New Course on CDISC Standards

May 7, 2013 by Clinovo    No Comments    Posted under: CDISC

Clinical information tends to be more complex, comes from multiple sources in different formats. As a result, clinical data submission has become time-consuming, costly and error-prone. CDISC® (Clinical Data Interchange Standards Consortium) established new data standards to speed up data-review and improve clinical data exchange, storage and archival. Our technology edge combined to our experience in standards implementation allows us to develop tailored CDISC solutions to accelerate your FDA review. Clinovo introduced a new opportunity to learn these recognized clinical data standards!

Clinovo’s new “CDISC Standards: Theory and Application” class is an 8-week training program starting in June 11th, 2013. The TechTrainings are technical hands-on classes for entry-level or experienced clinical trial professionals designed to help them reach the next step in their professional career. The class will be held in Palo Alto at Dentons Offices or remotely.

Taught by Sy Truong, President at Meta-Xceed and author of award-winning papers, this new course will give an overview of CDISC standards: ODM, SDTM, ADaM and Define.XML. Students will learn how to transform legacy data into these clinical standards through real-life examples. Case studies will include data exchange, archival, and electronic submission to regulatory agencies such as the FDA.

Clinovo will continue to offer the “Base Clinical SAS Programming” class to help entry-level programmers prepare the Base SAS certification, as well as the “Advanced Clinical SAS Programming” class to tackle advanced real-world SAS programming challenges. Clinovo offers $50 gift cards for referrals.

More information on the class can be found on clinovo.com/techtrainings.

Olivier Roth launched the TechTrainings by Clinovo in 2012, a series of hands-on courses for clinical trial professionals, leveraging his company’s years of on-field experience and industry expertise. He is the Marketing & Communication Coordinator at Clinovo, a CRO based in Sunnyvale, focused on streamlining clinical trials for life science companies through technology solutions. Olivier helps managing Clinovo’s marketing and communication from marketing strategy to partnership management, lead generation, event planning and new business opportunities. Prior to Clinovo, Olivier was working as a Strategic Marketing Consultant at VivaSante, an international consumer healthcare company based in Paris.

Mobile Devices Pave the Path for Clinical Research Evolution

Sep 19, 2012 by Clinovo    No Comments    Posted under: New Technologies, Trends

Clinical trial sponsors looking to stay at the forefront of efficiency and accuracy should consider whether they are making the best use of the growing trend of access to clinical data on mobile devices. From the secure sharing of electronic patient reported outcome (ePRO) data, to creating more flexible clinical data management, mobile technology has the potential to improve processes across the clinical research process. In many cases, sponsors are already seeing the benefits – including real-time alerting capabilities and increased efficiencies – of incorporating mobile technology in their research process.

Real-time results – delivered to the right people at the right moment

Real-time alerting can dramatically improve a trial’s overall success rate. Alerts can be configured to automatically send an email or text message to a mobile device when a pre-specified event occurs, such as when a serious adverse event (SAE) is entered into the system. It is important that alerts notify mobile devices; most people are not always logged into their computer workstation, but many keep their smartphone or tablet close by. This helps ensure that all relevant stakeholders are informed as quickly as possible when their action is required. For example, if a patient in Sweden reports symptoms via their iPad after intake of Drug X, their information can be instantly analyzed in California, where a data manager will be notified that he or she needs to take appropriate next steps, which may include alerting sites across the globe to suspend the use of Drug X. With the use real-time notifications delivered through mobile devices and the ability to act upon this feedback from any web-enabled device, response times can be reduced from days or weeks to hours or minutes, giving clinical teams the opportunity to address problems before they put a study in jeopardy.

Consumer-based efficiency – taking advantage of familiar technology

Increasing trial efficiency and correctness are common requirements for CROs and trial managers when implementing new clinical trial technologies. Luckily, mobile devices and their efficiency benefits can be easily introduced into the research process without costly hardware investments or extensive user training. Most trial participants and managers currently utilize mobile devices in their everyday life, so the functionality is already available. Because participants are using a technology they already understand, it becomes easy for them to enter data directly. In addition, trial participants will be more likely to engage with tools they’re already familiar with, enabling increased accuracy and improved reporting. And because of the connectivity of mobile devices, it is easy for trial managers to retrieve data from patients without costly delays.

