Roche Cobas 4800 1.02

cobas 4800 system

Host Interface Manual

Software Version 1.02

DRAFT

Table of Contents

General

1

... 1 Target audience ... 1 References ... 1 Document Revision History

... 2 Contacts, Trademarks ... 3 Glossary

Overview

4

... 4 Communication Overview ... 5 Communication layers

Workflow

6

... 6 Communication Scenarios ... 6 Work Order Inquiry

... 8 Result export

Message types

8

... 8 General Information ... 8 Full Run Inquiry

... 8 Full Order Response

... 10 Test Result Export

... 13 FLAGS

ASTM Protocol

17

... 19 COBAS 4800 ASTM Record Definitions

... 20 Inquiry records Mappings (ASTM)

... 20 H Segment ... 21 P Segment ... 21 Q Segment ... 21 L Segment ... 22 Inquiry Response Mapping

... 22 H Segment ... 23 P Segment ... 23 O Segment ... 24 L Segment ... 25 Inquiry/response examples ... 26 Results Mapping (ASTM)

... 26 H Segment ... 27 P Segment ... 27 O Segment ... 28 R Segment ... 28 L Segment ... 29 Results Example ASTM

HL7 Protocol

31

... 32 COBAS 4800 HL7 Record Definitions

... 33 Inquiry Records mapping (HL7)

... 33 Inquiry Mapping

... 35 Inquiry Response Mapping

... 37 Results Mapping (HL7)

... 40 Result Example HL7

Communication setup

42

... 42 Network connection ... 42 Instrument Setup

Simulator

43

... 43 Installing simulators ... 43 HL7 Simulator ... 46 Setting up the simulator connection

... 49 Connection test

... 50 Sending an order to the system

... 54 Receiving results from the system.

... 57 ASTM Simulator

Troubleshooting / logfiles

58

General

General

1

Target audience

The intended audience for this manual is Host Interface programmers and the Roche Field engineers supporting the system.

References

[1] HL 7 Documentation Version 2.4, Health Level Seven, Ann Arbor MI, USA, www.HL7.org [2] ASTM Documentation 1394 LIS2

Note: Although ASTM and HL7 are the base of the data exchange, the result transmission is not a strict ASTM or HL7 format.

The system presents CT/NG or HPV as global blocks of results and transmits them as such. See the Result topics for the respective ASTM and HL7 formats for details.

Document Revision History

Document Version Revision Date

1.0 January 2009

1.02 Manual rev 02 March 2010

Copyright 2009, 2010, Roche Diagnostics Ltd. All rights reserved. Rev 02: Corrected some errors and omissions.

Clarified the target audience of manual and simulators. Added definition Client / server.

Added complete results fields tables Added examples multiple flags

Added information regarding media types

Added information regarding order handling (Tubes without orders) at various places. Timeout for order response from LIS increased to 180 seconds.

This manual applies to Software Version 1.02

Information in this document is subject to change without notice. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without the express written permission of Roche Diagnostics GmbH.

Every effort has been made to ensure that all the information contained in this manual is correct at the time of publishing. However, Roche Diagnostics Ltd. reserves the right to make any changes necessary without notice as part of ongoing product development.

Document references

These are internal Roche references DVS Number: 05702950001

Contacts, Trademarks

Contact Addresses

Manufacturer Roche Diagnostics Ltd. Forrenstrasse

CH-6343 Rotkreuz Switzerland

Distribution Roche Diagnostics GmbH Sandhofer Straße 116 D-68305 Mannheim Germany

Distribution in the US Roche Diagnostics 9115 Hague Road PO Box 50457 Indianapolis, IN 46250 USA

Questions or comments regarding the contents of this manual can be directed to the address below or to your Roche representative.

Roche Diagnostics Ltd. Global Service Support Forrenstrasse

6343 Rotkreuz, Switzerland email: [email protected]

Trademarks

cobas is a trademark of Roche.

General

Glossary

MTS Medium Throughput System This name is sometimes used inside the protocol. Where the Acronym MTS is used, it means the cobas ®4800 system..

A&D Amplification and detection. The system will only perform Amplification and detection on already prepared MWP, using the z 480 instrument.

The A&D runs are not supported by the LIS workflow.

AnD Same meaning as A&D - Often used inside records as the "&" character would be interpreted as separator and therefore cannot be used.

Full run Samples will be prepared into a MWP by the cobas x 480, then the plate will be transferred manually to the cobas z 480 for the A&D run.

GUID Stands for Global Unique Identifier.

A unique identifier created by the system. It is a 128 bits number written in a pattern of hexadecimal numbers similar to :

3F2504E0-4F89-11D3-9A0C-0305E82C3301

It is used to identify a unique run in the transmission records. MWP Microwell plates.

Transformer A software module that conforms XML communication files to the communication server. cobas x 480

instrument

The cobas x 480 prepares the samples.

The cobas x 480 is loaded with samples, consumables and reagents. After sample preparation, the multiwell plate with the PCR-ready samples is unloaded, sealed, and transferred to the cobas z 480 for amplification and detection.

cobas z 480 analyzer

The cobas z 480 utilizes fluorescence to detect nucleic acids amplified by using realtime PCR methodology. the loading and unloading of the multiwell plate is done manually.

Overview

2

The structure of the document is as follow

The topic General describes general functions of the subsystem or the unit having influence on the implementation. This chapter contains no specifications but provides background information and context information for the specifications stated in the next chapter. The goal is to increase the legibility of the document.

Topic HL7 contains all the specifications for the HL7 protocol. Topic ASTM contains all the specifications for the ASTM protocol.

Communication Overview

The physical connection used by the cobas 4800 host interface is the standard network card (N.I.C) with Ethernet protocol. The connection is TPC/IP over ethernet.

The RS-232 connection is not supported by the system.

The cobas 4800 system offers two transmission protocols: -ASTM -HL 7

The communication is realized by xml files which are exchanged and evaluated between cobas 4800 sw <-> Transformer and Transformer <-> cobas 5000 IT Communications Server.

Client /Server structure

The communication is always established by the cobas 4800 control unit; the cobas 4800 system is always the TCP/IP client and the LIS is always the TCP/IP server.

Overview

Communication layers

As all the communication is based on network connections, this manual addresses mostly the upper layer (application) related topics.

Workflow

3

Communication Scenarios

The following table shows the communication scenarios existing for the cobas 4800. Table 1 Communications Scenarios

Name Description Input Output

Work Order

Inquiry Full The cobas 4800 ask the LISto get order details for one or more Samples

Run Type, Test Type, Sample

Id’s For each sample: SubTest Type, Media Type Work Order

Inquiry A&D Only

This mode is not supported by the LIS workflow

Run Type, Test Type, Id of the MWP

For each sample: Sub Test Type, Media Type, MWP Position Test Result

Upload

The cobas 4800 System sends the test result of a Run to the LIS

Run Id, Run Type, Test Type Sub Test Type, Media Type, Test Result, Flags, Sample Id, Test Time Stamp, Order Time Stamp, Accepted Flag

-Once the LIS has been enable by Roche support, the LIS must always respond to order requests. There is no possibility to work with "results sending only" and manually ordering.

If the LIS cannot respond to order requests, the system cannot run tests unless the LIS is disabled again to work completely offline.

Work Order Inquiry

Figure 1 Work Order Inquiry

The Work Order Inquiry Scenario is described In Figure 1.

If a cobas 4800 user starts a run to test samples it loads the samples or the MWP plate. After the plate loading, the cobas 4800 system starts the above inquiry sequence to the LIS server.

Workflow

Missing orders:

When sample numbers are received that do not have a corresponding test request in the Host system, the whole sample record must be skipped.

No "empty" orders shall be sent to the cobas 4800, otherwise it will result into a complete order upload failure. See in Each protocol for details.

