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Importing Lab Normal Values:

A Case StudyHenrik Dittmann & Maxime Steisel

IT Department, Institut Jules Bordet, Brussels, Belgium

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Session Overview

Who are we?

What do we do with OpenClinica?

Why are we concerned about lab normal values?

What does our system do with them?

What would we like to do in the future?

What would you like to do?

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Research IT at IJB

Institut Jules Bordet:

public and research hospital,

specializing in oncology

Research IT group:

provides IT systems and tools

for clinical and translational research

investigates new technologies in these areas

CTSU (Clinical Trial Support Unit):

provides operational support, data management,

monitoring, etc. for investigator-initiated clinical trials

sponsored by IJB

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OpenClinica at IJB

OpenClinica Enterprise Edition, employed largely for

investigator-initiated clinical trials since May 2013

Currently 4 active trials, 1 in preparation

Typically phase II, 20-200 subjects, multi-centric, multi-

country

Rather complex eCRFs: 15-40 CRFs, 10-20 study

events

CRFs built on the base of CDISC CDASH:

standardization

reusability

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Lab Normal Values

It is time consuming to have to enter the lab normal

values on every lab CRF.

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Variation in Lab Normal Values

LNVs will stay the same across many visits for a subject

LNVs will stay the same across many subjects for a site

Changes can occur when

lab instruments are changed or recalibrated

the site switches to another lab

the site regularly uses more than one lab

+ a test is exceptionally done at another lab

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Lab Normal Value References

Rather than to enter the LNVs each time, references can

be made:

to the previous / a specified visit that uses the same LNVs

(per subject)

to a repository of LNV sheets stored elsewhere in the CRF

(per subject)

to a repository of LNV sheets independent of subjects (per

site, not possible in OpenClinica)

Our solution:

store LNV sheets in a repeating event

allow specification of LNVs in the lab page as well as a

reference to an occurrence of the repeating event

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LNV Reference Sheets

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Subject-Independent LNVs

Provide users with an external interface for the upload of

LNVs:

enter and update (in case

of data entry errors)

LNV sheets that will be

applicable for all subjects

Users can still enter LNVs directly in OpenClinica:

in the lab page itself (per lab CRF)

as an individual page in the LNV event (per subject)

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OpenClinica

LNV

Upload

WS

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User Interface

Web interface:

authenticate against OpenClinica

select site

enter CRF data for a new or as an update to an existing

LNV sheet

Upload of CSV data (planned)

Import of HL7 messages (e.g. from LIMS, long-term

goal)

Scheduled process to add the LNV sheets that have

been defined already to any new patients

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Importing an LNV Sheet

Implemented as a layer of Web services

on top of OpenClinica’s SOAP services

using a database for recording import data and success as

well as study-specific metadata

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Web Service OC Web Service Internal DB

getSites Study: listAll

getOccurrences imports

getTests tests

getUnits units

updateLNVs StudySubject: listAllByStudy,

Event: schedule, Data: import

oids, imports, values,

patients

completePatients StudySubject: listAllByStudy,

Event: schedule, Data: import

oids, imports, values,

patients

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Import process

1) Schedule a new LNV event for each subject in the site;

OCC = max(occurrences)

2) While min(occurrences) ≠ OCC: Schedule a new LNV

event for each subject where occurrence ≠ OCC

3) Upload data into the OCCth event for each subject

Record OCC, the data itself and success/failure per

subject in DB, together with username and timestamp

Provide metadata per study in DB: OIDs used, list of

tests, list of units

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Examples I

Add a new LNV sheet:

Update an LNV sheet:

