Nacci - SDTM Implementation Best Practices - BIAS

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SDTM Implementation - Best Practices
Pantaleo Nacci, Head Statistical Safety & Epidemiology/PV
Biometristi Italiani Associati (BIAS) Seminar:
CDISC, SDTM and ADaM: Moving from theory to practice
SAS Institute - Milano, 14 March 2014
Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
The CDR Project
 In 2010 Novartis Vaccines (NVx) initiated a very ambitious
project to pool together all legacy studies for which data
are electronically available in-house, as well as all new
EDC trials, within the framework of a Clinical Data
Repository (CDR)
 A slightly adapted variant of CDISC SDTM 3.1.2 was
selected as common standard for final storage, analysis
and reporting, which allows storing of study metadata as
well
 All legacy study data are being remapped to this standard
in two phases, and their metadata retrieved (mostly from
protocols) and entered, for a total of around 400 studies
3 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
The CDR Project (2)
 All EDC panels have been redesigned to collect data in a
format compliant with CDASH standards, which allows
easy remapping to SDTM
 After a careful and lengthy selection process among three
candidates, the solution chosen as the basis of the CDR
has been SAS Drug Development (SDD) as a hosted
environment
 The re-mapping is done using custom-written SAS
programs rather than SAS Clinical Data Integration (CDI),
as initially planned
4 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
The CDR Project (3)
 (Re-)coding of adverse events, concomitant medication,
medical history, etc. is performed in Oracle Thesaurus
Management System (TMS)
 Our home-grown Standard Reporting Software suite of
validated SAS programs was adapted to run in the new
SDD environment AND to use the new CDISC data
structures
 Last but not least, all our existing processes were
migrated to the new platform, and several new ones
mapped and documented
5 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Two years later...
 More than two years after the CDR went live, all new
clinical studies are now running completely in it
• Data get pushed automatically into the system at regular intervals
• SDTM data are then obtained directly from CDASH dumps nightly,
so that the latest version is always available online
• Deviations from the NVx standard are dealt with using a set of studyspecific ‘rules’, and approval by a technical committee is necessary
 Standard Reporting Software has finally been tested on
real data, necessary fixes have been applied and new
enhancements are actively being worked on as we speak
 Special techniques are being developed to speed up
operations in SDD
6 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Two years later... (2)
 Phase 2 of the Legacy Data Conversion sub-project has
started, and data from 191 legacy studies, dating back as
far as 1992, are now available for use, of course in
addition to those from CDR-native ones
 Utilities to create and maintain complete and ongoing
dynamic ‘oceans’ have been fully validated, and jobs to
maintain them are scheduled to run nightly
 Other utilities to create static ‘data poolings’ have been
validated too, and are available for use
• Several data poolings have now been created and released for
analysis
7 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
CDR - The Full Picture
Phasing out
•TGROUPS
TMS Coding
Paper CRFs
Scanned
CRFs (ICRF)
Clintrial
(AE, MEDHX, CMED)
•Lab norms
Submission
Data sets
•Randomization
•Exclusions
•Stat. Populations
Stat. Analysis
Monitor listings
Adapter
eCRFs – EDC
Periodic
Updates
CRO data,
eDiaries
Ext. Labs
Serology Lab
Clinical Data Repository CDISC
Data sets
SAS Drug Development
Serology database
Future wish:
SAE ->EDC->
CDR-> PV DB
Pooled analysis
CTMS
Rapid Pooling
Data Mining
Signal Detection.
SAE coding *
8 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
SAEs
PV Safety database
PV Safety reports
* Ideally all coding in 1 system
Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
Regulatory Requirements
 It was in October 2007, while attending the PhUSE annual
conference in Lisbon, that I heard for the first time about
JANUS from an FDA speaker
 The message was clear even then: the need to adopt nonproprietary data standards was not a question of ‘if’, but
just of ‘when’
 It took longer than expected, but on 6th February 2014
FDA officially published several guidance documents for
electronic regulatory submissions, with a 90-day window
for public comment
• Various CDISC data standards (CDASH, SDTM, SEND, ADaM) are
specifically mentioned as required
10 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Effects on Submission Reviews
 Even after adopting CDISC standard more pitfalls might
be present in (therapeutic) areas not well characterized
 E.g., given the degree of latitude still left to the single
companies by the gaps in the current standards as
regards vaccines data, an FDA reviewer might be faced
with widely differing structures (and possibly codelists)
representing the same data but coming from different
companies
• E.g., in vaccine trials solicited AEs can be stored in AE, CE, FA, etc.