When order numbers are skipped, the mismatch will be signaled on the screen as shown below (1): (Mismatch occurred between loaded and expected samples

Please press "Unload Sample" ) The sample positions are indicated in (2)

Possible correcting actions :

1. Unload the sample rack(s), remove the indicated sample tubes (2), reload the sample rack. or

2. Unload the sample rack, add orders to the indicated samples into the LIS system, reload the sample rack(s)

Work order inquiry timeout:

The timeout after a work order inquiry from the instrument is currently set at 180 seconds and cannot be changed. The complete work order list has to be completely transmitted within these 180 seconds, otherwise a timeout message will

Result export

The results can be manually exported to the LIS using the selected protocol (ASTM or HL7). The LIS has to be enabled to be able to export the results.

If the system works in offline mode and tests are ordered manually , results cannot be exported via LIS. The total transmission time should not exceed 120 seconds otherwise the last results may not be transmitted.

Message types

4

General Information

The Full run, the A&D Only run and the result export have different data to transfer. The following tables show the detail of this data.

Full Run Inquiry

Table 2 Full Run Inquiry

cobas 4800 Query Example HL7-Mapping ASTM-Mapping

Run Type Full QPD-3-2 Q-5-6

Test Type CT/NG QPD-3-1 Q-5-4

Software MTS MSH-3 H-5-3

Version 0.9.1.0843 MSH-4 H-5-4

Sample Id’s (1-94) 100101001 QPD-4 Q-3

Full Order Response

Table 3 Full Order Response

cobas 4800 Query Example HL7-Mapping ASTM-Mapping

Run Type Full OBR-4-3 O-5-6

Test Type CT/NG OBR-4-1 O-5-4

Software LIS MSH-3-1 H-5-3

Version 6.3 MSH-4-1 H-5-4

Sample Id 0010212 OBR-3-1 O-3-1

SubTestType NG OBR-4-2 O-5-5

Message types

Table 4 Possible values SubTestType (order response)

Type Possible values for subtype field (order response)

CT/NG CT/NG

CT NG

HPV HPV High Risk Panel + Genotyping

HPV High Risk Panel

Table 5 * Possible values media

Type Test subtype Possible value

field Media Type Media names

CT/NG CT UT UUT = UniTrans = Urine UniTrans NG CT/NG HPV HPV High Risk Panel PC SP = PreserveCyt

= SurePathoriginal tube is not validated on cobas 4800

PC and SP are used, whether the samples are in original containers or in secondary tube round base 13mL

HPV16 HPV18

Test Result Export

Table 6 Test Result Export

Test Result

Export Example HL7Mapping ASTMMapping

Start Time 2008-10-14T13:49:39 OBR-7 R-12

End Time 2008-10-14T13:50:45 OBR-8 R-13

Test Type CT/NG OBR-4 R-3

Run Type Full OBR-4 O-4

Run Id 83b6f32c-d31b-49a8-8239-13be65486ea3 MSH-10 O-4;H-5-1

User Id Laboperator OBX-16 R-11

Software MTS MSH-3 H-5-3

Version 0.9.3.0847 MSH-4 H-5-4

Created Admin ORC-10 O-17

Creation Date 2008-06-11T15:56:58 ORC-7-4 O-8

Plate Id (A&D Only)

AD000012 OBX-3;OBR-3 O-3;H-5

For each Sample

Test Result Examples: Invalid ; CT POS, NG POS ;

See Test results combination tables for all possibilities.

OBX-5-1 R-4-1

Flag Pattern M1,M3 OBX-5-2 R-4-2

Sub Test Type CT OBR-4 R-3

Sample Id 100101001 OBX-3;OBR-3 O-3;H-5

Media Type UUT OBR-15 O-16

Order Date 2008-10-14T13:50:38 OBR-27 O-15

Accepted Flag False OBX-11 O-26

MWP Position A5 OBX-3;OBR-3 O-3;H-5

Test result Possible values (Samples)

invalid positive (POS) negative (NEG)

Test result Possible values (Controls)

invalid Valid

Message types

Test results combination tables

:

Table 7

cobas® 4800 CT/NG Test Result Report and Interpretation

CT POS, NG POS CT Positive, NG Positive. Specimen is positive for the presence of both CT and NG DNA.

CT NEG, NG NEG CT Negative*, NG Negative*. Neither CT nor NG DNA, if present, could be detected.

CT POS, NG NEG CT Positive, NG Negative*. Specimen is positive for the presence of CT DNA.

NG DNA, if present, could not be detected. CT POS, NG Invalid CT Positive, NG Invalid.

Specimen is positive for the presence of CT DNA.

NG result is Invalid. Original specimen should be re-tested to obtain valid NG result.

CT NEG, NG POS CT Negative*, NG Positive. CT DNA, if present, could not be detected. Specimen is positive for the presence of NG DNA.

CT Invalid, NG Positive.

CT Invalid, NG POS CT result is Invalid. Original specimen should be re-tested to obtain valid CT result.

Specimen is positive for the presence of NG DNA.

CT Invalid, NG NEG CT Invalid, NG Negative*. CT result is Invalid. Original specimen should be re-tested to obtain valid CT results.

NG DNA, if present, could not be detected.

CT NEG, NG Invalid CT Negative*, NG Invalid. CT DNA, if present, could not be detected. NG result is Invalid. Original specimen should be re-tested to obtain valid NG result.

Invalid CT Invalid, NG Invalid. Both CT and NG results are Invalid. Original specimen should be re-tested to obtain valid CT and NG results. Failed No Result for Specimen Consult the cobas® 4800 system Operator’s

Manual for instructions to review run flags and recommended actions. Original specimen should be re-tested to obtain valid CT and NG results.

Table 8

cobas® 4800 HPV Test Result Report and Interpretation SubTest “HPV High Risk Panel”:

HR HPV POS High Risk HPV Positive Specimen is positive for the DNA of any one of, or combination of, the following high risk HPV types: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68.

HR HPV NEG High Risk HPV Negative* HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set threshold.

Invalid High Risk HPV Invalid Results are invalid. Original specimen should be_{re-tested to obtain valid result.} Failed No Result for Specimen Consult the cobas® 4800 system Operator’s

Manual for instructions to review run flags and recommended actions. Original specimen should be re-tested to obtain valid result.

SubTest “HPV High Risk Panel Plus Genotyping”:

Other HR HPV POS, HPV16 POS, HPV18 POS

Other High Risk HPV Positive, HPV16 Positive, HPV18 Positive. Specimen is positive for HPV types 16 and 18 DNA and the DNA of any one of, or combination of, the following high risk HPV types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68.

Other HR HPV POS, HPV16 POS, HPV18 NEG

Other High Risk HPV Positive, HPV16 Positive, HPV18 Negative*. Specimen is positive for HPV type 16 DNA and the DNA of any one of, or combination of, the following high risk HPV types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68. HPV type 18 DNA was undetectable or below the pre-set threshold.

Other HR HPV POS, HPV16 NEG, HPV18 POS

Other High Risk HPV Positive, HPV16 Negative*, HPV18 Positive. Specimen is positive for HPV type 18 DNA and the DNA of any one of, or combination of, the following high risk HPV types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68. HPV type 16 DNA was undetectable or below the pre-set threshold.

Other HR HPV POS, HPV16 NEG, HPV18 NEG

Other High Risk HPV Positive, HPV16 Negative*, HPV18 Negative*. Specimen is positive for the DNA of any one of, or combination of, the following high risk HPV types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68. HPV types 16 and 18 DNA were undetectable or below the pre-set threshold.

Other HR HPV NEG, HPV16 POS, HPV18 POS

Other High Risk HPV Negative*, HPV16 Positive, HPV18 Positive. HPV types 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set threshold. Specimen is positive for HPV types 16 and 18 DNA.

