OpenCDISC Rules for Discussion
March 18-19, 2012
CDER’s Top Issues
• Wasted Space
• Description:
– Currently, sponsors pad column widths by arbitrarily
pre-allocation column widths to 200, loosely based on
the previous IG example
– IG is updated, as is the FDA’s CID
– Ideally, column widths should only be the maximum
length used in that column across records
• Solution:
– Should we use extra characters used or %?
– Exceptions?
CDER’s Top Issues
• Dataset Sizes
• Description:
– Based on FDA’s SDS and CID
• Solution:
– Limit set to 1 gb
– Warning acceptable for this?
– Should warning/error be based on certain limits?
• Warning 1 gb to 1.25 gb
• Error > 1.5?
CDER’s Top Issues
• Expected –DY variable when –DTC present
• Description:
– Are these three situations enough?
• --DY variable value is not populated
• --DY variable value is imputed
• Incorrect value for --DY variable
• Solution:
– Someone brought up an issue with this
– Extra rule check or edit of existing rule check?
– Is warning appropriate?
CDER’s Top Issues
• Duplicate USUBJID/--DECOD/--STDTC record
• Description:
– E.g. AEs with same start date
– Situation for imputed dates?
• Solution:
– Add rule or modify to exclude any partial dates in
records
– Change to information if partial date?
CBER’s Top (open) Issues
Project Breakout Session
March 18-19, 2013
CBER’s Top Issues
• * SD0002: Required variable is null
• Description:
– This issue occurs across domains (LB, AE, TS, FA, etc.)
– Why does this occur? EDC system issue? Quality
Control?
– If value not taken/recorded, how to avoid “null”
entry? Screen failure? Explanation in Reviewer’s
Guide?
– Should check be adjusted if all/majority of values in a
variable column are null/missing? Different check?
CBER’s Top Issues
• * SD0006: No Baseline Result in [domain] for
subject
• Description:
– While SDTM requires baseline, not all tests have a
“baseline” value
– Is this a CBER issue, or is it ubiquitous?
• Proposal:
– Should existing rule be split for different LBTESTCDs
that do not have a baseline to avoid false positives?
– Is this currently in progress?
CBER’s Top Issues
• * SD0026/29/35: Standard unit null when standard
result is provided
• Description:
– Implementation issue? EDC?
– Or is the issue that not all LBTESTs have associated unit?
• Proposal:
1.
2.
3.
4.
Identify rules with no units and update implementation
Define.xml or TS domain for list of tests w/o unit
Add additional variable to indicate LBTEST has no unit
Utilize screen failure if applicable?
CBER’s Top Issues
• SD0031: Missing values for --STDTC and --STRF, when -ENDTC or --ENRF is provided
• Description:
– Data collection issue
– Con meds for ongoing, so have ENRF but no start information
• Proposal:
– Adjust business rule on how to represent exposures that happen
in a “moment in time”
– CT for situations where started before trial but now ongoing
– STRTPT could be used to represent event/intervention occurred
prior, but would need to amend IG for clarification
CBER’s Top Issues
• SD0063: SDTM/Dataset variable label mismatch
• Description:
– Variable label should match label described in SDTM
– When creating a new domain Variable Labels could be
adjusted as appropriate to properly convey the
meaning in the context of the data being submitted
– There was an issue in OpenCDISC v.1.3 that was
resolved -> false positive resolved? Does anyone else
see this issue now?
– When would this issue arise at your company?
CBER’s Top Issues
• SD0070: No EX record for subject
• Description:
– Typical for follow-on studies where exposure occurred in
first study so no exposure in “this” study
– Randomized but not “treated” -> perhaps subject died
– Phase 0 study looking at population but no treatment
being provided
• Solution:
– ACTARMCD provided in 3.1.3 which allows NOTTRT
– OpenCDISC can check this to increase accuracy of rule
validation
– Important review piece for FDA reviewers
CBER’s Top Issues
• SD0087/88: RFSTDTC/RFENDTC is not provided
for a randomized subject
• Description:
– Why does this issue occur?
– What do you all use this information to relay?
– Data not collected? Study Design? EDC?
• If not collected, is screen failure viable option with
explanation in reviewer’s guide?
• Proposal:
– Smart checks based on study design? Is this possible
to even implement?
