Analysis Data Model (ADaM)_SEP2012

Report
Analysis Data Model
(ADaM)
Case Studies
Wouter van Wyk, 27 Sep 2012
Copyright © 2012 Quintiles
Case Studies
Specific to Basic Data Structure (BDS)
With the increased adoption of the Analysis Data Model
(ADaM) we are facing a shift in our approach to creating
Analysis datasets, as we are encouraged to create
records rather than adding additional variables as we
might have in the past. With these Case Studies I hope
to address some of the questions around:
• Mapping multiple SDTM Variables to the same ADaM variable
• Creating derived records
• Multiple baseline definitions in the same ADaM domain
2
Mapping multiple SDTM Variables to
the same ADaM variable
• Finding domains
> Eg. LB, VS, EG
> **ORRES, **STRESN
• Map to BDS
> AVAL, AVALC
• Multiple variables mapping to a single ADaM BDS Result variable
• Traceability
> SRCDOM, SRCSEQ, SRCVAR
3
Mapping multiple SDTM Variables to
the same ADaM variable
SDTM VS Dataset
DOMAIN
VSSEQ
VISIT
VSTEST
VSORRES
VSORRESU
VSSTRESN
VSSTRESU
VS
1
SCR
WEIGHT
158.7
LB
72
kg
VS
2
V1
WEIGHT
162
LB
73.5
kg
VS
3
V2
WEIGHT
161.8
LB
73.4
kg
VS
4
V3
WEIGHT
161.6
LB
73.3
kg
VS
5
V4
WEIGHT
162.3
LB
73.6
kg
VS
6
V5
WEIGHT
163
LB
74
kg
4
Mapping multiple SDTM Variables to
the same ADaM variable
SRCDOM
SRCSEQ
SRCVAR
VISIT
PARAM
AVAL
VS
1
VSORRES
SCR
WEIGHT (LB)
158.7
VS
1
VSSTRESN
SCR
WEIGHT (kg)
72
VS
2
VSORRES
V1
WEIGHT (LB)
162
VS
2
VSSTRESN
V1
WEIGHT (kg)
73.5
VS
3
VSORRES
V2
WEIGHT (LB)
161.8
VS
3
VSSTRESN
V2
WEIGHT (kg)
73.4
VS
4
VSORRES
V3
WEIGHT (LB)
161.6
VS
4
VSSTRESN
V3
WEIGHT (kg)
73.3
VS
5
VSORRES
V4
WEIGHT (LB)
162.3
VS
5
VSSTRESN
V4
WEIGHT (kg)
73.6
VS
6
VSORRES
V5
WEIGHT (LB)
163
VS
6
VSSTRESN
V5
WEIGHT (kg)
74
5
Mapping multiple SDTM Variables to
the same ADaM variable
• Traceability
> The property that enables the understanding of the data’s lineage and/or the
relationship between an element and its predecessor(s).
> Where did the data come from?
• SRCDOM: Identifies the SDTM domain
• SRCSEQ: Identifies the record in the SDTM domain
• SCRVAR: Identifies the SDTM variable used to create AVAL/AVALC
6
Creating derived records
• Derived Parameters
> Test is not present in SDTM
- BMI, BSA,
- Calculated Creatinine Clearance
- QTcF, QTcB
• Derived Value
> Test is in SDTM, but the record is not
- Baseline,
- Endpoint
- Last Observation Carried Forward
• Traceability
> PARAMTYP vs. DTYPE
7
Creating derived records
• DTYPE
• LOCF
Row
USUBJID
VISIT
AVISIT
ADY
PARAM
AVAL
1
1001
BASELINE
BASELINE
-4
SUPINE SYSBP (mm Hg)
145
2
1001
WEEK 1
WEEK 1
3
SUPINE SYSBP (mm Hg)
130
3
1001
WEEK 2
WEEK 2
9
SUPINE SYSBP (mm Hg)
133
4
1001
WEEK 3
WEEK 3
20
SUPINE SYSBP (mm Hg)
125
5
1002
BASELINE
BASELINE
-1
SUPINE SYSBP (mm Hg)
145
6
1002
WEEK 1
WEEK 1
7
SUPINE SYSBP (mm Hg)
130
7
1002
WEEK 3
WEEK 3
22
SUPINE SYSBP (mm Hg)
135
8
1003
BASELINE
BASELINE
1
SUPINE SYSBP (mm Hg)
150
9
1003
WEEK 1
WEEK 1
8
SUPINE SYSBP (mm Hg)
140
8
Creating derived records
Row
USUBJID
VISIT
AVISIT
ADY
PARAM
AVAL
DTYPE
1
1001
BASELINE
BASELINE
-4
SUPINE SYSBP (mm Hg)
145
2
1001
WEEK 1
WEEK 1
3
SUPINE SYSBP (mm Hg)
130
3
1001
WEEK 2
WEEK 2
9
SUPINE SYSBP (mm Hg)
133
4
1001
WEEK 3
WEEK 3
20
SUPINE SYSBP (mm Hg)
125
5
1002
BASELINE
BASELINE
-1
SUPINE SYSBP (mm Hg)
145
6
1002
WEEK 1
WEEK 1
7
SUPINE SYSBP (mm Hg)
130
7
1002
WEEK 1
WEEK 2
7
SUPINE SYSBP (mm Hg)
130
8
1002
WEEK 3
WEEK 3
22
SUPINE SYSBP (mm Hg)
135
9
1003
BASELINE
BASELINE
1
SUPINE SYSBP (mm Hg)
150
10
1003
WEEK 1
WEEK 1
8
SUPINE SYSBP (mm Hg)
140
11