Other HR HPV NEG, HPV16 NEG, HPV18 POS

Other High Risk HPV Negative*, HPV16 Negative*, HPV18 Positive. HPV types 16, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set threshold. Specimen is positive for HPV type 18 DNA.

Other HR HPV NEG, HPV16 POS, HPV18 NEG

Other High Risk HPV Negative*, HPV16 Positive, HPV18 Negative*. HPV types 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set threshold. Specimen is positive for HPV type 16 DNA.

Other HR HPV NEG, HPV16 NEG, HPV18 NEG

Other High Risk HPV Negative*, HPV16 Negative*, HPV18 Negative*. HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set threshold.

Invalid Invalid. The results are Invalid. Original specimen should be re-tested to obtain valid results.

Failed No Result for Specimen Consult the cobas® 4800 system Operator’sManual for instructions to review run flags and recommended actions. Original specimen should be re-tested to obtain valid results.

Message types

FLAGS

Result Interpretation

Table 9 Flag

Code Source Severity Description

R1 RI Error General exception raised.

R2 RI Error The Well Result List is null or empty. R3 RI Error The Well Result Node is invalid.

R4 RI Error The Result Interpretation Parameters Node is null. R5 RI Error The Result Interpretation Parameters Node is invalid. R6 RI Error Input Xml Nodes mapping failed.

R7 RI Error The Result Interpretation provides 4-dyes result interpretation. 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.

R11 RI Error The Well Result Node attributes are invalid. R12 RI Error The Algorithm Results Node is incomplete.

R13 RI Error The Qualitative Interpretation Tables Node is invalid. R14 RI Error The Result Table Node is invalid.

R15 RI Error The SubTest type or the ResultTable is invalid. R16 RI Error The Intermediate-Result Interpretation failed. R17 RI Error The Well-Result Interpretation failed. R18 RI Error The Multi-Well Result Interpretation failed.

R19 RI Error The Ct ranges for the intermediate interpretation are invalid. R20 RI Warning The positive external control is invalid.

R21 RI Warning The negative external control is invalid.

Multiple or other reason

Table 10 Flag

Code Source Severity Description

M1 SW Error Software error. Additional information can be found in messages and the trace log files.

M2 Other Error Aborted by the user

M5 SW Warning PCR run only with a user defined sample preparation M6 SW Warning The connection to the instrument was temporarily lost

Calculation

Table 11 Flag

Code Source Severity Description

C1 CP Error General exception raised. C2 CP Error The RawData node is null.

C3 CP Error The CalculationParameters node is null. C4 CP Error The RawData node is invalid.

C5 CP Error The CalculationParameters node is invalid. C6 CP Error Input XmlNodes mapping failed.

C7 CP Error The HpvCtng-CalculationPackage provides 4-dyes result interpretation. 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.

C101 XT Error The CrossTalk compensation has failed. C102 XT Error The CrossTalkMatrix is null.

C103 XT Error The Background vector is null. C104 XT Error CrossTalk Matrix has invalid entries.

C105 XT Error The length of the background vector is not equal with CrossTalkMatrix filter combinations count.

C106 XT Error Matrix coefficients calculation has failed. C107 XT Error Matrix inversion has failed.

C108 XT Error Resolution matrix size and channel count do not match. C121 XT Error The RawData node is null.

C122 XT Error The CalculationParameters node is null. C123 XT Error The RawData node is invalid.

C124 XT Error The CalculationParameters node is invalid. C125 XT Error General exception raised.

C221 KA2 Error The RawData node is null.

C222 KA2 Error The AlgorithmParameters node is null. C223 KA2 Error The RawData node is invalid.

Message types

C224 KA2 Error The AlgorithmParameters node is invalid. C225 KA/KA2 Error General exception raised.

C301 ELCA Warning CurvatureFailure C302 ELCA Error InterceptOutOfRange C303 ELCA Error SlopeOutOfRange C304 ELCA Warning CurveFitFailure C305 ELCA Warning AFIMinFailure C306 ELCA Error DataRangeFailure C307 ELCA Info InsufficientCurvature C308 ELCA Info DeclineCorrected C309 ELCA Error CTOutOfRange

C321 ELCA Error The RawData node is null.

C322 ELCA Error The CalculationParameters node is null.

A&D errors

Table 12 Flag

Code Source Severity Description

Z1 AnDI Error Hardware or software error from the instrument. The run was aborted.

SPI errors

Table 13 Flag

Code Source Severity Description

X1 SPI Error Hardware or software error from the instrument. The run was aborted. X2 SPI Info Barcode was entered manually.

X3 SPI Error Clot detected for a sample. This sample will have an invalid result.

X4 SPI Error Not enough liquid while processing a sample. This sample will have an invalid result.

X5 SPI Error Reagent onboard time exceeded when the user tried to start the sample preparation process. The run was aborted.

X6 SPI Error Working Master Mix with extract timed out after sample preparation has finished. The run was aborted.

X7 SPI Error Error during processing of external control. Run results will be invalid. X8 SPI Error Hardware or software error from the instrument. Processing of the sample was

Test Result Export workflow

5

Figure 2 Test Result Export

Test Result Export workflow

ASTM Protocol

6

The cobas 4800 ASTM protocol also implements the ASTM E1381-91 Low Level Protocol, although this is not the focus of this manual. 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.

Message example with intermediate frame:

c4800 00:08:17,763 [ENQ] HOST 00:08:17,763 [ACK] c4800 00:08:17,883 [STX]1H|\^&|||MTS^c9507f52-37bc-43d4-bba6-360fb 74bd898^OrderFileValidator^1.0.0.0918^1394.LIS2 |||||LIS|TSREQ^REAL|P|1|20091001085217|[CR][ETX ]80[CR][LF] HOST 00:08:17,883 [ACK] c4800 00:08:17,983 [STX]2P|1|[CR][ETX]BB[CR][LF] HOST 00:08:17,983 [ACK] c4800 00:08:18,103 [STX]3Q|1|^RDR0003406\RDR0003408\RDR0003407\RDR 0003405\RDR0003404\RDR0003403\RDR0003424\RDR000 3423\RDR0003422\RDR0003421\RDR0003420\RDR000341 9\RDR0003418\RDR0003417\RDR0003416\RDR0003415\R DR0003414\RDR0003413\RDR0003412\RDR0003411\RDR0 003410\RDR0[ETB]5D[CR][LF] HOST 00:08:18,113 [ACK] c4800 00:08:18,203 [STX]4003409\RDR0000829\RDR0003494||^^^CT/NG^^F ull|[CR][ETX]FB[CR][LF] HOST 00:08:18,203 [ACK] c4800 00:08:18,314 [STX]5L|1|[CR][ETX]BA[CR][LF] HOST 00:08:18,314 [ACK] c4800 00:08:18,414 [EOT] Frame Configurations For Middle Frame <STX> FN text <ETB> C1 C2 <CR><LF> For Last Frame <STX> FN text <ETX> C1 C2 <CR><LF>

C1C2 represent the checksum characters. Control character (characters enclosed in < > <ENQ> is control character (HEX 05)

<STX> is control character (HEX 02) <ETB> is control character (HEX 17) <CR> is control character (HEX 0D) <LF> is control character (HEX 0A) <ETX> is control character (HEX 03) <ACK> is control character (HEX 06)

Maximum Length of the Frame

For one frame, maximum of 240 characters for text, 7 characters for frame control characters (not included in the 240). Messages equal to or less than 240 characters are transmitted as one final frame.

Messages greater than 240 characters are split into frames that have character lengths that fall within the 240-character limit.

The only or final remaining frame becomes the last frame and is indicated by <ETX>. All others are intermediate (middle) frames and are indicated by <ETB>.

