Sunday, November 13, 2011

SDTM Compliance Checks

Validation checks or tools to check the compliance of SDTM data

JANUS is a standard database model which is based on the CDISC’s SDTM standard. JANUS is used by the FDA to store the submitted SDTM clinical data. As a part of data definition file submission pharmaceutical companies have to submit SAS datasets in transport file (.xpt) format along with annotated CRF and Define.xml file. The reason being this is… to properly load the clinical data into JANUS database which is maintained by the FDA. It is very easy for FDA reviewers to review the clinical data once they load the clinical data into their JANUS database. They can even produce ad-hoc reports and perform cross-study review at the same time. FDA runs compliance checks on the data submitted to make sure the data was collected as per the SDTM standard. FDA checks the compliance of data by running the WebSDM™ developed by PhaseForward). WebSDM™ is a SDTM compliance check validation tool performs a set of SDTM compliance checks on clinical data before it’s gets loaded into the JANUS database.


SDTM Validation tools verifies that the clinical data is in compliance with the standards and the assumptions of the SDTM implementation guide v3.1.1 or v3.1.2. They also verifies that the Define file created is in compliance with the ODM v 1.2.

WebSDM™ is an application, tests the compliance of submission-ready files (in SAS V5 Transport format or Oracle® views) according to the SDTM IG. The FDA has been using the WebSDM™ since 2004 to review the clinical data. Users load SDTM-compliant files into WebSDM™ tool which can then check for errors and or inconsistencies in the structure and content of the data.

The checks available include detection of structural and consistency errors rated by severity (high, medium and low). We can get the details of the compliance checks performed by the WebSDM™ from Phase forward website.

It will be very useful for the sponsor to run the WebSDM checks on the clinical data because the FDA reviewers also use the same application to review the data. The one negative point of this application is .. it cannot be used for near SDTM complaint or client specific standard datasets.

2) SAS - Proc CDISC:

SAS provides Proc CDISC to perform SDTM compliance checks on the clinical data. Proc CDISC is already included in the software as a procedure, If you use newer version of SAS (Version 9.1.3 Service Pack 3 and above).

Proc CDISC only supports few domains to run the compliance checks (15 out of the 23 domains outlined in CDISC SDTM version 3.1. It supports the

Interventions (CM, EX, SU),
Events (AE, DS, MH),
Findings (EG, IE, LB, PE, QS, SC, VS), and
Special purpose (DM, CO) class of domains.

Proc CDISC does not support the trial design domains, custom-defined domains or other new SDTM domains like MB, MC, PC and PK etc.

3) OpenCDISC Validator:

OpenCDISC is a new application which has been released by openCDISC to run the compliance checks on the clinical data. OpenCDISC validator is an open source java based project that provides validation of datasets against SDTM datasets. The advantage of this software application is ..It is open software so can be downloaded for free. The second advantage of this application is, It includes the combination of WebSDM and Janus checks. It can also check the ADaM compliance standards.

OpenCDISC can check the compliance of SAS transport as well as delimited files (.CSV etc) as per the SDTM v3.1.1 or SDTM v3.1.2 standards. One major advantage of this tool, this can perform compliance checks on all sorts of datasets (ex: SDTM compliant, SDTm non-compliant).

Here are few other nice SUGI papers that have lots of information regarding .. Open CDISC SDTM compliance checks:

Open CDISC Plus
A Standard SAS® Program for Corroborating OpenCDISC Error Message


Study Data Specifications document V 1.6 by FDA.
In-Depth Review of Validation Tools to Check Compliance of CDISC SDTM-Ready Clinical Datasets
SAS and Open Source Tools for CDISC SDTM Compliance Checks for Regulatory Submissions
Validating CDISC SDTM-Compliant Submission-Ready Clinical Datasets with an In-House SAS® Macro-Based Solution
Max Kanevsky (2008), “Validating SDTM, an open source solution”, proceeding of the CDISC Interchange 2008