 This might result in longer times for review, even with the
help of JANUS or similar systems
11 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Evolution of the NVx Data Standards
How an unstable reference can ultimately be a liability
 It is now almost exactly two years since the first native
CDISC study data entered the CDR
 Only once that milestone was reached it was finally
possible to fully test the reporting software, which had
been developed using mock data
• As expected, many issues, small and not so small, surfaced
 The next slide show an overview of the changes applied
to the initial production version of the NVx SDTM standard
until June 2012
• A few further changes, mostly adoption of new domains, have been
applied since then
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Evolution of the NVx Data Standards (2)
Adapting to changing requirements is a must
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Evolution of the NVx Data Standards (3)
How a pilot phase can save a lot of time later
 In practice, these are a few examples:
• Information which in the old data structures was contained in one
variable is now spread over several ones, e.g.:
- EDTTEST = ‘HI_B_BRISBANE08_CC’
- LBCAT=‘IMMUNOLOGY’
- LBMETHOD=‘HEMAGGLUTINATION INHIBITION’
- LBTEST=‘INFLUENZA B BRISBANE/2008 CC AB ‘
• Re-assaying of samples, only identifiable using the date when an
assay was run, was not accommodated for until a new TSTDTC
variable was added in SUPPLB
14 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Usage of SDTM Data
 As mentioned earlier, two data ‘oceans’, inherently
dynamic, are maintained within it and have been used
multiple times to create static ‘data poolings’
• Complete ocean: contains all available data from studies which are
not active anymore; data for newly completed studies are added to
those of existing ones
• Ongoing ocean: contains all available data for studies not yet
completed, and is recreated from scratch every night
• All AE/MH verbatims can be updated to the latest MedDRA version
in one go
 These ‘data poolings’ are used to support submissions,
but also papers, etc., i.e., whenever there is the possible
need to go back to a known status to perform additional
analyses
15 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
Basic Requirements - General
• The scope of such projects must be well defined at the beginning, so
that all necessary functions are involved from early on
• Proper resourcing levels are needed from the beginning, and all
interested systems must be identified and properly covered
• Think boldly when looking at the big picture and drawing your longterm plans, but don’t be ashamed to take only the steps you can
afford at any given time
• It is extremely dangerous to have all knowledge on a certain topic
concentrated in only one or two persons, and it can also create
unnecessary bottlenecks at the wrong time
• A target reference framework must be clearly identified early on
• While it is possible to implement CDISC structures from scratch just
looking at the documentation, choosing the right system will make it
easier to implement, e.g., the inevitable tweaks linked to the
peculiarities in your legacy data
17 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Basic Requirements – Legacy Data
• The criteria to include/exclude studies and the overall timelines
should be well understood and shared by top management to avoid
creating excessive or plainly wrong expectations
• Putting study data together takes a lot of time, patience and attention
to detail, even when most of the electronic data are already more or
less in the right format
• Finding actual evidence about old studies can be a challenge (!)
• Original documentation (at least annotated CRF and protocol/CSR,
including all amendments) must be available for all studies before
the coding starts, to avoid misinterpreting the data
• Metadata are important as much as data themselves, so, e.g., make
absolutely sure your T-domains are correct
• If at all possible plan for a pilot phase, it will most probably save a lot
of time and grief later
18 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
What About All Those Studies in the Archive?
 We decided that data from all new studies would be
collected and stored according to CDISC standards, but
this still left us with data from over 400 studies lying in our
archives gathering dust
 In this case the skill set required for the remapping was
different, needing both good knowledge of the new CDISC
standards and a lot of experience with the old one(s)
 As described earlier, the first step was to decide which
studies to convert first
20 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Interpreting Old Data
 A data inspection step was then undertaken, with the aim
to identify all the legacy datasets and variables used
 In our case we could further split the studies in pre- and
post-Clintrial adoption:
• Pre-Clintrial ones were managed by several different CROs in the
first half of the 90’s, so that today existing knowledge is extremely
limited and fragmentary
• Post-Clintrial ones are on the contrary based on relatively minor
variations of the current internal standard, which is known and
understood by most members of the programming group
 Study data were either re-extracted again from Clintrial or
retrieved from our electronic archives
21 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Necessary Tools
 We correctly identified the need to retrieve all protocols,
protocol amendments, (annotated) CRFs and CSRs from
the archives, but underestimated the difficulty of getting
them, especially the very old ones
 The initial programming approach, agreed with our Quality
partners, was based on random sampling of results, but a
radical change to double-programming was requested
well into the process
• This caused a sudden shortage of experienced programmers
22 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Remapping Your Existing Data
Another source of possible issues for your SDTM implementation
 The LDC Phase 1 exercise, restricted to 153 high priority
studies, took considerably longer than planned, but why?