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1 2 3

PTN-301 L1.0 L1.1

PTN-302 L1.0 L1.1

PTN-303 L1.0 L1.1

PTN-304 L1.0 L1.1 LX1.0

PTN-305 L1.0 L1.1

PTN-306 L1.0 L1.1

PTN-307 L1.0 L1.1

PTN-308 L1.0 L1.1

PTN-309 L1.0 L1.1

PTN-310 L1.0 L1.1

PTN-311 L1.0 L1.1

1 2 3 4

PTN-301 L1.0 L1.1 --- L2.0

PTN-302 L1.0 L1.1 --- L2.0

PTN-303 L1.0 L1.1 --- L2.0

PTN-304 L1.0 L1.1 LX1.0 L2.0

PTN-305 L1.0 L1.1 --- L2.0

PTN-306 L1.0 L1.1 --- L2.0

PTN-307 L1.0 L1.1 --- L2.0

PTN-308 L1.0 L1.1 --- L2.0

PTN-309 L1.0 L1.1 --- L2.0

PTN-310 L1.0 L1.1 --- L2.0

PTN-311 L1.0 L1.1 --- L2.0

1 2 3 4

PTN-301 L1.0 L1.1' --- L2.0

PTN-302 L1.0 L1.1' --- L2.0

PTN-303 L1.0 L1.1' --- L2.0

PTN-304 L1.0 L1.1' LX1.0 L2.0

PTN-305 L1.0 L1.1' --- L2.0

PTN-306 L1.0 L1.1' --- L2.0

PTN-307 L1.0 L1.1' --- L2.0

PTN-308 L1.0 L1.1' --- L2.0

PTN-309 L1.0 L1.1' --- L2.0

PTN-310 L1.0 L1.1' --- L2.0

PTN-311 L1.0 L1.1' --- L2.0

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Examples II

Add a new study subject:

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1 2 3 4

PTN-301 L1.0 L1.1' --- L2.0

PTN-302 L1.0 L1.1' --- L2.0

PTN-303 L1.0 L1.1' --- L2.0

PTN-304 L1.0 L1.1' LX1.0 L2.0

PTN-305 L1.0 L1.1' --- L2.0

PTN-306 L1.0 L1.1' --- L2.0

PTN-307 L1.0 L1.1' --- L2.0

PTN-308 L1.0 L1.1' --- L2.0

PTN-309 L1.0 L1.1' --- L2.0

PTN-310 L1.0 L1.1' --- L2.0

PTN-311 L1.0 L1.1' --- L2.0

PTN-312

1 2 3 4

PTN-301 L1.0 L1.1' --- L2.0

PTN-302 L1.0 L1.1' --- L2.0

PTN-303 L1.0 L1.1' --- L2.0

PTN-304 L1.0 L1.1' LX1.0 L2.0

PTN-305 L1.0 L1.1' --- L2.0

PTN-306 L1.0 L1.1' --- L2.0

PTN-307 L1.0 L1.1' --- L2.0

PTN-308 L1.0 L1.1' --- L2.0

PTN-309 L1.0 L1.1' --- L2.0

PTN-310 L1.0 L1.1' --- L2.0

PTN-311 L1.0 L1.1' --- L2.0

PTN-312 L1.0 L1.1' --- L2.0

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Referencing LNVs in Rules

Custom Rules Generator:

allows data managers to specify rules in an Access

database, using generic item names

extracts OIDs from metadata exports of testing and

production environments

creates XML files

Syntax extension for rule expressions: “$X” variableLBREFID eq $X and LBORRES * 2 gt SE_LNV[$X].F_LNV.LBORNHI

will be replaced by (using pseudocode here):(LBREFID eq 1 and LBORRES * 2 gt SE_LNV[1].F_LNV.LBORNHI) or

(LBREFID eq 2 and LBORRES * 2 gt SE_LNV[2].F_LNV.LBORNHI) or

(LBREFID eq 3 and LBORRES * 2 gt SE_LNV[3].F_LNV.LBORNHI) or

...

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Working with OC…

…or against it?

We don’t want to interfere with OpenClinica, modifying or

extending the system directly

Major architectural change to allow data that is not

specific to a study subject

Web Services provide an API that (in this case) gives

access to all necessary functions

Solution does not make use of EE-specific features

► Working around OC

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Pros and Cons

+ Support for

both site-wide and per-subject LNVs

corrections to a LNV sheet

propagation to subjects created afterwards

o Can be referenced through rules (not efficient, though)

– Data is really not subject-specific but specific to the site

– Queries must be addressed for each subject individually

– Time windows during which manual entry into a subject’s

LNV sheets can cause the import to fail for this subject

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Outlook

1) Currently, OpenClinica does only cater for study data

that is specific to a subject

except for some metadata (which is not accessible to rules)

► ODM provides a place for study-specific reference data

in the ReferenceData element

2) Build interfaces to other systems with OpenClinica’s

web services, e.g., to get LNVs and lab data from LIMS

interoperability (read HL7, convert tests, units, …)

remove patient information from lab data before importing

that

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Thank you for your attention!

What would you like to do?

dealing with lab normal values

dealing with data that are not patient-specific

interfacing OpenClinica

…

henrik.dittmann@bordet.be

maxime.steisel@bordet.be

www.bordet.be

www.br-e-a-s-t.org

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