1003
WEEK 1
WEEK 2
8
SUPINE SYSBP (mm Hg)
140
LOCF
12
1003
WEEK 1
WEEK 3
8
SUPINE SYSBP (mm Hg)
140
LOCF
LOCF
9
Creating derived records
• Duplicate the needed record
• Populate DTYPE to indicate new record
> Use something descriptive like, LOCF, BASELINE, ENDPOINT, WCCF
• SCRDOM, SRCVAR, SRCSEQ populated as with original record
• Do not modify SDTM variables
10
Creating derived records
• PARAMTYP
Row
PARAM
PARAMCD
AVISIT
AVISITN
AVAL
PARAMTYP
1
Weight (kg)
WEIGHT
SCR
-4
99
2
Weight (kg)
WEIGHT
RUN-IN
-2
101
3
Weight (kg)
WEIGHT
BASELINE
0
100
4
Weight (kg)
WEIGHT
WEEK 24
24
94
5
Weight (kg)
WEIGHT
WEEK 48
48
92
6
Weight (kg)
WEIGHT
WEEK 52
52
95
7
Log10(Weight (kg))
L10WT
SCR
-4
1.9956
DERIVED
8
Log10(Weight (kg))
L10WT
RUN-IN
-2
2.0043
DERIVED
9
Log10(Weight (kg))
L10WT
BASELINE
0
2
DERIVED
10
Log10(Weight (kg))
L10WT
WEEK 24
24
1.9731
DERIVED
11
Log10(Weight (kg))
L10WT
WEEK 48
48
1.9638
DERIVED
12
Log10(Weight (kg))
L10WT
WEEK 52
52
1.9777
DERIVED
11
Creating derived records
• Add records needed
• New value for PARAM and AVAL
• SRCSEQ, SRCDOM, SRCVAR will be NULL
> AVAL did not have SDTM as source
• SDTM variables can be populated as appropriate
• Do not modify SDTM variables
12
Multiple baseline definitions in the
same ADaM domain
• Multiple definitions of Baseline
>
>
•
•
Last value prior to very first dose of active
Last value prior to Run-in
Last value prior to Double-Blind
Last value prior to Open Label
• In case there is more than one definition of baseline, new rows must be created for
each additional alternative definition of baseline
• Some data redundancy is expected
• BASETYPE
13
Multiple baseline definitions in the
same ADaM domain
CDISC ADaM IG v1.0 Table 4.2.1.11
Row
BASETYPE
EPOCH
AVISIT
AVAL
ABLFL
BASE
CHG
1
RUN-IN
RUN-IN
BASELINE
34.5
Y
34.5
0
2
RUN-IN
RUN-IN
DAY 10
11.6
34.5
-22.9
4
RUN-IN
STABILIZATION
DAY 15
13.1
34.5
-21.4
6
RUN-IN
DOUBLE BLIND
DAY 20
13.7
34.5
-20.8
7
RUN-IN
DOUBLE BLIND
DAY 25
19.7
34.5
-14.8
8
RUN-IN
DOUBLE BLIND
DAY 30
28.1
34.5
-6.4
10
RUN-IN
OPEN LABEL
DAY 35
28.4
34.5
-6.1
11
RUN-IN
OPEN LABEL
DAY 40
30.5
34.5
-4
14
Multiple baseline definitions in the
same ADaM domain
Row
BASETYPE
EPOCH
AVISIT
AVAL
ABLFL
BASE
CHG
1
RUN-IN
RUN-IN
BASELINE
34.5
Y
34.5
0
2
RUN-IN
RUN-IN
DAY 10
11.6
34.5
-22.9
4
RUN-IN
STABILIZATION
DAY 15
13.1
34.5
-21.4
6
RUN-IN
DOUBLE BLIND
DAY 20
13.7
34.5
-20.8
7
RUN-IN
DOUBLE BLIND
DAY 25
19.7
34.5
-14.8
8
RUN-IN
DOUBLE BLIND
DAY 30
28.1
34.5
-6.4
10
RUN-IN
OPEN LABEL
DAY 35
28.4
34.5
-6.1
11
RUN-IN
OPEN LABEL
DAY 40
30.5
34.5
-4
12
DOUBLE BLIND
DOUBLE BLIND
DAY 20
13.7
13.7
0
13
DOUBLE BLIND
DOUBLE BLIND
DAY 25
19.7
13.7
6
14
DOUBLE BLIND
DOUBLE BLIND
DAY 30
28.1
13.7
14.4
15
DOUBLE BLIND
OPEN LABEL
DAY 35
28.4
13.7
14.7
16
DOUBLE BLIND
OPEN LABEL
DAY 40
30.5
13.7
16.8
Y
15
Multiple baseline definitions in the
same ADaM domain
• Duplicate all records affected
• Populate BASETYPE with something descriptive
• SRCVAR, SRCDOM, SRCSEQ will be populated as records can be traced back to
SDTM
• Some data redundancy is expected
16
Summary
• SRCVAR, SRCDOM, SRCSEQ used when multiple SDTM variables map to
AVAL
> E.g. **ORRES and **STRESN
• DTYPE used when new record is created but AVAL is not modified.
> E.g. LOCF
• PARAMTYP used when new parameter is created and value of AVAL can not
be traced back to SDTM
• BASETYPE used when there are multiple baseline definitions that require
additional records to be added
17
Questions?
18

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