Data security concerns – succeed with caution

In order to make mobile capabilities a research reality, we can’t ignore the possibility of security threats and regulatory concerns. However, mobile software can be very secure if written properly, and the clinical trial industry can benefit from the great strides other industries such as online banking have made in mobile security. Similarly, regulatory concerns can also be addressed by ensuring mobile software is fully Title 21 CFR Part 11 compliance. Data security is a risk in any electronic platform, but when addressed carefully, its risks need not outweigh the vast benefits that electronic technologies provide.

Propelling into a mobile-charged future

As the clinical industry becomes more dependent on technology, waiting for results or data batches to be complete will no longer be acceptable or considered the norm. The ability to increase efficiency, analyze live data and implement results immediately demonstrates collectively the key benefits of utilizing mobile devices in clinical trials. Taking advantage of new and innovative technologies is a key to the future of clinical trials, and mobile capabilities will pave the way.

Rick Morrison
CEO, Comprehend Systems

Rick Morrison is the co-founder and chief executive officer of Comprehend Systems. Prior to founding Comprehend Systems, Rick served as the chief technology officer of an internet-based data aggregator, where he was responsible for product development and operations. Rick has over a decade of experience writing software for clinical trials, including tools that are now used by the FDA and top pharma. Rick holds a bachelor’s degree in computer science from Carnegie Mellon University.

Are you prepared for CDISC?

Jul 17, 2012 by Clinovo    No Comments    Posted under: CDISC, Trends

CDISC® (Clinical Data Interchange Standards Consortium) is establishing data standards to speed up data-review and improve clinical data exchange, storage and archival. Today, 60% of FDA submissions are already done in CDISC standards. The FDA is getting more and more involved into CDISC standards, a meaningful signal for the industry. Theresa Mullin, Director of Office of Planning and Informatics within CDER, claimed that “the FDA is committed to using CDISC standards for the foreseeable future”. These data standards are expected to be mandatory by 2016 for every drug submission.

CDISC standards hold the clinical data to a greater level of readability and compliancy in regards to FDA requirements. Carey Smoak, Senior Manager of SAS Programming at Roche Molecular and CDISC Device Team Leader, points out that “a submission without CDISC standards can have a review period twice as long as one under standards”. Indeed, they facilitate the FDA review process since they are known and understood by reviewers.

A 2009 study conducted by Gartner in collaboration with the CDISC organization shows that the overall clinical trial duration is divided by two when using CDISC standards. Thus CDISC standards ultimately speed up time to market.

So if the benefits of using CDISC standards are so obvious, how can we explain that so many sponsor companies are still not adopting them?

Converting legacy data to CDISC standards is expensive

Clinical data standardization is no simple process:  It is time consuming and proves to be tedious. However, a few open source CDISC conversion tools have been launched to address this problem. One successful example is the OpenCDSIC validator software, recognized by the FDA and freely available. CDISC Express, Clinovo’s free SAS-based SDTM mapping tool, has been downloaded 600 times.

In the future, standards can be adopted smoothly if the industry works harder at incorporating them earlier in the process. Indeed, the next challenge is to push CDISC standards upfront in the clinical trial process. CDISC experts agree the best timing to implement CDISC standards is the database built.

CDISC standards are still evolving

Standards are still being built and are in constant evolution. The CDISC organization is still releasing new versions of its clinical standards. Sponsors companies are often scared that if they convert their clinical data to a format, it will be obsolete a year later. Clinical trial experts still state however that sponsor companies should shift to CDISC standards as soon as possible.

Companies often lack the internal expertise

In order to be efficiently used and maintained, Carey Smoak points out that “the wiser choice is to hire people with expertise on CDISC standards”. Companies should educate themselves on this topic and exclusively hire experts from CDISC Registered Solutions Providers organizations.