CBER’s Top Issues
• * CTxxxx: Many Codelist Issues
• Description:
– Invalid codelist value not found in codelist
– This is not necessarily an extensible codelist vs. SDTM
codelist issue
• Proposal:
– When using extensible codelists, reference needs to be
made in define.xml
– This will eliminate “most” CT issues in your OpenCDISC
report which arose due to faulty define.xml
– Update define.xml code specifying external code list
dictionary
CDER’s Top Issues
Project Breakout Session
March 18-19, 2013
CDER’s Top Issues
• File System Checks
• Description:
– Although OpenCDISC v1.4 checks CID for checks, what
about other relevant documents, such as the Study
Data Specifications?
– Folder structure is one avenue to consider as FDA
automates processes that require these items
– Define.xml is another
• Solution:
– Create new checks? Is this business rule specific?
CDER’s Top Issues
• SD0003/1011: ISO Dates
• Description:
– ISO date field used as duration spec, not just
start/stop (i.e. AE)
– Partial dates are difficult to interpret/analyze
– If duration field is inputted in expected start/stop,
is this detected?
• Solution:
– Create new checks? Is this business rule specific?
CDER’s Top Issues
• Traceability
• Description:
– Being able to trace data between
CRFs/SDTM/ADaM
– FDA reviewers want this, but how do you provide?
– Very, very difficult to solve this issue
• Solution:
–?
CDER’s Top Issues
• SD0064: Invalid subject
• Description:
– Subject in non-DM domain but no record in DM
– Recorded information but subject did not receive
treatment? Withdrew prematurely?
• Solution:
– Does ACTARMCD provide solution?
– Use screen failure and add information to
ACTARMCD?
CDER’s Top Issues
• SD0038: Study Day value = 0
• Description:
– IG is clear that Study Day can be -1 or 1, but not 0
– Understanding or implementation issue?
• Solution:
– Discuss OpenCDISC v1.4’s new checks for this
CDER’s Top Issues
• SD0080: AE start date is after the latest
Disposition date
• Description:
– Sometimes, this last disposition date not recorded
– Other times, protocol requires follow-up period
for AEs while the disposition date is listed in
original trial schedule
• Solution:
– Modify checks?
CDER’s Top Issues
• SD1005: Invalid StudyID
• Description:
– StudyID values don’t match StudyID in DM
– This seems like a simple issue to resolve -> why does this
happen?
– This metadata checking is important to FDA processes
– Issues can include: dashes, added date, abbreviated study
names, etc…
• Proposal:
– Add additional checks for other StudyID locations
(define.xml, index.xml, stf.xml?) for additional accuracy
CDER’s Top Issues
• SD0065: Invalid subject visit/visit number
• Description:
– All Unique Subject Identifier (USUBJID) + Visit
Name (VISIT) + Visit Number (VISITNUM)
combination values in data should be present in
the Subject Visits (SV) domain
– Is this a data quality check issue?
CDER’s Top Issues
• SD0040: Inconsistent value for --TEST within -TESTCD
• Description:
– All values of Name of Measurement, Test or
Examination (--TEST) should be the same for a
given value of Short Name of Measurement, Test
or Examination (--TESTCD)
– 1:1 relationship between test code and name
– Why would this be different?
CDER’s Top Issues
• SD0005: Duplicate --seq
• Description:
– The value of Sequence Number (--SEQ) variable
must be unique for each record within a subject
– Why would this occur?
– Is this because a subject comes in twice for a
single sequence because no data reported in first
sequence?
CDER’s Top Issues
• SD0004: Inconsistent value for DOMAIN
• Description:
– Domain Abbreviation (DOMAIN) variable should
be consistent with the name of the dataset
– Why would this ever break?
– Due to split domains?
CDER’s Top Issues
• SD0007: Inconsistent value for Standard Units
• Description:
– Standard Units (--STRESU) must be consistent for
all records with same Short Name of
Measurement, Test or Examination (--TESTCD) and
Category (--CAT)
– Same test in different category is considered, so
why does this rule still break?
CDER’s Top Issues
• SD0018: Invalid value for --TESTCD variable
• Description:
– The value of a Short Name of Measurement, Test
or Examination (--TESTCD) variable should be
limited to 8 characters, cannot start with a
number, and cannot contain characters other than
letters in upper case, numbers, or underscores
– Clear and concise explanation -> why does this
rule still break so often?