• Not all studies had available protocol and CRF at the time
programming started, forcing the team to a dangerous guessing
game
• The NVD data standard was still evolving rapidly, so that some
important assumptions proved grossly wrong when new studies
were designed and run in the new system, sometimes requiring
extensive rewriting of almost validated programs
• One domain in particular proved a nightmare, LB/SUPPLB, as
several old test codes, as well as free text descriptions, were not
included in the new so-called lab metadata tables
23 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Remapping Your Existing Data (2)
Still something you want to do?
 Even with all these issues and delays, this is still one of
the core business reasons why NVx started the CDR
project
 Safety signaling across vaccines, therapeutic areas and
even single vaccine components can now be performed
using data in the oceans
• This is meaningful only for projects where all data are already
available in SDTM
24 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
Future Developments
What’s next on the CDR plate
 The current implementation of CDR is based on SDD 3.5,
which does not exactly shine for speed
• A new, revised version of SDD (4.3) has been out for a while, and we
have been getting a feel for it for some time
 The set of available CDISC standards currently
implemented is restricted to CDASH 1.1 and SDTM 3.1.2
• Two main tasks have been identified here, upgrading to SDTM
3.1.3/3.2 and adopting ADaM 2.1
 The Standard Reporting Software we use is still a
revamped version of very old programs ported to
SDD+SDTM
• We are in the process of redesigning the reporting system from
scratch, embedding in it the creation of ADaM datasets
26 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Future Developments (2)
What’s next on the CDR plate
 Until now we have remapped only part of the available
legacy data
• Lessons learned from the Phase 1 have been put to good use to reengineer the process
• Many things have changed to the better in the CDR environment:
- The reference standard is much more stable
- OpenCDISC consistency checks are readily available to check the
progress all along
- Basic documentation has been retrieved for all remaining studies
(no more guessing games!)
- Programmers know better both sets of data structures
27 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
What is Happening on the SDTM Front
Lately CDISC has been very active too!
 SDTM 3.1 was released on 14 July 2004, SDTM 3.1.1 on
26 August 2005 and SDTM 3.1.2 on 12 November 2008
 After a hiatus of almost four years, during which more and
more companies have adopted it, SDTM 3.1.3 has been
finally released on 16 July 2012, followed by an utterly
unexpected version 3.2 on 26 November 2013
• According to their previous roadmap, we should have seen
SDTM 3.1.4 last July, and 3.1.5 roughly one year later
• An updated roadmap has been published in late February
 Stated long-term aim is to have two updates per year, à la
MedDRA
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CDISC Planned Activities and Releases
What we can expect for the next year
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Agenda
The story so far
Benefits of implementing SDTM
Basic requirements
Legacy data conversion: a missed opportunity?
The way forward
Conclusions
Conclusions
 The old SAS server is still in service, but we are reducing
the number of both business processes and users using it
 We have plenty of exciting developments on our plate
 CDR is a long-term project, which is evolving and will take
years to reach a stable status
 More and more activities are now moved completely to
CDR
 Safety signaling using all available data for selected
vaccines/products is now possible, and by the end of 2014
this should be possible for most of our major products
currently on the market
31 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Conclusions (2)
 Using capabilities already built in SAS we should be able
to create necessary documentation for the submission
data (e.g., define.xml) with much less effort than in the
past, and with a higher quality
 In the meantime SDTM is moving again
 Changes to existing processes have always a cost, and
resources are not always a viable alternative to time
 It will be crucial to understand how much change is
introduced by each new version, and calculate the
business impact in each company scenario
• It might make sense to skip some ‘minor’ versions
32 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Useful Links
 CDISC:
• http://www.cdisc.org
• Technical Plan Project Schedule
 SAS Clinical Standards Toolkit
• http://support.sas.com/rnd/base/cdisc/cst/
 FDA/PhUSE Computational Science Symposium 2014
• http://www.phuse.eu/css
33 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Useful Links (2)
 FDA:
• FDA-2014-D-0092 - Study Data Technical Conformance Guide and
Data Standards Catalog
• FDA-2012-D-0097 - Guidance on Electronic Submissions:
Standardized Study Data
• FDA-2014-D-0085 - Guidance on Submissions in Electronic
Format--Submissions under the Federal Food, Drug, and Cosmetic
Act
34 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
Questions?
35 | BIAS Meeting | P. Nacci | 14 March 2014 | SDTM Implementation - Best Practices
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