Results timeout:

Timeout for messages sent by the cobas 4800 system: From the ENQ, the transmission including multiple frames should not exceed 120 seconds. Intermediate frames sent past this time will not be sent, the system will close the transmission with an EOT,

ASTM Protocol

COBAS 4800 ASTM Record Definitions

Message Structure

The Message structures are defined in the syntax also used in [2 ]

Work order inquiry

H Record MESSAGE HEADER SEGMENT

P Record Patient Record (empty, needed by protocol) Q Record Query information

L Record ASTM message closing record

Work order response

H Record MESSAGE HEADER SEGMENT

P Record Patient Record (empty, needed by protocol) O Record Order information

: :

Following O records until end of message L Record ASTM message closing record

Test result export

H Record MESSAGE HEADER SEGMENT

P Record Patient Record (empty, needed by protocol) O Record Order information

R Record Result information O Record Order information R Record Result information :

:

Following O / R records until end of message L Record ASTM message closing record

cobas 4800 – Field mappings

The tables in topic Inquiry records Mappings (ASTM) are showing the mappings between the cobas 4800 xml file and the xml file which the host interface needs to work with.

Inquiry records Mappings (ASTM)

H Segment

Table 14 ASTM Inquiry Message Header Segment

Name and Number

Type Comment Values Required

H-1 String The character H identifies the record as a message

header record H Yes

H-2 String Component, Repetition, Escape and Subcomponent

delimiter – exactly in this order |^ \ & Yes

H-5-1 String Name of the application which sent this message MTS Yes

H-5-2 GUID GUID representing the unique identifier of this

message given from MTS by it’s xml-filename 128-Bit-IntegerMin. Value = 0 Max. Value = FFFF FFFF-FFFF-FFFFFFFFFFFF

Yes

H-5-3 String The name or shortcut of the user which create the message

Any string Yes

H-5-4 String The version of the sending software 0.9.4.0847 Yes

H-5-5 Number Protocol version – used as a version check to make sure that this message is interpreted correctly

1394.LIS2 Yes

H-10 String Name of the application which has to receive this

message LIS Yes

H-11-1 String Message type

used to delegate the tasks to the analyzer TSREQ (e.gTSREQ^REAL) Yes

H-11-2 String Event trigger

used to delegate the tasks to the analyzer

REAL (e.g TSREQ^REAL)

Yes

H-12 String Processing mode (processing priority) P = Production

P Yes

H-13 Number Version number – currently a constant number set

to 1 1 Yes

H-14 DateTime DateTime of the message put by the creating system

on creation of this message YYYYMMDDhhmmss

e.g.

20081122121212 Yes

ASTM Protocol

P Segment

The MTS software doesn’t have any patient informations – but the ASTM protocol does need a P record.

Table 15 ASTM Inquiry Patient Information Segment

Name and Number

Type Comment Values Required

P-1 String The character P identifies the record as a patient record

P Yes

P-2 Number For the first patient transmitted, 1 shall be entered,

for the second, 2, ... until the last as defined 1 Yes

Q Segment

Table 16 ASTM Inquiry Request Information Segment

Name and Number

Type Comment Values Required

Q-1 String This field is coded as Q. Q Yes

Q-2 Number For the first patient transmitted, 1 shall be entered,

for the second, 2, ... until the last as defined 1 Yes

Q-3-2 String List of specimens separated by \ or

The Plate Id for AnD Only runs (AnD workflow not supported)

020404~789043 2~098398 or AD0000034

Yes

Q-5-4 String Test type. Example CT/NG or HPV ^^^CT/NG ^^Full

Yes

Q-5-6 Run type - Can only be Full (Not supported SpiOnly, AnDiOnly)

^^^CT/NG^^

Full

Yes

L Segment

ASTM Inquiry L Segment (Message Terminator) Segment

Name and Number

Type Comment Values Required

L-1 String This field is coded as L. L Yes

Inquiry Response Mapping

H Segment

This table is showing the field mappings between the MTS xml file / Transformer and the ASTM message header segment.

Table 17 ASTM Response Message Header Segment

Name and Number

Type Comment Values Required

H-1 String The character H identifies the record as a

message header record H Yes

H-2 String Component, Repetition, Escape and

Subcomponent delimiter – exactly in this order

|^ \ & Yes

H-5-1 String Name of the application which sent this message LIS Yes

H-5-2 GUID GUID representing the unique identifier of this

message given from MTS by it’s xml-filename 128-Bit-IntegerMin. Value = 0

Max. Value = FFFFFFFF- FFFF-FFFF-FFFF-FFFFFFFFFFFF

Yes

H-5-3 String The name or shortcut of the user which create the message

Any string Yes

H-5-4 String The version of the sending software 6.2 Yes

H-5-5 Number Protocol version – used as a version check to make sure that this message is interpreted correctly

1394.LIS2 Yes

H-10 String Name of the application which has to receive this

message MTS Yes

H-11-1 String Message type

used to delegate the tasks to the analyzer

TSREQ (e.g TSREQ^REAL)

Yes

H-11-2 String Event trigger

used to delegate the tasks to the analyzer

REAL (e.g TSREQ^REAL)

Yes

H-12 String Processing mode (processing priority) P = Production

P Yes

H-13 Number Version number – currently a constant number

set to 1 1 Yes

H-14 DateTime DateTime of the message put by the creating system on creation of this message

YYYYMMDDhhmmss e.g. 20081122121212

ASTM Protocol

P Segment

The cobas 4800 software does not have any patient information – but the ASTM protocol does need a P record.

Table 18 ASTM Response Patient Information Segment

Name and Number

Type Comment Values Required

P-1 String The character P identifies the record as a patient

record P Yes

P-2 Number For the first patient transmitted, 1 shall be entered,

for the second, 2, ... until the last as defined 1 Yes

O Segment

This table is showing the field mappings between the MTS xml file / Transformer and the ASTM test order segment. 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.

Table 19 ASTM Response Test Order Segment

Name and Number

Type Comment Values Required

O-1 String The character assigned to the order record shall be O

O Yes

O-2 Number Set ID – for each order which is transmitted a

own number is set starting from 1 to n Continuous ID starting by 11, 2, …n Yes

O-3-1 String Unique identifier of the sample – usually a barcode assigned to the sample (Specimen ID)

0001301^AD0000013^A6 Yes

O-3-2 String _{Plate ID – only for "AnD Only" runs}

_(see

Note 1)

0001301^AD0000013^A6 NO

O-3-3 String MWP Position only for "AnD Only" runs 0001301^AD0000013^A6 NO

O-5-4 String Identifies the ‘testtype’ of the sample Known values are:

- CT/NG - HPV

^^^CT/NG^NG^Full Yes

O-5-5 String Identifies the sub test type of a sample. Can be different for each sample but must be a sub type of the TestType.