Ale Gicqueau, CEO at Clinovo

Dive into CDISC Express (2) : Create a new study

Jul 21, 2011 by Clinovo    No Comments    Posted under: Best-Practices, Case studies, CDISC, Code, Tips & Techniques

Here is the second part of ‘Dive into CDISC Express’, written by Jiangtang Hu. You can read the first part here.

Step 1 of 6: Create a new study (create_new_study.sas)

Open create_new_study.sas in C:\Program Files\CDISC Express\programs\, you can see only one line of a macro call:

%addnewstudy(studyname=my new study);

Just assign a study name to the macro variable, &studyname, e.g, “CLINCAP”:

%addnewstudy(studyname= CLINCAP);

Submit the codes, you can find a folder named “CLINCAP” with the same structure as the two demo studies imbedded in this application(example1 and example2) in C:\Program Files\CDISC Express\studies\, see(the left and right panels are folders and files before and after the execution of  create_new_study.sas. The following the same):

Folder ‘doc’ is used to hold the mapping files;

Folder ‘log’ used to hold log files generated by following macro calls, such as generate SDTM domains;

Folder ‘results’ and its subfolder will hold all the outputs, such as define.xml, SAS transport file, validation reports and SDTM datasets;

Folder ‘source’ holds all the clinical raw data used as inputs for SDTM domains;

Folder ‘tempdata’ holds all the temporary datasets generated by following macro calls.

Also, a configuration file named CLINCAP_configuration.sas put in C:\Program Files\CDISC Express\programs\study configuration\. This file is used to set some study level parameters, such as lab and toxicity specifications (details in C:\Program Files\CDISC Express\specs\Lab specs\).

Two versions of SDTM implementation guides are supported by CDISC Express, CDISC SDTM Implementation Guide Version 3.1.1 and Version 3.1.2. You can find the corresponding specification files in C:\Program Files\CDISC Express\specs\SDTM specs\:

SDTM_Specs_3_1_1.xls

SDTM_Specs_3_1_2.xls

The choosing of SDTM implementation version is also coded in the configuration file, in Line 41:

%LET SDTMSPECFILE=SDTM_Specs_3_1_1.xls;

Version 3.1.1 is used by default. You can also choose Version 3.1.2 if needed:

%LET SDTMSPECFILE=SDTM_Specs_3_1_2.xls;

Assign a study name and choose a SDTM implementation version. That’s all needed in step 1. Let’s take few minutes to navigate the software. CDISC Express is a set of macros and Excel files. It is important to know the file structure.

C:\Program Files\CDISC Express\

├─documentation : FAQ, Quick Start, User Guide

├─macros

│  ├─ClinMap : system level macros

│  └─function_library : study level macros

├─programs : “action taken” macros

│  ├─study configuration : study parameters configuration, e.g, choose SDTM version

├─SDTM Validation : For validation of SDTM domains

│  └─study1

├─specs : specification files

│  ├─Excel engine : ExcelXP tagset file

│  ├─Lab specs : lab and toxicity

│  ├─Mapping validation : validation rules

│  ├─SDTM specs : hold two versions of SDTM implementation

│  └─SDTM Terminology : SDTM codelist(including NCI terminology)

├─studies

│  ├─example1

└─temp : hold temporary data not specified to any studies

As we already got, all the “action taken” programs such as create_new_study.sas are located in C:\Program Files\CDISC Express\programs\. In create_new_study.sas, one macro is called, %addnewstudy, which is in C:\Program Files\CDISC Express\macros\ClinMap\.

Note that in C:\Program Files\CDISC Express\macros\, there are two sets of macros in different folders:

C:\Program Files\CDISC Express\macros\ClinMap\: this folder holds all “system” level macros used by the application only. No modification encouraged.

C:\Program Files\CDISC Express\macros\function_library\: macros used for mapping among studies. You can also create you own macro in this folder. The application imbedded macros also documented in user guide.

