How to validate sdtm suppqual

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How to validate sdtm suppqual

  1. 1. How to validate SDTM SUPPQUAL Data set May 24th, 2010 by Kevin Lee 1
  2. 2. Covance Periapproval Services GM, every1 (Good Morning, Everyone) 2
  3. 3. Covance Periapproval Services What will be discussed The Introduction of SUPPQUAL The Issues in validating SUPPQUAL The Recommendation SDTM+SUPP procedure Overall steps for Validation Concerns Conclusion 3
  4. 4. Covance Periapproval Services Introduction of SUPPQUAL The SDTM does not allow any new variables beside ones assigned to each SDTM domain. So, the supplemental data set is introduced to supplement each SDTM domain. Its type: • a single SUPPQUAL dataset • The separate supplementary data sets (SUPP) such as SUPPDM, SUPPAE, and SUPPEX. 4
  5. 5. Covance Periapproval Services Structure of SUPPQUAL Name Label Type Role Codelist Mandatory STUDYID Study Identifier Text Identifier NONE Req RDOMAIN Related Domain Abbreviation Text Identifier DOMAIN Req USUBJID Unique Subject Identifier Text Identifier NONE Req IDVAR Identifying Variable Text Identifier NONE Req IDVARVAL Identifying Variable Value Text Topic NONE Req QNAM Qualifier Variable Name Text Record Qualifier NONE Req QLABEL Qualifier Variable Label Text Record Qualifier NONE Req QVAL Data Value Text Qualifier NONE Req QORIG Origin Text Qualifier NONE Req QEVAL Evaluator Text Qualifier NONE Perm 5
  6. 6. Covance Periapproval Services The Relation of SUPPQUAL to each domain The SUPPQUAL data set is linked back to a parent record using RDOMAIN, USUBJID, IDVAR and IDVARVAL. IDVAR and IDVARVAL is usually the sequence number (ex. AESEQ, VSSEQ and so on) except DM and SV. 6
  7. 7. Covance Periapproval Services The Issues in Validating SUPPQUAL Some of SUPPQUAL variables could be originally captured as numeric – for example, QVAL and IDVARVAL. SUPPQUAL data set could be very large • • For example, DM – 417KB, but SUPPQUAL – 858,529KB The running Time in PC could be 0.5 to 1 hour. It is really difficult to visually link the SUPPQUAL data back to a parent record for the review. 7
  8. 8. Covance Periapproval Services The recommendation For QVAL and IDVARVAL • Consistent conversion from numeric to character type – using the same format on input statement • All the converted variables should be leftaligned. Better hardware (Unix is known more than 2 time faster than PC) Create the separate SUPP for each domain for easier validation, not just a single SUPPQUAL. Set up the friendly environment for the validation – SDTM+SUPP procedure/data sets. 8
  9. 9. Covance Periapproval Services Advantage to create individual SUPP data sets The supplementary data sets won’t be as big as a single SUPPQUAL, so it takes less time to review, to update, and to validate. 9
  10. 10. Covance Periapproval Services The Advantages to create SDTM+SUPP data sets SDTM+SUPP keeps all the variables related to SDTM domain. Much easier to link back to a parent record of the supplementary variables. Much easier when creating ADaM Data set. 10
  11. 11. Covance Periapproval Services The Flow Chart of Data SDTM (EX) SAS Raw Data Sets (EXPOSURE) SDTM+SUPP (EX) ADaM (ADEX) SUPP (SUPPEX) SDTM+SUPP Procedure 11
  12. 12. Covance Periapproval Services The Options to validate SUPPQUAL Validate all 3 of them - EX in SDTM+SUPP, EX and SUPPEX. Validate only 2 SDTM data sets – EX and SUPPEX Validate only EX in SDTM+SUPP Our recommendation is to validate all 3 of them. However, the best way to validate is to start validating EX in SDTM+SUPP in the initial stage and validating all 3 of them in the later stage of the trials. 12
  13. 13. Covance Periapproval Services The advantages in validating SDTM+SUPP data sets much easier to validate the numeric supplementary variables. Less time to validate. If there are any issues in the supplementary variables, it is much easier to link back to parent records for the review. 13
