure B 50 mL reagent reservoir.
Reagent reservoirs Deepweli plate The deepweil plate is used for sample processing. The deepweil plate hoids up to 96 samples. The deepweil plate is placed in the plate carrier on position 1 prior to a run. For details about the plate carrier, see Plate carrier p. Original specimen should be re-tested to obtain valid CT and NG results. Original specimen should be Invalid re-tested to obtain valid result.
Original specimen should be re-tested to obtain valid result. Invalid Invalid. The results are Invalid. Original specimen should be re-tested to obtain valid results. R8 RI Error The test ingredients have not been specified. R9 RI Error The test should have at least one target and at least one internal control. R10 RI Error The probes have not been specified. R20 RI Warning The positive external control is invalid. R21 RI Warning The negative external control is invalid.
Additional information can be found in messages and the trace log files. C8 CP Error The test ingredients have not been specified. C9 CP Error The test should have at least one target and at least one internal control. C10 CP Error The probes have not been specified. C11 CP Error The computation algorithm has not been specified. C12 CP Error The specified algorithm is not supported by this calculation package. C13 CP Error The specified algorithm version is not supported by this calculation package.
C14 CP Error The calculation parameters for the numeric algorithm are incomplete. C15 CP Error The fluorescence measurements data is incomplete. C XT Error Matrix coefficients calculation has failed. C XT Error Matrix inversion has failed. C XT Error Resolution matrix size and channel count do not match. C XT Error General exception raised. The run was aborted. This sample will have an invalid result. X5 SPI Error Reagent onboard time exceeded when the user tried to start the sample preparation process.
Run results will be invalid. Processing of the sample was aborted. Figure 2 shows this scenario. No changes can be made at this level and because the system is implemented over a network communication, it just acts as an intermediate level inside the application layer, transmitting the data to the upper ASTM layer. The short description of the ASTM lower layer is here for information. Messages equal to or less than characters are transmitted as one final frame. Messages greater than characters are split into frames that have character lengths that fall within the character limit.
Results timeout: Timeout for messages sent by the cobas system: From the ENQ, the transmission including multiple frames should not exceed seconds. The test order segment is holding all information related to a sample. Note: Missing orders. For samples that do not have a corresponding test request in the Host system, the whole O segment record must be skipped. Example: If the sample numbers and do not have a test for cobas , the lines marked in bold in the ASTM response from the Host would not exist.
The Host system may have to further parse the result block if a further separation of individual subcomponents is required. See the tables 11 for details and possible combinations inside result blocks. HL7 messages are embedded in block delimited by special non printable characters.
See table below. The observation request segment is holding all information related to a sample. The network address of the instrument is normally determined by the installation of a cobas IT firewall.
To change the network address, you must log into the operating system as local Administrator. Please ask the Roche service representative. Instrument Setup By default the HIF modules are not installed, for the instrument setup, please refer to the Network Configuration Guide cobas system. This installation has to be performed by qualified Roche service personnel. Once the software for host interface has been installed, some parameters can be changed to match the requirements of the LIS system.
The default protocol after installation is HL7. This software can be installed on Windows computers and are intended to be used only by Roche trained personnel. When used as an instrument simulator, the goal is to provide only a quick test tool for testing the transmission formats. Please keep in mind that the simulator does not react like a real instruments in all situations. The simulator is intended to be used for several Roche instruments, periodically new ones will be added.
From version 2. They will be installed by default under Host Interface tools. The user needs administrator rights to be able to install the host tools package properly. After the basic installation of the "Host tools" package, some patches may be required depending on the simulator you intend to use. Please ask the Roche service representative for further information.
Network card HL7 Simulator Roche has developed a specific host simulator to make simple testing of the HL7 protocol, for the cobas Instrument. To start the simulator, simply select from the stat menu as shown.
The simulator must be set up as a server. That is, it will listen on a defined port. Port is often used as a default. The server IP address is the address of the network card and cannot be changed for a server.
It comes from the network settings of the computer hosting the simulator. This is the same as the LIS address that must be set on the cobas when installing or setting up the Host. This has the effect of enabling the correct responses from the simulator to the selected type of instrument. Once every minute, the cobas communication server will attempt a connection on the defined IP address and port.
If the simulator is reached, the connection indicator will turn from yellow to green as shown. Additionally, the IP address of the connected system will appear in the lower part of the blue box Remote. At this point the simulator can be used and will display the HL7 records received and sent.
In some circumstances, the simulator may erroneously indicate an active connection. This can be the case if there are elements in the network that where temporarily disconnected. If the LIS seems unresponsive although the connection is displayed as active, make the connection check.
