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Discussion: sdtm updates

Discussion: sdtm updates. MARCH 2013. Public comments. Comments were requested from CDISC for the new and updated domains for SDTM v3.1.4 Batch 1 : RD - Reproduction Details / RP – Reproductive System Findings IS - Immunogenicity Specimen Assessment SR - Skin Response

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Discussion: sdtm updates

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  1. Discussion: sdtm updates MARCH 2013

  2. Public comments • Comments were requested from CDISC for the new and updated domains for • SDTM v3.1.4 Batch 1 : • RD -Reproduction Details / • RP – Reproductive System Findings • IS - Immunogenicity Specimen Assessment • SR - Skin Response • EX - Exposure • EC - Exposure as Collected CDISC response available No response from CDISC available yet Overview of the comments: Most comments were about : Label inconsistencies, Incorrect Type, CORE and Controlled Term/Codelist/Format information Spelling errors Controlled Terminology updates Questions Suggestions

  3. Public comments Update : EX / EC domain IG v 3.1.4, batch 1 Interventions domain Comments (EXOCCUR/EXREASND): EX domain is an Interventions domain and therefore --PRESP, --OCCUR, --STAT and --REASND are already available, they were only excluded from EX because according to the current Implementation Guide page 85: ‘EX should contain only medications received’ - as this concept is now changed, it's making sense to allow these variables in EX and fill them as in all other domains.

  4. Public comments Update : EX / EC domain IG v 3.1.4, batch 1 Comments (EXOCCUR/EXREASND): • Also the SDTMIG V3.1.2 section 4.1.5.7 should be updated to document the use of a --REASND in combination with an --OCCUR=N. The table listed in this section is used by many electronic compliance checking tools as the set of allowed situations. It should be clearly stated that for EX/EC an exception is to be made. (Please note I refered to the SDTMIG V3.1.2 as there is not yet an updated version of this part of the IG available)

  5. Public comments Update : EX / EC domain IG v 3.1.4, batch 1 Comments (EXOCCUR/EXREASND): EXSTAT/EXREASND - In every other SDTM domain, REASND is used for the reason that an observation was not made. In findings domains, this is the reason a test was not done. In events domains, this is the reason that a question about a pre-specified event was not asked. In other interventions domains, this is the reason that a question about a pre-specified intervention was not asked. REASNDis populated when STAT=NOT DONE. In this proposal, REASND would be populated when OCCUR = N. If it is desired to record the reason why a dose was not given, then a new variable for "reason not given" (or some such) should be created, instead of overloading the existing variable REASND. Even if we don't foresee using REASND for its original purpose in EX, this proposal would create a domain-specific exception to the general mapping of REASND to BRIDG, complicating the process of mapping future BRIDG-based SHARE content to SDTM.

  6. Public comments Update : EX / EC domain IG v 3.1.4, batch 1 Comments (EC Domain): It's also good to have the CRF collected dose/units and the protocol specified ones, but in my opinion it would be a lot easier to introduce something like Standard Dose and Standard Units like in the Finding domains, and there the dosage and units as specified in the protocol. The original collected dosage and unit can be kept in EXDOSE and EXDOSU. That would be more clear than making two very similar domains and linking them via RELREC.

  7. Public comments Update : EX / EC domain IG v 3.1.4, batch 1 ADaM? Comments (EC Domain): Another argument for the EC/EX solution was that the values from EC can be summarized in EX to support analysis. In my opinion this should not be part of SDTM - as SDTM is usually not preparing tables for analysis but should reflect the CRF data as entered, sure some values are derived as well but to put one whole domain which is only derived and summarizing/pooling treatment data is maybe not what SDTM was intended for, for me that sounds more like ADaM. Update : EX / EC domain IG v 3.1.4, batch 1 It is indicated that EXVAMT will be deprecated, but it is not clear to me what replaces it. There are no examples showing collected doses based on a preparation step such as an infusion where study drug is diluted to a certain concentration in a vehicle such as saline.

  8. Public comments Update : RD domain IG v 3.1.4, batch 1 Comments : In the NCI Terminology Codelists there is a RP (Reproductive System Findings) domain assigned, why did it change to RD ? The Response: It was decided by CDISC that this domain will be renamed to RP (Reproductive System Findings) as per CDISC controlled terminology.