  14. 14. Covance Periapproval Services The automatic procedure to create SDTM and SUPP The flag document (the best option is to create the flag variable column in Define document) The macro that split SDTM and SUPP from SDTM+SUPP according to the flag document. 14
  15. 15. Covance Periapproval Services The sample Define Doc Domain Name Label Type Role Codelist Core Origin EX STUDYID Study Identifier Char Identifier NONE Req CRF EX DOMAIN Domain Abbreviation Char Identifier DOMAIN Req Derived EX USUBJID Unique Subject Identifier Char Identifier NONE Req Sponsor Defined EX EXSEQ Sequence Number Num Identifier NONE Req Derived EX EXTRT Name of Actual Treatment Char Topic NONE Req Derived EX EXDOSE Dose per Administration Num Record Qualifier NONE Perm CRF EX EXDOSU Dose Units Char Variable Qualifier DOSU Exp CRF EX EXDOSFRQ Dosing Frequency Per Interval Char Variable Qualifier DOSFRQ Perm Derived EX EXROUTE Route of Administration Char Variable Qualifier ROUTE Perm CRF EX EXSTDTC Start Date/Time of Treatment Char Timing ISO8601 Perm CRF EX VISIT Visit Name Char Timing NONE Perm Derived EX VISITNUM Visit Number Num Timing NONE Perm Derived EX TAETORD Order of Element within Arm Num Timing NONE Perm Derived EX EPOCH Trial Epoch Char Timing EPOCH Perm Derived EX EXSPID2 Vial or Component ID Char Plus NONE Perm Derived Y EX EXSTDTI Start Date/Time of Treatment Imputed Char Plus ISO8601 Perm Derived Y EX ELEMENT Description of Element Char Plus NONE Perm Derived Y EX ETCD Element Code Char Plus NONE Perm Derived Y EX STDYRLEP Start Day Rel to Epoch Num Plus NONE Perm Derived Y 15 Suppqual Flag
  16. 16. Covance Periapproval Services The sample codes to create SDTM and SUPP from SDTM+SUPP **** Create SDTM EX domain; data sdtm.ex; set sdtmsupp.ex; drop exspid2 exstdti element etcd stdyrlep; run; **** Create SDTM SUPPEX domain; proc transpose data=sdtmsupp.ex out=_suppex(rename=(_name_=qnam _label_=qlabel col1=qval exseq=_exseq)); by studyid domain usubjid exseq; var exspid2 exstdti element etcd stdyrlep; run; data sdtm.suppex(drop=_exseq); set _suppex; idvarval = trim(left(put(_exseq, best30.))); idvar = ‘EXSEQ’; qorig = ‘Derived’; run; 16
  17. 17. Covance Periapproval Services Overall steps to validate in using SDTM+SUPP Create the Define document including the flags to indicate the supplementary variables. Create the macro that split SDTM+SUPP data sets into SDTM and SUPP. Create SDTM+SUPP data sets and using the macro and Define document, create SDTM and SUPP from SDTM+SUPP. Validate SDTM+SUPP data sets first and then SDTM and SUPP. 17
  18. 18. Covance Periapproval Services Concerns for SDTM+SUPP procedure One single SUPPQUAL is requested by a sponsor. • Special attention on the truncations. One to many relationship between a parent record to corresponding supplementary variables • When SUPP and SDTM are split by macro, the SAS programmer puts the procedure that the duplicate records be removed from SDTM. • When annotating eCRF, the SAS programmer do not include one to many relationship in the SDTM+SUPP. 18
  19. 19. Covance Periapproval Services Conclusions The validation of SUPPQUAL data set takes a lot of time and resource because of its size and complexity. However, through the automatic procedure and a special attention on possible SUPPQAUL related issues, the validation will take less time and less resource. 19
  20. 20. Covance Periapproval Services Contact Information Kevin Lee Covance Periapproval Services. 555 North Lane Suite 6000 Conshohocken, PA (610) 832 - 5751 Email:Kevin.lee@covance.com 20
  21. 21. Covance Periapproval Services Thanks and any Question??? 21

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