metadata and adam
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Metadata and ADaM
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Disclaimer
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Any views or opinions presented in this presentation are solely those of the author and do not necessarily represent those of the company.
www.cytel.com ©2012 Cytel Statistical Software & Services Pvt. Ltd.
Agenda
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• Introduction of ADaM Metadata
• Clincial Trial Process
• Examples of how to create Metadata
• Goal of ADaM Metadata
• Pros and Cons
• Conclusion
• Questions & Answers
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ADaM Metadata
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• Definition – Information of ADaM(Analysis Data Model) datasets
• Types– Analysis Dataset Metadata– Analysis Variable Metadata – Analysis Parameter Value-Level Metadata– Analysis Results Metadata
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Normal Clinical Trial Process
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Protocol SAP Mock Up Tables
CRF
DMDB Raw TFLDerived
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CDISC Clinical Trial Process
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Protocol SAP Mock Up Tables
eCRF
EDC SDTM
ADaMMetadata
TFLADaM
ADaM Related Process
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ADaM Related Process
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Analysis Dataset
Metadata
TFLADaM
Analysis Variable
Metadata
Analysis Parametervalue-levelMetadata
Analysis Results
Metadata
ADaM Metadata
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Example 1 - Time to Event Mock Up table
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Table 14.2.1
Time to Death by Treatment
PARAM = ‘Days to Death’, TRTP
Analysis Population: Intent to Treat
ITTFL=‘Y’
Drug 1Drug 2 p-value
__________________________________________________________________________________________N xxx
xxxMedian xx
xx x.xxQ1, Q3 xx, xx xx,
xx__________________________________________________________________________________________
AVAL(Days to Event), CNSR(Censor information)
proc lifetest data=ADTTEOS; where PARAM=“Days to Death” and ITTFL=“Y”;
time AVAL*CNSR(1);strata TRTP;
run;
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Time to Event Analysis Dataset Metadata
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Dataset Name
Dataset Description
Dataset Location
Dataset Structure
Key Variables of Dataset
Class of Dataset
Documentation
ADTTEOS Overall Survival Analysis Dataset
adtteos.xpt One record per subject per parameter
STUDYID, USUBJID, PARAM
BDS adtteos.txt
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Example 1 : Time to Event Analysis Variable Metadata including Analysis Parameter Value-Level Metadata (1)
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[CB1]Note to ADaM team: We have elected to use this format for the program names. According to the Study Data Specifications, since the programs created by SAS use a file extension for ASCII text files other than .txt, the file name should include the native file extension generated by the analysis tool for ASCII text program files, e.g. mySAScode.sas.
Dataset Name
Parameter Identifier
Variable Name
Variable Label Variable Type
Display Format
Codelist / Controlled
Terms
Source / Derivation
ADTTEOS *ALL* STUDYID Study Identifier text $20 ADSL.STUDYID
ADTTEOS *ALL* USUBJID Unique Subject Identifier
text $20 ADSL.USUBJID
ADTTEOS *ALL* ITTFL Intent-To-Treat Population Flag
text $1 Y, null ADSL.ITTFL
ADTTEOS *ALL* TRTP Planned Treatment
text $40 Drug 1, Drug 2 ADSL.TRT01P
ADTTEOS *ALL* TRTPN Planned Treatment (N)
integer 1.0 1 = Drug 1, 2 = Drug 2
ADSL.TRT01PN
ADTTEOS PARAMCD PARAM Parameter text $50 Days to Death
ADTTEOS *ALL* PARAMCD Parameter Code text $8 DEATH
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Example 1 : Time to Event Analysis Variable Metadata including Analysis Parameter Value-Level Metadata (2)
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[CB1]Note to ADaM team: We have elected to use this format for the program names. According to the Study Data Specifications, since the programs created by SAS use a file extension for ASCII text files other than .txt, the file name should include the native file extension generated by the analysis tool for ASCII text program files, e.g. mySAScode.sas.
Dataset Name
Parameter Identifier
Variable Name
Variable Label
Variable Type
Display Format
Codelist / Controlled Terms
Source / Derivation
ADTTEOS *ALL* AVAL Analysis Value float 8.2 ADT – STARTDT + 1
ADTTEOS *ALL* STARTDT Time to Event Origin Date for Subject
integer YYYYMMDD10.
ADSL.RANDDT
ADTTEOS *ALL* ADT Analysis Date integer YYYYMMDD10.