Values, see Table

^^^CT/NG^NG^Full YES

O-5-6 String Identifies the ‘runtype’ of the sample Allowed values are:

- Full = Full run of all system components - AnDiOnly = AmpDetect only. See Note 1

^^^CT/NG^NG^Full Yes

O-8 DateTime Contents the Time when the order was created YYYYMMDDHHMMSS e.g. 20081203143400

Yes

(Note see

restriction

)

O-16 String Media Type. Allowed values, see Table String ex: UT Yes

O-17 String Contents the user who has created the order admin Yes

Note 1: A&D mode not supported by LIMS workflow

9

58

L Segment

ASTM response L Segment (Message Terminator) Segment

Name and Number

Type Comment Values Required

L-1 String This field is coded as L. L Yes

ASTM Protocol

Inquiry/response examples

outgoing - ASTM: H|\^&|||MTS^65745d86-7a00-49ae-98b3-8a67d18f8e31^none^0.9.8.0912^1394. LIS2|||||LIS|TSREQ^REAL|P|1|20090403081313| P|1| Q|1|^15200049\15200059\15200043\15200073\15200013\15200071\15200041 \15200011\15200069\15200039\15200009\15200067\15200037\15200007\15200065 \15200035\15200005\15200093\15200063\15200033\15200003\15200091\15200061 \15200031\15200027||^^^CT/NG^^Full| L|1| incoming - ASTM: H|\^&|||LIS^65745d86-7a00-49ae-98b3-8a67d18f8e31^none^0.9.8.0912^1394. LIS2|||||MTS|TSREQ^REAL|P|1|20090403083315| P|1 O|1|15200049^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|2|15200059^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|3|15200043^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|4|15200073^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|6|15200071^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|7|15200041^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|8|15200011^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|9|15200069^^||^^^CT/NG^CT^Full|||20090403083315||||||||UT|none O|10|15200039^^||^^^CT/NG^NG^Full|||20090403083315||||||||UT|none O|11|15200009^^||^^^CT/NG^CT/NG^Full|||20090403083315||||||||UT|none O|12|15200067^^||^^^CT/NG^CT/NG^Full|||20090403083315||||||||UUT|none O|13|15200037^^||^^^CT/NG^NG^Full|||20090403083315||||||||UUT|none O|14|15200007^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|15|15200065^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none O|16|15200035^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|17|15200005^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|18|15200093^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|19|15200063^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|20|15200033^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|21|15200003^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|22|15200091^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|23|15200061^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|24|15200031^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none O|94|15200027^^||^^^CT/NG^CT^Full|||20090403083316||||||||UUT|none L|1

Note: When sample numbers are received that do not have a corresponding test request in the Host system, the whole

sample record must be skipped.

No "empty" orders shall be sent to the cobas 4800, otherwise it will result into a complete order upload failure.

Example: If the sample numbers 15200065 and 15200027 do not have a test for cobas 4800, the lines marked in bold in the ASTM response from the Host would not exist.

Results Mapping (ASTM)

H Segment

This table is showing the field mappings between the MTS xml file / Transformer and the ASTM message header segment.

Table 20 ASTM Response Message Header Segment

Name and Number

Type Comment Values Required

H-1 String The character H identifies the record as a

message header record H Yes

H-2 String Component, Repetition, Escape and

Subcomponent delimiter – exactly in this order

|^ \ & Yes

H-5-1 String Name of the application which sent this message LIS Yes

H-5-2 GUID GUID representing the unique identifier of this

message given from MTS by it’s xml-filename 128-Bit-IntegerMin. Value = 0

Max. Value = FFFFFFFF- FFFF-FFFF-FFFF-FFFFFFFFFFFF

Yes

H-5-3 String The name or shortcut of the user which create the message

Any string Yes

H-5-4 String The version of the sending software 6.2 Yes

H-5-5 Number Protocol version – used as a version check to make sure that this message is interpreted correctly

1394.LIS2 Yes

H-10 String Name of the application which has to receive this

message MTS Yes

H-11-1 String Message type

used to delegate the tasks to the analyzer

TSREQ (e.g TSREQ^REAL)

Yes

H-11-2 String Event trigger

used to delegate the tasks to the analyzer

REAL (e.g TSREQ^REAL)

Yes

H-12 String Processing mode (processing priority) P = Production Yes

H-13 Number Version number – currently a constant number set to 1

1 Yes

H-14 DateTime DateTime of the message put by the creating system on creation of this message

YYYYMMDDhhmmss e.g. 20081122121212

ASTM Protocol

P Segment

The cobas 4800 software does not have any patient information – but the ASTM protocol does need a P record.

Table 21 ASTM Response Patient Information Segment

Name and Number

Type Comment Values Required

P-1 String The character P identifies the record as a patient record P Yes

P-2 Number For the first patient transmitted, 1 shall be entered, for the second, 2, ... until the last as defined

1 Yes

O Segment

This table is showing the field mappings between the MTS xml file / Transformer and the ASTM test order segment. The test order segment is holding all information related to a sample.

Table 22 ASTM Test Order Segment

Name and Number

Type Comment Values Required

O-1 String The character assigned to the order record shall be O O Yes

O-2 Number Set ID – for each order which is transmitted a own

number is set starting from 1 to n Continuous ID starting by1 1, 2, …n

Yes

O-3-1 String Unique identifier of the sample – usually a barcode

assigned to the sample (Specimen ID) 0001301^AD0000013^A6 Yes

O-3-2 String Plate ID – only for AnD Only runs 0001301^AD0000013^A6 NO

O-3-3 String MWP Position only for AnD Only runs 0001301^AD0000013^A6 NO

O-4 String Run type of the test Full or AnD Only Yes

O-5-4 String Identifies the ‘testtype’ of the sample allowed values are:

- CTNG - HPV

^^^CT/NG^NG^Full Yes

O-5-5 String Identifies the sub test type of a sample. Can be diffrent for each sampl but must be a sub type of the TestType. See Table

^^^CT/NG^NG^Full YES

O-5-6 String Identifies the ‘runtype’ of the sample Allowed values are:

- Full = Full run of all system components - AnDiOnly = AmpDetect only

^^^CT/NG^NG^Full Yes

O-8 DateTime Contents the Time when the order was created YYYYMMDDHHMMSS e.g. 20081203143400

Yes

O-16 String Media Type

Allowed values see Table

String ex: UT Yes

O-17 String Contents the user who has created the order admin Yes

O-26 String Type of Results: F=Final Results; P=preliminary results – depends of the result export flag “Áccepted”.

F Means result was accepted P Means result was not accepted (yet)

F or P Yes

9

.

R Segment

Note:

The system presents CT/NG or HPV as global blocks of results and transmits them as such.

The Host system may have to further parse the result block if a further separation of individual subcomponents is required . See the tables for details and possible combinations inside result blocks.

Table 23 ASTM Result Record Segment

Name and Number

Type Comment Values Require

d

R-1 String The record type ID is coded as R. R Yes

R-2 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1

1, 2, …n

Yes

R-3-4 String Identifies the ‘testtype’ of the sample Known values are:

- CT/NG - HPV

^^^CT/NG^NG^Full Yes

R-3-5 String Identifies the sub test type of a sample. Can be diffrent for each sampl but must be a sub type of the TestType Ex: CT see table

^^^CT/NG^NG^Full YES

R-3-6 String Identifies the ‘runtype’ of the sample Allowed values are:

- Full = Full run of all system components - AnDiOnly = AmpDetect only

^^^CT/NG^NG^Full Yes

R-4-1 String Application package defined test result e.g. Positive, see

table .

Positive^M1\M2 Yes

R-4-2 String Flags for the test result See example Positive^M1\M2 Yes

R-4-3 String CT-Values of the controls CT_DYE1^NaN^ CT_DYE5^NaN^ CT_DYE3^NaN^ CT_DYE0^NaN

NO

R-11 String User who has run the test laboperator Yes

R-12 DateTime Time when the test was started on the instrument YYYYMMDDHHMMS S

e.g. 20081203143400 Yes

R-13 DateTime Time when the test was finished on the instrument YYYYMMDDHHMMS S e.g. 20081203143400 Yes