  9. Public comments Update : RD domain IG v 3.1.4, batch 1 Comments : • “Why RDSTDTC is not spelled out in the list of variables, given that one might want to know when a particular ‘finding’ occurred. What's being collected is RDDTC, the collection date. For some ‘tests’, like PREGNT, it is important to know when a pregnancy began, not simply the collection date. Reconsider this as a findings class.” The Response: RDDTC is the date of the reproductive finding and should not be confused with the collection date relative to when it was recorded on a CRF.

  10. Public comments Update : RD domain IG v 3.1.4, batch 1 • Control Terminology Suggestions: • RDTESTCD – PREGSTAT / RDTEST- Pregnancy Status • RDTESTCD - EARLYTRM / RDTEST - Early Termination • RDTESTCD – LIVEBRTH / RDTEST- Live Birth PREGSTAT -PREGNANCY ONGOING, LIVE BIRTH, STILLBIRTH, EARLY TERMINATION EARLYTRM - SPONTANEOUS ABORTION, THERAPEUTIC ABORTION, ELECTIVE ABORTION, OTHER LIVEBRTH - NORMAL, BIRTH DEFECT, OTHER The Response: Suggestions for controlled terminology should be send to the NCI EVS for consideration upon the release of the domain in provisional status.

  11. Public comments Update : IS and SR domains IG v 3.1.4, batch 1

  12. Public comments Update : IS and SR domains IG v 3.1.4, batch 1 • Comments: • IS needs controlled terminology. Many of the tests used as examples are existing LBTESTCD codes - either existing terminology e.g. HCAB or extensible e.g. as in Example 3. Will they be copied from LBTESTCD terms? Will they then be removed from LBTESTCD terminology? • Will ALL Serology and Immunology tests now reside in this domain rather than LAB? How about VIROLOGY? Can you provide a list of tests which will move? I think this needs clear guidance as the definition of serology/immunology in relation to specific testing can be rather vague. Defining the CAT for each LBTESTCD/ISTEST would be helpful. • Please explain why you don't have an upper limit of quantitation. We have serology data that requires this • .

  13. Public comments Update : IS and SR domains IG v 3.1.4, batch 1 • Comments: • I am concerned about moving categories of data out of LAB into their own domain. Generally all the categories fit well within the existing LAB domain and may only need a few extra variables. My preference would have been to keep serology and immunology and viral within LAB but add extra optional variables to LAB e.g. ISLLOQ & ASSAYV with examples of how to use them. Dividing the data up too much leads to problems when people have different opinions as to whether this data is immunology or virology or biomark. We end up having the same data in different dataset domains due to study team preference. Does LAB just end up being haem, chem and urine? • ISTEST: Immunoglobulin E is given as an example in the CDISC notes and HCAB in example 1. These are already a lab test codes. Will ISTESTCD/ISTEST share same codelist as LB? If so, how will users know whether to report results in LB vs IS? Does purpose of test determine domain to use? • Any specific reason why the data from IS can't be included in • LB, differentiated by LBCAT?

  14. Public comments Summary of comments on v3.1.4 batch 1: For the EX/EC/IS domains a lot more thought should go in there so that there is no duplication of information and a review of the quality of work to be reviewed by users should be done.

  15. Non-standard variables Supplemental Qualifier Datasets

  16. Non-standard variables Update : Non-standard variables IG v 3.1.4, batch 2 • Biggest Concerns: • Dataset Size • Validation • Cost Impact

  17. NSVs in standard domains Update : Non-standard variables IG v 3.1.4, batch 2 Practical

  18. NSVs in standard domains Update : Non-standard variables Practical IG v 3.1.4, batch 2 Validation

  19. NSVs in standard domains Update : Non-standard variables Cost IG v 3.1.4, batch 2

  20. NSVs in standard domains Update : Non-standard variables Cost IG v 3.1.4, batch 2

  21. NSVs in standard domains Update : Non-standard variables Cost IG v 3.1.4, batch 2

  22. NSVs in standard domains Update : Non-standard variables IG v 3.1.4, batch 2 General

  23. Any Comments ?

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