SAS Date of DS.DSDTC
ADTTEOS *ALL* CNSR Censor integer 1.0 0, 1 0 for DS.DSDECOD = ‘DEATH’, 1 for any other study completion
ADTTEOS *ALL* EVNTDESC Event or Censoring Description
text $40 DEATH, COMPLETED THE STUDY, LOST TO FOLLOW-UP, AE, PD
DS.DSDECOD
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Example 1 : Time to Event ADaM Dataset
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[CB1]Note to ADaM team: We have elected to use this format for the program names. According to the Study Data Specifications, since the programs created by SAS use a file extension for ASCII text files other than .txt, the file name should include the native file extension generated by the analysis tool for ASCII text program files, e.g. mySAScode.sas.
USUBJID TRTP PARAM AVAL STARTDT ADT CNSR EVNTDESC001-01-001 Study Drug 1 Days to
Death157 2011-01-04 2011-06-10 1 COMPLETED
THE STUDY
001-01-002 Study Drug 2 Days to Death
116 2011-02-01 2011-05-28 1 AE
001-01-003 Study Drug 2 Days to Death
88 2011-02-05 2011-05-04 0 DEATH
001-01-004 Study Drug 1 Days to Death
102 2011-03-20 2011-06-30 1 PD
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Example 1 : Time to Event Analysis Results Metadata
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Metadata Field Metadata
DISPLAY IDENTIFIER
Table 14.2.1
DISPLAY NAME Time to Death by Treatment, Analysis Population: Intent to Treat
RESULT IDENTIFIER
Days to Death
PARAM Days to Death
PARAMCD DEATH
ANALYSIS VARIABLE
AVAL
REASON Primary efficacy analysis
DATASET ADTTEOS
SELECTION CRITERIA
ITTFL=“Y” and PARAM = ‘Days to Death’
DOCUMENTATION See SAP Section XX for details. Program: t-14-012-001-death.txt
PROGRAMMING STATEMENTS
proc lifetest data= ADTTEOS; where ITTFL=‘Y’ and PARAM = “Days to Death”; time AVAL*CNSR(1); strata TRTP;run;
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Example 2 : Time to Event Mock Up table
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Table 14.2.2
Time to Progression Free Survival : Cox Proportional Hazard Model
PARAM = ‘Days to Progression Free Survival’, TRTP
Analysis Population: Intent to Treat
ITTFL=‘Y’
Drug 1Drug 2 p-value
__________________________________________________________________________________________N xxx
xxxMedian xx
xx x.xxQ1, Q3 xx, xx xx,
xx__________________________________________________________________________________________
AVAL(Days to Event), CNSR(Censor information)
proc phreg data=ADTTEOS; where PARAM=“Days to Progression Free Survival” and ITTFL=“Y”;
model AVAL*CNSR(1) = TRTP AGE SEX ;run;
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Example 2 : Time to Event Analysis Variable Metadata including Analysis Parameter Value-Level Metadata (1)
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[CB1]Note to ADaM team: We have elected to use this format for the program names. According to the Study Data Specifications, since the programs created by SAS use a file extension for ASCII text files other than .txt, the file name should include the native file extension generated by the analysis tool for ASCII text program files, e.g. mySAScode.sas.
Dataset Name
Parameter Identifier
Variable Name
Variable Label Variable Type
Display Format
Codelist / Controlled Terms
Source / Derivation
ADTTEOS *ALL* STUDYID Study Identifier text $20 ADSL.STUDYID
ADTTEOS *ALL* USUBJID Unique Subject Identifier
text $20 ADSL.USUBJID
ADTTEOS *ALL* AGE Age integer 3.0 ADSL.AGEADTTEOS *ALL* SEX Sex text $1 ADSL.SEXADTTEOS *ALL* ITTFL Intent-To-Treat
Population Flagtext $1 Y, null ADSL.ITTFL
ADTTEOS *ALL* TRTP Planned Treatment
text $40 Drug 1, Drug 2 ADSL.TRT01P
ADTTEOS *ALL* TRTPN Planned Treatment (N)
integer 1.0 1 = Drug 1, 2 = Drug 2
ADSL.TRT01PN
ADTTEOS PARAMCD PARAM Parameter text $50 Days to DeathDays to Progression Free Survival
ADTTEOS *ALL* PARAMCD Parameter Code text $8 DEATHPFS
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Example 2 : Time to Event Analysis Variable Metadata including Analysis Parameter Value-Level Metadata (2)
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Dataset Name
Parameter Identifier
Variable Name
Variable Label
Variable Type
Display Format
Codelist / Controlled Terms
Source / Derivation
ADTTEOS *ALL* AVAL Analysis Value float 8.2 ADT – STARTDT + 1
ADTTEOS *ALL* STARTDT Time to Event Origin Date for Subject
integer YYYYMMDD10.