L Segment

Segment Name and Number

Type Comment Values Required

L-1 String This field is coded as L. L Yes

L-2 int The Terminator field 1 Yes

11

9

10

ASTM Protocol

Results Example ASTM

(Simulator log)

outgoing - ASTM: c4800 00:11:52,652 [ENQ] HOST 00:11:52,652 [ACK] c4800 00:11:52,762 [STX]1H|\^&|||MTS^e5052475-cdb3-4c13-97d4-2bb43 467e75f^^1.0.0.0918^1394.LIS2|||||LIS|TSREQ^REA L|P|1|20091001085550|[CR][ETX]FA[CR][LF] HOST 00:11:52,782 [ACK] c4800 00:11:52,872 [STX]2P|1|[CR][ETX]BB[CR][LF] HOST 00:11:52,872 [ACK] c4800 00:11:52,982 [STX]3O|1|0NCL010145A03DC^AD6002095^B1||CT/NG^F ull|||20090825020548|||||||20090825143017|NegCt rl||||||||||F|[CR][ETX]B0[CR][LF] HOST 00:11:52,992 [ACK] c4800 00:11:53,092 [STX]4R|1|^^^CT/NG^N/A^Full|Valid^^CT_DYE0\NaN\ CT_DYE5\34.949874877929688\CT_DYE1\NaN|||||||La bmanager|20090825140628|20090825170656|[CR][ETX ]7F[CR][LF] HOST 00:11:53,102 [ACK] c4800 00:11:53,203 [STX]5O|2|1C1M014196A012R^AD6002095^A1||CT/NG^F ull|||20090825020548|||||||20090825143017|PosCt rl||||||||||F|[CR][ETX]B4[CR][LF] HOST 00:11:53,213 [ACK] c4800 00:11:53,313 [STX]6R|1|^^^CT/NG^N/A^Full|Valid^^CT_DYE0\36.5 50521850585938\CT_DYE5\35.303115844726562\CT_DY E1\35.388565063476562|||||||Labmanager|20090825 140628|20090825170656|[CR][ETX]B4[CR][LF] HOST 00:11:53,323 [ACK] c4800 00:11:53,423 [STX]7O|3|RDR0003428^AD6002095^H1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT|||||||| ||F|[CR][ETX]98[CR][LF] HOST 00:11:53,433 [ACK] c4800 00:11:53,533 [STX]0R|1|^^^CT/NG^CT/NG^Full|CT·POS,·NG·POS^|| |||||Labmanager|20090825140628|20090825170656|[ CR][ETX]B4[CR][LF] HOST 00:11:53,543 [ACK] c4800 00:11:53,643 [STX]1O|4|RDR0003430^AD6002095^G1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT|||||||| ||F|[CR][ETX]8B[CR][LF] HOST 00:11:53,653 [ACK] c4800 00:11:53,753 [STX]2R|1|^^^CT/NG^CT/NG^Full|CT·POS,·NG·POS^|| |||||Labmanager|20090825140628|20090825170656|[ CR][ETX]B6[CR][LF] HOST 00:11:53,753 [ACK] c4800 00:11:53,854 [STX]3O|5|RDR0003432^AD6002095^F1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT|||||||| ||F|[CR][ETX]8F[CR][LF] HOST 00:11:53,864 [ACK] c4800 00:11:53,964 [STX]4R|1|^^^CT/NG^CT/NG^Full|CT··NEG,·NG·POS^| ||||||Labmanager|20090825140628|20090825170656| [CR][ETX]C0[CR][LF] HOST 00:11:53,974 [ACK] c4800 00:11:54,074 [STX]5O|6|RDR0003433^AD6002095^E1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT||||||||

||||||Labmanager|20090825140628|20090825170656| [CR][ETX]C2[CR][LF] HOST 00:11:54,194 [ACK] c4800 00:11:54,294 [STX]7O|7|RDR0003435^AD6002095^C1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT|||||||| ||F|[CR][ETX]95[CR][LF] HOST 00:11:54,304 [ACK] c4800 00:11:54,404 [STX]0R|1|^^^CT/NG^CT/NG^Full|CT··NEG,·NG··NEG^ X2|||||||Labmanager|20090825140628|200908251706 56|[CR][ETX]4E[CR][LF] HOST 00:11:54,414 [ACK] c4800 00:11:54,515 [STX]1O|8|RDR0003436^AD6002095^D1||CT/NG^Full|| |20090825020548|||||||20090825141222|UT|||||||| ||F|[CR][ETX]92[CR][LF] HOST 00:11:54,525 [ACK] c4800 00:11:54,625 [STX]2R|1|^^^CT/NG^CT/NG^Full|CT··NEG,·NG··NEG^ |||||||Labmanager|20090825140628|20090825170656 |[CR][ETX]C6[CR][LF] HOST 00:11:54,635 [ACK] c4800 00:11:54,725 [STX]3L|1|[CR][ETX]B8[CR][LF] HOST 00:11:54,735 [ACK] c4800 00:11:54,835 [EOT]

Note: The bullet character inside results is just a placeholder to visualize the spaces inside strings.

example |CT·POS,·NG··NEG^| should look in reality: |CT POS, NG NEG^|

The character used in the transmission is a regular space (Hex 20).

Example multiple flags (R segment only, simulator log)

outgoing - ASTM:

c4800 06:53:16,137 [STX]6R|1|^^^HPV^HPV·High·Risk·Panel·+·Genotypi ng^Full|Failed^X3\X4\X1|||||||GT|20091211133042 |20091211153236|[CR][ETX]69[CR][LF]

ASTM Protocol

HL7 Protocol

7

Minimal Layer Protocol

The data framing uses the MLLP, Minimal Lower Layer Protocol defined in the HL7 standard.

HL7 messages are embedded in block delimited by special (non printable) characters. <start_block>data<end_block><CR>

The values of the special characters are <VT> for the start block and <FS> for the end block. See table below.

<start_block> Start Block character (1 byte) ASCII <VT>

Data (variable number of bytes) The HL7 data is comprised of any displayable ASCII characters and the carriage return character, <CR>.

<end_block> End Block character (1 byte) ASCII <FS>. .

<CR> Carriage Return (1 byte)

Char (ASCII) Décimal Octal Hex Name

VT 011 013 0B Vertical Tab

FS 028 034 1C File Separator

CR 013 015 0D Carriage Return

Graphical representation of data framing:

COBAS 4800 HL7 Record Definitions

The tables in the topic Inquiry Records mapping (HL7) show the mappings between the cobas 4800 xml file and the HL7 segment / records file which the host interface needs to work with.

Message Structure

The Message structures are defined in the syntax also used in [1]

Work order inquiry

MSH MESSAGE HEADER SEGMENT

QPD QUERY PARAMETER DEFINITION

RCP RESPONSE CONTROL PARAMETER SEGMENT

Work order response

MSH MESSAGE HEADER SEGMENT

{

ORC COMMON ORDER SEGMENT - Multiple times ORC + OBR {

OBR OBSERVATION REQUEST SEGMENT }

}

Test result export

MSH MESSAGE HEADER SEGMENT

{

ORC COMMON ORDER SEGMENT - Multiple times ORC + OBR + OBX {

OBR OBSERVATION REQUEST SEGMENT OBX OBSERVATION/RESULT SEGMENT }

}

33

HL7 Protocol

Inquiry Records mapping (HL7)

Inquiry Mapping

MSH Segment (Message Header)

Table 24 HL7 Inquiry Message Header Segment

Name and Number

Type Comment Values Required

MSH-1 String Field delimiter | Yes

MSH-2 String Component, Repetition, Escape and Subcomponent delimiter – exactly in this order

^ ~ \ & Yes

MSH-3 String Name of the application which sent this message MTS Yes

MSH-4 String The version of the sending software e.g. 1.3.5 Yes

MSH-5 String Name of the application which has to receive this message LIS Yes

MSH-7 DateTime DateTime of the message YYYYMMDDhh mmss

e.g.

20081122121212 Yes

MSH-9-1 String Message type code – see HL7 Doc.:

[1] Table 0076 - Message type QBP (QBP^Q11) Yes

MSH-9-2 String Trigger event code – see HL 7 Doc.: [1] Table 0003 - Event type

Q21 (QBP^Q11) Yes

MSH-10 GUID Message Id – Generated by the Transformer Software 128-Bit-Integer Min. Value = 0 Max. Value = FFFF FFFF-FFFF-FFFFFFFFFFFF Yes

MSH-11 String Processing mode (processing priority) see HL7 Doc.:

[1] Table 0103 - Processing ID

P = Production Yes

MSH-12 Number HL7 Version ID – used as a version check to make sure that this message is interpreted correctly

see HL7 Doc.:

[1] Table 0104 – Version ID

2.4 Yes

MSH-17 String Country ISO code used for currency-, datetime- and other specifications.

