Transcript 06-How to deal with data from local labs

How to deal with data from local labs
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Laboratory Data Transfer with SDTM to the LB domain
• Overview of topics:
• Challenge getting lab results into LB
• SDTM Requirements
• Data provided by Central Laboratories
• Data provided by Local Laboratories
•
Standardized units
•
Conversion factors
•
Non-Convertible Units
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SDTM Requirement
• The task: beside the original result and original unit coming from the DB
add
• LBTESTCDs when the lab test is not part of the CT
• Original ranges
• You need ONE standard unit per lab parameter
• Standardized section, including
•
•
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Converted result (if the standardized unit is different to the original unit)
Standardized unit
Converted ranges (if the standardized unit is different to the original unit)
• Reference range identicators
• Test methods and other supplemental information
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Variable Conversion
•Need to convert all data from Original to Standard
Original Variable
Standardized Variable
Results
LBORRES
LBSTRESC
LBSTRESN
Units
LBORRESU
LBSTRESU
Ranges
LBORNRLO
LBORNRHI
LBSTNRLO
LBSTNRHI
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Data provided by Central Laboratories
• Central Laboratories are normally uncomplicated
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Standardized exports from their database
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Normally already only a single unit per test
•
Ranges attached to values consistent with the timepoint of the test
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Reference range identicators in place
•
Additional information often given
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Data provided by Local Laboratories
• Local Laboratories are a challenge:
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Result and unit entered in CRF, Ranges often collected separately
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Every site could have their own unit per lab parameter
•
Conversion of „local“ unit to selected „standard“ unit needed
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Define conversion factors per original unit which is different
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Variability of syntax of local units
•
This includes similar units such as
g/L == mg/mL
or semantic differences such as
x10^6/L == 10E6/L == 10^6/L
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Use of „other unit“ fields
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Both original and standard unit must be mapped to Controlled Terminology
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Example for Multiple Units per Parameter
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Data provided by Local Laboratories (2)
•
Need to collect the ranges per investigator per lab parameter
•
Need to collect each range per gender and age of the subject
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Ranges have to be consistent with the unit of the value
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Ranges sometimes are valid only for a period - have to be updated
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Ranges may be from their lab, but they may have other references.
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Inconstitencies between result units and range units possible
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Data validation necessary for results out of range
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Investigator assessments must be included
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Data provided by Local Laboratories (3)
•
Other interesting things that could happen…
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The site changes the unit and/or ranges from visit to visit per subject
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Typos of units which has been entered per hand
•
Do you know „LAKHS/CMM“ ?
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Handle exotic local units – and find conversion factors
Identify the meaning for some abbrivated units
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You have to spend lots of resources to get the local lab part into a good shape
•
Paper CRFs are much harder to handle than eDC eCRFs
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Standardized units
• You need ONE standard unit per lab parameter
• Who determines this standard unit?
• There is no library to check for the correct unit per parameter
• Only for some lab parameter a „SI unit“ is defined
• Often a misunderstanding between „SI unit“
and
„standardized unit“
• Different terms and syntax for the same unit
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Standardized units (2)
• Sponsor defined the standard unit for „his“ submission
• Standard Unit must be defined -> sponsor specific
• often SI where available, but might be protocol or CRF driven as well
• Not all sponsors have such standardized unit per lab parameter
=> some times „standardized unit” per study
• Another problem: use of the same LBTEST for different LBCATs
• E.g. Glucose (GLUC) for Chemestry and Urinalysis
• Should the same LBTESTCD/LBTEST for the different categories?
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Conversion factors
• Same problems and questions
• Who determines this conversion factors?
• There is no library to check for the correct conversion factors
• Need to validate each conversion factor
• Has to be hardcoded in the transfer program
• New data could mean: update of transfer program - because of new units
• Has to be used for values and ranges
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What would make our life easier…
• General consideration: each sponsor should have a lab model defined,
e.g. a library, that defines…
• LBTESTCDs for non-CT lab parameter
• Laboratory categories for each lab test (need a concept of categorizing tests)
• Standardized units per lab parameter
• Conversion factors
• Question: is there a need to create such library within CDISC?
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Special Issue: Non-Convertible Units
• Check for mixture of absolute and relative results for one parameter
• e.g. Basophils: given in “X 10*9/L” and “%”
• There are two different SDTM CT entries for Basophils:
• absolute
Basophils
BASO
• relative
Basophils/Leukocytes
BASOLE
• Depending on the original unit use the correct LBTESTCD/LBTEST
• Never convert such values since these are two separate parameters
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Special Issue: Non-Convertible Units - Example
• Incorrect dataset
LBTESTCD LBTEST
LBORRES LBORRESU
LBSTRESC LBSTRESN LBSTRESU
BASO
BASO
BASO
BASO
BASO
BASO
BASO
BASO
0
0
1
1
2
0.028
0.041
0.056
0
0
1
1
2
0.028
0.041
0.056
Basophils
Basophils
Basophils
Basophils
Basophils
Basophils
Basophils
Basophils
%
%
PER 100 BLOOD CELLS
PER 100 BLOOD CELLS
PER 100 BLOOD CELLS
X 10*9/L
X 10*9/L
X 10*9/L
0 X 10*9/L
0 X 10*9/L
1 X 10*9/L
1 X 10*9/L
2 X 10*9/L
0.028 X 10*9/L
0.041 X 10*9/L
0.056 X 10*9/L
• Correct dataset
LBTESTCD LBTEST
LBORRES LBORRESU
LBSTRESC LBSTRESN LBSTRESU
BASOLE
BASOLE
BASOLE
BASOLE
BASOLE
BASO
BASO
BASO
0
0
1
1
2
0.028
0.041
0.056
0
0
1
1
2
0.028
0.041
0.056
Basophils/Leukocytes
Basophils/Leukocytes
Basophils/Leukocytes
Basophils/Leukocytes
Basophils/Leukocytes
Basophils
Basophils
Basophils
%
%
PER 100 BLOOD CELLS
PER 100 BLOOD CELLS
PER 100 BLOOD CELLS
X 10*9/L
X 10*9/L
X 10*9/L
0%
0%
1%
1%
2%
0.028 X 10*9/L
0.041 X 10*9/L
0.056 X 10*9/L
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It’s not only LB…
• This standardized requirement may occurs for all Finding Domains
• Everywhere using different units for one parameter check for issues
• e.g. VS domain:
• Temperature collected in
°C and °F
• Weight collected in
kg and lbs
• Height collected in
cm and inch
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Thank you
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