ADSL.RANDDT
ADTTEOS *ALL* ADT Analysis Date integer YYYYMMDD10.
SAS Date of DS.DSDTC
ADTTEOS DEATH CNSR Censor integer 1.0 0, 1 0 for DS.DSDECOD = ‘DEATH’, 1 for any other study completion
ADTTEOS PFS CNSR Censor integer 1.0 0, 1 0 for DS.DSDECOD in(‘DEATH’ , ‘PD’), 1 for any other study completion
ADTTEOS *ALL* EVNTDESC Event or Censoring Description
text $40 DEATH, COMPLETED THE STUDY, LOST TO FOLLOW-UP, AE, PD
DS.DSDECOD
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Example 2 : Time to Event ADaM Dataset
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[CB1]Note to ADaM team: We have elected to use this format for the program names. According to the Study Data Specifications, since the programs created by SAS use a file extension for ASCII text files other than .txt, the file name should include the native file extension generated by the analysis tool for ASCII text program files, e.g. mySAScode.sas.
USUBJID
AGE SEX TRTP PARAM AVAL
STARTDT
ADT CNSR EVNTDESC
001-01-001
43 M Study Drug 1
Days to Death 157 2011-01-04
2011-06-10
1 COMPLETED THE STUDY
001-01-002
57 F Study Drug 2
Days to Death 116 2011-02-01
2011-05-28
1 AE
001-01-003
71 M Study Drug 2
Days to Death 88 2011-02-05
2011-05-04
0 DEATH
001-01-004
55 F Study Drug 1
Days to Death 102 2011-03-20
2011-06-30
1 PD
001-01-001
43 M Study Drug 1
Days to Progression Free Survival
157 2011-01-04
2011-06-10
1 COMPLETED THE STUDY
001-01-002
57 F Study Drug 2
Days to Progression Free Survival
116 2011-02-01
2011-05-28
1 AE
001-01-003
71 M Study Drug 2
Days to Progression Free Survival
88 2011-02-05
2011-05-04
0 DEATH
001-01-004
55 F Study Drug 1
Days to Progression Free Survival
102 2011-03-20
2011-06-30
0 PD
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Example 2 : Time to Event Analysis Results Metadata
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Metadata Field Metadata
DISPLAY IDENTIFIER
Table 14.2.2
DISPLAY NAME Time to Progression Free Survival : Cox Proportional Hazard Model
RESULT IDENTIFIER
Days to Progression Free Survival
PARAM Days to Progression Free Survival
PARAMCD PFS
ANALYSIS VARIABLE
AVAL
REASON Secondary efficacy analysis
DATASET ADTTEOS
SELECTION CRITERIA
ITTFL=“Y” and PARAM=“Days to Progression Free Survival’
DOCUMENTATION See SAP Section XX for details. Program: t-14-002-002-pfs.txt
PROGRAMMING STATEMENTS
proc phreg data= ADTTEOS; where ITTFL=‘Y’ and PARAM = “Days to Progression Free Survival’; model AVAL*CNSR(1) = TRTP AGE SEX;run;
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Summary of Examples
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Mock Up Tables 14.2.1 14.2.2
ADaM Metadata Dataset ADTTEOS
Variables STUDYDI, USUBJID
ITTFL
TRTP, TRTPN
PARAM, PARAMCD
AVAL
STARTDT, ADT
CNSR
EVNTDESC
AGE
SEX
Parameter DEATH PFS
Results Days to Death Days to Progression Free Survival
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Goal of Metadata
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• Serve as Spec and Define – Spec : provide the programmers how ADaM and some TFL
can be created– Define : datasets information for sponsors
• Central document for all programmers and statisticians
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Goal of Metadata (2)
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• Minimize the communication traffic in virtual office setting– Philadelphia Office– Boston Office– India Office– Remote Programming
• Reconciliation between ADaM datasets and Metadata – use macros to check wether ADaM datasets follow ADaM Metadata.
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Cons
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• Who will prepare and maintain the metadata• CDISC expert(SDTM, ADaM and so on)• Programmer Lead• Statistician
• The initial investment on resource and time at the early stage of the study
• Two many metadata?
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Pros (1)
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• Consistency in ADaM datasets– Label– Name– Format– # of variables
• Help the inexperience personnel – ADaM is new• The central document between developers and
validators – especially for the virtual office setting• Helps the programmers on efficacy analysis.
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Pros (2)
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• Better estimate on the number of ADaM datasets – help the planning and resourcing.
• Review on Mock Up tables and SAP
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Conclusion
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• The concept of Metadata is “Plan your work and work your plan”
• ADaM Metadata is ongoing until all are done.
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Questions?
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