[1] Table 0399 – Country code

[A-Z]{3} e.g. CHE = Switzerland, USA = United States

Yes

MSH-18 String Character char set used for the whole message - see HL7 Doc.:

[1] Table 0211 – Alternate character sets

The COBAS 4800 project has decided to use the not documented character set UTF-8

QPD - Query Parameter Definition

Table 25 HL7 Inquiry Query Parameter Definition Segment

Name and Number

Type Comment Values Required

QPD-1 String This field contains the name of the query FullRunQuery or AnDOnlyQuery

YES

QPD-3 String Test Specification contains the Test Type and the Run

Type (only "Full" supported) CT/NG^FULL YES

QPD-4 String All Samples or the Plate ID of the MWP Plate AD0000012 or 0001~0002~000 3~0004

YES

RCP - Response Control Parameter Segment

Table 9 HL7 Inquiry Response Control Parameter Segment Segment

Name and Number

Type Comment Values Required

RCP-1 String Query priority – For cobas 4800 always I=Immediate I YES

HL7 Protocol

Inquiry Response Mapping

MSH Segment (Message Header)

Table 26 HL7 Response Message Header Segment

Name and Number

Type Comment Values Required

MSH-1 String Field delimiter | Yes

MSH-2 String Component, Repetition, Escape and Subcomponent delimiter – exactly in this order

^ ~ \ & Yes

MSH-3-1 String Name of the application which sent this message LIS Yes

MSH-4-1 String The version of the sending software 6.2 Yes

MSH-5-1 String Name of the application which has to receive this message MTS Yes

MSH-7 DateTime DateTime of the message YYYYMMDDhhm mss

e.g.

20081122121212 Yes

MSH-9-1 String Message type code – see HL7 Doc.:

[1] Table 0076 - Message type OML (OML^O21) Yes

MSH-9-2 String Trigger event code – see HL 7 Doc.:

[1] Table 0003 - Event type O21 (OML^O21) Yes

MSH-10 GUID Message Id – Generated by the Transformer Software 128-Bit-Integer Min. Value = 0 Max. Value = FFFF FFFF-FFFF-FFFFFFFFFFFF Yes

MSH-11 String Processing mode (processing priority) see HL7 Doc.:

[1] Table 0103 - Processing ID

P = Production Yes

MSH-12 Number Version ID – used as a version check to make sure that this message is interpreted correctly

see HL7 Doc.:

[1] Table 0104 – Version ID

2.4 Yes

MSH-17 String Country ISO code used for currency-, datetime- and other specifications.

The value is mapped from the current thread of the Transformer application

[1] Table 0399 – Country code

[A-Z]{3} e.g. CHE = Switzerland, USA = United States

Yes

MSH-18 String Character char set used for the whole message - see HL7 Doc.:

[1] Table 0211 – Alternate character sets The cobas 4800 project has decided to use the not documented character set UTF-8

ORC Segment (Common Order)

Table 11 HL7 Response Common Order Segment

Name and Number

Type Comment Values Required

ORC-1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1 1, 2, …n

Yes

ORC-7-4 DateTime This field contains the creation time of the order out of the cobas 4800 order file

20081202154500 YES

ORC-10 String This field contains the identity of the user who actually

created the order out of the cobas 4800 order file. e.g ADMIN YES

OBR – Segment (Observation Request)

This table is showing the field mappings between the cobas 4800 xml file / Transformer and the HL7 message version 2.4 observation request segment.

The observation request segment is holding all information related to a sample.

Table 12 HL7 Response Observation Request Segment

Name Type Comment Values Required

OBR-1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1

1, 2, …n

Yes

OBR-3-1 String Unique identifier of the sample – usually a barcode assigned to the sample

0001301

^AD0000013^A6

YES

OBR-3-2 String Plate ID – only for A&D Only runs.

See Note 1

0001301^AD0000013 ^A6

NO

OBR-3-3 String MWP Position only for A&D Only runs 0001301^AD0000013^

A6 NO

OBR-4-1 String Identifies the ‘testtype’ of the sample Known values are:

CTNG - HPV

CT/NG^NG^Full Yes

OBR-4-2 String The sub test type of a sample. Values, see

Table

CT/NG^NG^Full YES

OBR-4-3 String Identifies the ‘runtype’ of the sample Allowed values are: See Note 1

- Full = Full run of all system components - SpiOnly = Sample Extraction only - AnDiOnly = AmpDetect only

CT/NG^NG^Full Yes

OBR-15 String Media Type

Allowed values : see Table

String ex: UT Yes

OBR-27 XML DateTime

Xml DateTime of the message put by the creating system on creation of this message

YYYYMMDDhhmmss e.g. 20081122121212

Yes

Note 1 : Only "Full" is supported by the HIF workflow.

Note 2 : Missing orders For samples that do not have a corresponding test request in the Host system, the whole ORC +

OBR segment records pair must be skipped. 9

HL7 Protocol

Results Mapping (HL7)

MSH Segment (Message Header)

Table 13 HL7 Result Message Header Segment

Name and Number

Type Comment Values Requir

ed

MSH-1 String Field delimiter | Yes

MSH-2 String Component, Repetition, Escape and Subcomponent delimiter

– exactly in this order ^ ~ \ & Yes

MSH-3-1 String Name of the application which sent this message MTS Yes

MSH-4-1 String The version of the sending software 0.9.4.847 Yes

MSH-5-1 String Name of the application which has to receive this message LIS Yes

MSH-7 DateTime DateTime of the message YYYYMMDDhh mmss

e.g.

20081122121212 Yes

MSH-9-1 String Message type code – see HL7 Doc.:

[1] Table 0076 - Message type ORU(ORU^O21) Yes

MSH-9-2 String Trigger event code – see HL 7 Doc.: [1] Table 0003 - Event type

O21 (ORU^O21) Yes

MSH-10 GUID Message Id – Generated by the Transformer Software TBD Yes

MSH-11 String Processing mode (processing priority) see HL7 Doc.:

[1] Table 0103 - Processing ID

P = Production Yes

MSH-12 Number Version ID – used as a version check to make sure that this message is interpreted correctly

see HL7 Doc.:

[1] Table 0104 – Version ID

2.4 Yes

MSH-17 String Country ISO code used for currency-, datetime- and other specifications.

[1] Table 0399 – Country code

[A-Z]{3} e.g. CHE = Switzerland, USA = United States

Yes

MSH-18 String Character char set used for the whole message - see HL7 Doc.: [1] Table 0211 – Alternate character sets

The cobas 4800 project has decided to use the not documented character set UTF-8

UTF-8 Yes

ORC – Segment (Common Order)

Table 14 HL7 Result Common Order Segment

Name and Number

Type Comment Values Requir

ed

ORC-1 Number Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1 1, 2, …n

Yes

ORC-7-4 DateTime This field contains the creation time of the order out of the cobas 4800 order file

20081202154500 YES

ORC-10 String This field contains the identity of the user who actually created the order out of the cobas 4800 order file.

OBR - Segment (Observation Request)

This table is showing the field mappings between the cobas 4800 xml file / Transformer and the HL7 message observation request segment.

The observation request segment is holding all information related to a sample.