CDER’s Top Issues
• SD0048: Value for --ORRES is populated, when
--STAT is 'NOT DONE'
• Description:
– Status (--STAT) should be NULL, when Result or
Finding in Original Units (--ORRES) is provided
– Seems simple to resolve -> why does this rule
break? Other points to consider? Special cases?
CDER’s Top Issues
• SD0077: Invalid referenced record
• Description:
– Reference record defined by Related Domain
Abbreviation (RDOMAIN), Unique Subject Identifier
(USUBJID), Identifying Variable (IDVAR) and Identifying
Variable Value (IDVARVAL) must exist in the target
Domain
– Does data belong in parent domain and not suppqual?
– This can (and does) happen -> data dumped into
suppqual because not sure where else to put it
– If no clear parent, should it be included?
– Custom domain?
CDER’s Top Issues
• SD0061: Domain referenced in define.xml but
dataset is missing
• Description:
– Domains referenced in data definition document
(define.xml) should be included in the submission
– Seems simple enough to implement
– Poor define.xml management or other reason?
– Can compare define metadata with SDTM data
library
CDER’s Top Issues
• SD0017(others): Variable lengths
• Description:
– The value of xxxx should be no more than yy
characters in length
• --TEST, --TESTCD, TSPARM, ARMCD,
– Are there extenuating circumstances to these
rules where character limits may not be enough?
• Adjust OpenCDISC checks to accommodate?
– What’s the difference between SD0017 and
SD1058? Duplicate rules?
CDER’s Top Issues
• New check ideas
– Check for domains with no records
• Why did sponsor submit this domain for ‘review’?
– No define.xml present (although define.pdf exists)
• Warning for now until included in some documentation
or IG
• Allows for maximum use of standardized data
CAB/VP OpenCDISC
Reconciliation – Open Issues
Project Breakout Session
March 18-19, 2013
CAB/VP OpenCDISC
• SD0031
• Description:
– Start Date/Time of Observation (--STDTC), Start Relative to Reference Period
(--STRF) or Start Relative to Reference Time Point (--STRTPT) should not be
NULL, when End Date/Time of Observation (--ENDTC), End Relative to
Reference Period (--ENRF) or End Relative to Reference Time Period (-ENRTPT) is not NULL
• Proposed Solution/Action:
– Requires additional discussion originally sent to CBER Top 20 Validation Rule
Failures project team for further discussion.
CAB/VP OpenCDISC
• SD0046
• Description:
– All values of Qualifier Variable Label (QLABEL) should be the same for a given
value of Qualifier Variable Name (QNAM)
• Proposed Solution/Action:
– Send to the SDS Team to clarify what the IG should say regarding the
uniqueness of these one-to one relationships.
CAB/VP OpenCDISC
• SD0081
• Description:
– Date/Time of Collection (--DTC) should be less than or equal to the Start
Date/Time of the latest Disposition Event (DSSTDTC)
• Proposed Solution/Action:
– Requires additional discussion originally sent to CBER Top 20 Validation Rule
Failures project team for further discussion.
CAB/VP OpenCDISC
• SD0093
• Description:
– 'Age Units (AGEU) should be provided, when Age (AGE) is populated
• Proposed Solution/Action:
– Send to Change Control Board to be changed to an error.
CAB/VP OpenCDISC
• New Rules for Consideration
– RelationshipType (RELTYPE) populated as 'ONE' must not have
more than one record present in the RDOMAIN with the
corresponding IDVAR.
– A DATE/TIME OF COLLECTION is available, but the STUDY DAY
OF VISIT/COLLECTION/EXAM is missing.
– If both start date of observation and reference date are
populated with complete dates, then --STDY should be
populated.
CAB/VP OpenCDISC
• New Rules for Consideration
–
If both end date of observation and reference date are populated
with complete dates, then --ENDY should be populated.
–
Study Day variable(--DY) is not null but the variables required for the
calculation (DM.RFSTDTC and --DTC) are not complete. 2. Study Day
variable(--STDY) is not null but the variables required for the
calculation (DM.RFSTDTC and --STDTC) are not complete. 3. Study
Day variable(--ENDY) is not null but the variables required for the
calculation (DM.RFSTDTC and --ENDTC) are not complete.