Next part on the mapping file next week!

Dive into CDISC Express (1): Introductory

Jul 7, 2011 by Clinovo    No Comments    Posted under: Best-Practices, CDISC, Clinical Data Management, SAS Library, Tips & Techniques

Here is the first part of a post written by Jiangtang Hu, statistical SAS programmer at Sanofi Pasteur Beijing in the Biostatistics department. Jiangtang was one of the first to download CDISC Express. I have been interacting a lot with him. He is sharing on his personal blog his experience as a tester and user and offers the community a very practical guidance to use CDISC Express.

Thank you Jiangtang for this valuable input! This dive into CDISC Express is structured in four parts. I will be posting one every week. Don’t hesitate to comment this post and ask your questions to Jiangtang or myself.

Recently I did for my personal project some research on Clinovo’s open source application, CDISC Express, a SAS application based on Excel framework designed to map clinical data to CDISC SDTM domains automatically. Not perfect yet, but it is easily understandable and practically usable after few hours’ of exploration of user guide. And most important, it is on the right way: an automatic CDISC converter is the magic weapon in almost every clinical programmer’s dream.

CDISC Express is the first and only practically usable open source CDISC converter I even met. I wrote a post a month ago when I first tested it with great interests and reported some issues to its fix system. Then I also had the great opportunity to discuss the software via email with its core developer, Romain Miralles. This post is just my personal notes on how to use and dig into the software, and will be best serve as a working documentation. You can return to me for any questions and comments.

By the way, there is an opportunity for your practicing and you will also have a change to win an iPad2 from Clinovo’s CDISC Express Contest:

http://www.clinovo.com/cdisc/game

The due day is July 15th and I already submitted my work. That’s fun.

1. Download and Installation

You can get CDISC Express for free in

http://www.clinovo.com/cdisc/download

It is a window application and will be installed by default in

C:\Program Files\CDISC Express\

After installation, this path will be coded as a macro variable &CDISCPATH in the following six SAS files which are all located in C:\Program Files\CDISC Express\programs\:

• create_new_study.sas
• generate_Definexml.sas
• generate_mapping_template.sas
• generate_SDTM.sas
• Validate_Mapping_File.sas
• Validate_SDTM_Domains.sas

The macro variable reads as

%LET CDISCPATH = C:\Program Files\CDISC Express;

If you change the destination folder at the installation stage, e.g., to D:\CDISC Express\, the value of the macro variable &CDISCPATH will be changed accordingly in the six files mentioned before:

%LET CDISCPATH = D:\CDISC Express;

Note that if you want copy the whole folder of files to another destination, you should at least manually change the value of &CDISCPATH in such six files or add some codes to capture the path accordingly. From this point of view, the path setting of CDISC Express is not completely portable. Recommend that if you have such needs, just re-install the software in any destination you want. It will not write any records into registry and you can have many copies in one machine.

The following discussion assumes the software roots in C:\Program Files\CDISC Express\.

2. Working Flow

You can follow all the 6 action steps one by one coded in

C:\Program Files\CDISC Express\programs\

1) Create a new study (create_new_study.sas)

Simple and easy. Just assign a new study name in a macro call and run.

2) Generate mapping file (generate_mapping_template.sas)

This is the critical and most time consuming part. You should design mapping rules for every domain needed in Excel spreadsheets (the MAPPING FILE). If done, all other tasks, such as generate SDTM datasets, SAS transport files, define.xml and validation, can be well done by just clicking buttons.

3) Validate mapping file (Validate_Mapping_File.sas)

For validating the mapping file, just click the button. As mentioned, the most important work is designing mapping file. It would be back and forth to design mapping file and validate it.

4) Generate SDTM datasets (generate_SDTM.sas)

If mapping file is OK, click the button.

5) Validate SDTM datasets (Validate_SDTM_Domains.sas)

Click the button.

6) Generate Define.xml (generate_Definexml.sas)

Click the button.

Following part will dig into the software step by step.