Table 15 HL7 Result Observation Request Segment

Name and Number

Type Comment Values Require

d

OBR-1 Number Set ID – for each order which is transmitted a own

number is set starting from 1 to n Continuous IDstarting by 1 1, 2, …n

Yes

OBR-3-1 String Unique identifier of the sample – usually a barcode assigned to the sample

0001301^AD000001 3^A6

YES

OBR-3-2 String Plate ID – only for AnD Only runs 0001301^AD000001

3^A6 NO

OBR-3-3 String MWP Position only for AnD Only runs 0001301^AD000001 3^A6

NO

OBR-4-1 String Identifies the ‘testtype’ of the sample Known values are:

CT/NG - HPV

CT/NG^NG^FULL YES

OBR-4-2 String The sub test type of a sample See possible value table :

CT/NG^NG^FULL YES

OBR-4-3 String The run type of the test CT/NG^NG^FULL YES

OBR-7 DateTime Time the test was started on the instrument YYYYMMDDhhmms s

e.g. 20081122121212 YES

OBR-8 DateTime Time the test was finished on the instrument YYYYMMDDhhmms s

e.g. 20081122121212 YES

OBR-15 String Allowed values are:

See table

UUT YES

OBR-27 DateTime Time when the order was created YYYYMMDDhhmms s

e.g. 20081122121212 YES

9

HL7 Protocol

OBX - Segment (Observation / Result Segment)

Note:

The system presents CT/NG or HPV as global blocks of results and transmits them as such.

The Host system may have to further parse the result block if a further separation of individual subcomponents is required . See the tables for details and possible combinations inside result blocks.

Table 16 HL7 Result Observation / Result Segment Segment

Name and Number

Type Comment Values Require

d

OBX-1 String Set ID – for each order which is transmitted a own number is set starting from 1 to n

Continuous ID starting by 1 1, 2, …n

Yes

OBX-2 String This field contains the format of the observation value in OBX – For the cobas 4800 the format is ST = String Data

ST YES

OBX-3-1 String Unique identifier of the sample – usually a barcode assigned to the sample

0001301^AD000001 3^A6

YES

OBX-3-2 String Plate ID – only for AnD Only runs 0001301^AD000001 3^A6

NO

OBX-3-3 String MWP Position only for AnD Only runs 0001301^AD000001

3^A6 NO

OBX-5-1 String Application package defined test result e.g. Postive, Failed, … See table

Positive^M1~M2 YES

OBX-5-2 String Flags for the test result Positive^M1~M2 YES

OBX-5-3 String CT-Values of the controls CT_DYE1^NaN^ CT_DYE5^NaN^ CT_DYE3^NaN^ CT_DYE0^NaN

NO

OBX-11 String Accepted Flag possible values are: Final results = ‘F’ or ‘Final results = ‘P’ it depends on the accepted flags from the cobas 4800 result export file F Means result was accepted

P Means result was not accepted (yet)

F or P YES

OBX-16 String User of the instrument who run the test laboperator YES

11

Result Example HL7

HL7 Result Export (Simulator log)

c4800 10:14:27,257 [VT] c4800 10:14:27,257 MSH|^~\&|MTS|1.0.0.0918|LIS||20090918101319||OR U^O21|9a7b5dab-8049-4ba8-83b7-6e8aefcbbed1|P|2. 5.1|||||CHE|UTF-8|[CR] c4800 10:14:27,257 ORC|1||||||^^^20090826114803||||[CR] c4800 10:14:27,257 OBR|1||0NCL010145A037Y^AD6002084^B1|HPV^N/A^Ful l|||20090826120921|20090826154328|||||||NegCtrl ||||||||||||20090826114803|[CR] c4800 10:14:27,257 OBX|1|ST|0NCL010145A037Y^AD6002084^B1||Valid^^C T_DYE3~NaN~CT_DYE5~NaN~CT_DYE1~NaN~CT_DYE0~NaN| |||||P|||||Labmanager|[CR] c4800 10:14:27,273 ORC|2||||||^^^20090826114803||||[CR] c4800 10:14:27,273 OBR|2||R0000814^AD6002084^G1|HPV^HPV·High·Risk· Panel·+·Genotyping^Full|||20090826120921|200908 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,273 OBX|2|ST|R0000814^AD6002084^G1||Other·HR·HPV·NE G,·HPV16·POS,·HPV18·NEG^||||||P|||||Labmanager| [CR] c4800 10:14:27,288 ORC|3||||||^^^20090826114803||||[CR] c4800 10:14:27,288 OBR|3||R0000815^AD6002084^F1|HPV^HPV·High·Risk· Panel·+·Genotyping^Full|||20090826120921|200908 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,288 OBX|3|ST|R0000815^AD6002084^F1||Other·HR·HPV·NE G,·HPV16·NEG,·HPV18·POS^||||||P|||||Labmanager| [CR] c4800 10:14:27,288 ORC|4||||||^^^20090826114803||||[CR] c4800 10:14:27,304 OBR|4||R0000816^AD6002084^D1|HPV^HPV·High·Risk· Panel·+·Genotyping^Full|||20090826120921|200908 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,304 OBX|4|ST|R0000816^AD6002084^D1||Other·HR·HPV·PO S,·HPV16·NEG,·HPV18·NEG^||||||P|||||Labmanager| [CR] c4800 10:14:27,304 ORC|5||||||^^^20090826114803||||[CR] c4800 10:14:27,304 OBR|5||R0000817^AD6002084^E1|HPV^HPV·High·Risk· Panel·+·Genotyping^Full|||20090826120921|200908 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,320 OBX|5|ST|R0000817^AD6002084^E1||Other·HR·HPV·PO S,·HPV16·POS,·HPV18·NEG^||||||P|||||Labmanager| [CR] c4800 10:14:27,320 ORC|6||||||^^^20090826114803||||[CR] c4800 10:14:27,320 OBR|6||R0000819^AD6002084^C1|HPV^HPV·High·Risk· Panel·+·Genotyping^Full|||20090826120921|200908 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,335 OBX|6|ST|R0000819^AD6002084^C1||Other·HR·HPV·PO S,·HPV16·POS,·HPV18·POS^||||||P|||||Labmanager| [CR] c4800 10:14:27,335 ORC|7||||||^^^20090826114803||||[CR] c4800 10:14:27,335 OBR|7||R0000818^AD6002084^H1|HPV^HPV·High·Risk·

HL7 Protocol 26154328|||||||PC||||||||||||20090826114803|[CR ] c4800 10:14:27,335 OBX|7|ST|R0000818^AD6002084^H1||Other·HR·HPV·In valid,·HPV16·Invalid,·HPV18·POS^||||||P|||||Lab manager|[CR] c4800 10:14:27,351 ORC|8||||||^^^20090826114803||||[CR] c4800 10:14:27,351 OBR|8||2H1M015776A02IG^AD6002084^A1|HPV^N/A^Ful l|||20090826120921|20090826154328|||||||PosCtrl ||||||||||||20090826114803|[CR] c4800 10:14:27,351 OBX|8|ST|2H1M015776A02IG^AD6002084^A1||Valid^^C T_DYE3~37.381362915039062~CT_DYE5~35.7265472412 10938~CT_DYE1~36.203384399414062~CT_DYE0~35.940 170288085938||||||

Note: The bullet character inside results is just a placeholder to visualize the spaces inside strings.

example Other·HR·HPV·POS should look in reality: Other HR HPV POS

The character used in the transmission is a regular space (Hex 20).

Example multiple flags (OBX segment only, simulator log)

outgoing - HL7:

c4800 08:05:32,833 OBX|79|ST|A2482185^AD6201793^D3||Failed^X3~X4~X1|| ||||F|||||GT|[CR]

Communication setup

8

Network connection

The physical connection used by the cobas 4800 host interface is the standard network card (N.I.C) with Ethernet protocol. 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 4800 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. To change to ASTM, or back to HL7, change the target IP (LIS system) or the port, see the the Network Configuration Guide cobas 4800 system.