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Open Source Technologies for Clinical Trials

May 30, 2012 by     No Comments    Posted under: Business Best Practices, EDC, Trends

Clinical trials have become increasingly complex and, as a result, costly. Only 333 drugs and biologics have been approved between 2000 and 2010 due to stricter regulatory procedures while spending has increase by 15 in the same period of time.

The need for innovation is critical in the pharmaceutical and biotechnology industry. Life science companies and service providers are looking for innovative solutions to improve study performance and minimize their risks. This article will demonstrate how open source technology presents an innovative solution to this challenging environment, and ultimately helps bring medical innovations faster to patients.

What is open source? Open source is a type of software license. There are various types of open source licenses, but the common characteristic to all is allowing free distribution of the underlying source code. Famous open source systems include Linux, Apache, MySQL, and many others. Below is a definition of Open-Source Software:

Open Source Technologies for Clinical Trials

  1. Free redistribution
  2. Source code
  3. Derived works
  4. Integrity of the author’s source code
  5. No discrimination against persons or groups
  6. No discrimination against fields of endeavor
  7. Distribution of license
  8. License must not be specific to a product
  9. License must not restrict other software
  10. License must be technology-neutral

Taken from Opensource.org. See http://opensource.org/docs/definition.ph​p for an annotated description of the above points.

  

Open Source in the Clinical Trial Industry. Two pioneers in open source technology for clinical trials are Cynthia Brandt and Prakash Nadkarni of the YaleCenterfor Medical Informatics, with their TrialDB system (http://ycmi.med.yale.edu/trialdb/), an open-source Clinical Study Data Management System (CSDMS) for the storage and management of clinical data initiated in the 1990’s.

The US National Cancer Institute launched a wide-ranging, open-source friendly initiative named CaBIG (Cancer Biomedical Informatics Grid - https://cabig.nci.nih.gov), that aims to develop a collaborative information network to accelerate the detection, diagnosis, treatment, and prevention of cancer.

Open source software is also used for electronic data capture (OpenClinica, ClinCapture), clinical research (LabKey Server), Electronic health or medical record (OpenEMR), analysis (R project), and CDISC conversion (CDISC Express, OpenCDISC).

Benefits of open source technologies for clinical trials. While open source is prevalent in many industries, this technology is still emerging in the field of clinical trials. The development of open source technology in the clinical arena has been quickly growing. Eric Morrie, Manager for Clinical Programming in one of the worldwide leading medical device companies, shared his extensive experience on open source technologies at a Silicon Valley BioTalks (http://www.clinovo.com/biotalks/open-source/article). Eric explained how open source technologies save time, improve re-usability and simplify the customization of systems to a company’s needs.

  • Provide state-of-the-art, cost-effective solutions

Proprietary systems for clinical data management are often too expensive for individual researchers and smaller companies. As a result, they often use slow, error-prone paper-based methods.

Ale Gicqueau, President and CEO of Clinovo, a CRO based in the Bay Area, explains that with open source technologies, the license fee for proprietary systems is no longer a barrier entry for small and mid-size companies (http://www.clinovo.com/biotalks/open-source/article). Open source clinical data management systems save money by eliminating the reliance of using expensive proprietary systems, while insuring the same levels of quality. It provides a means for smaller companies to access high quality technologies for clinical data management and comply with international regulatory standards.

  • Avoids the risks of vendor lock-in

Proprietary systems lock a customer into a vendor’s product from which they cannot escape without substantial switching costs. Such dependence includes reliance for maintenance and support, and the necessity to accept version upgrades that the buyer may not need.

Widely adopted open source systems on the other hand have multiple vendors supporting it. Surveys demonstrate that early adopters of open source technologies are driven by the “reduced dependence on software vendors”, often seen as one of the most important advantages of open source technology.

  • Enables a larger community to maintain and enhance the source code

The open source model enables quick improvements by giving access to the underlying source code to a large community of talented developers. In the open source community, developers are encouraged to produce derived works to enhance the existing source code.

“The Open Source community attracts very bright, very motivated developers”, explains the UK software consultancy company GB Direct (http://open-source.gbdirect.co.uk/migration/benefit.html). “Highly prized factors are clean design, reliability and maintainability, with adherence to standards and shared community values preeminent.”

A rising trend: Open source for electronic data capture: One of the most famous and number one open source system for clinical trials is OpenClinica, with a community of over 12,000 developers.EDC systems are often prohibitively expensive, ranging in the hundreds of thousands of dollars. As a result, open source technology has been particularly well-received in the field of electronic data capture. Open source EDC platforms deliver the same benefits as proprietary EDC systems but without the license fee.

The one I am most familiar with is an open source EDC system developed by Clinovo : ClinCapture. It is a validated and enhanced version of the #1 open source EDC platform, fully customizable to any clinical study. Learn more

This open source EDC system has been successfully implemented by major pharmaceutical, medical device and biotech companies. Victor Chen, Director of Clinical Affairs at Intuitive Surgical, explains that he decided to use this technology due to the low price and the flexibility that suits adaptive clinical trials. However, he emphasizes on the importance of rigorously assessing any open source system vs. proprietary systems and evaluating the cost for validation. Read case study

The emergence of open source based tools for CDISC: Converting clinical data to the widely recognized CDISC SDTM standard is often done manually, which can quickly become tedious, error-prone, and time-consuming.CDISC SDTM data is the standard format recommended by the FDA for clinical trial data submission. The mission of CDISC is to develop and support global, platform-independent data standards to improve medical research.

Clinovo developed an open-source system to help with this conversion to CDISC SDTM: CDISC Express. CDISC Express is a powerful open source SAS®-based system that automatically converts clinical data into CDISC SDTM using an Excel framework.

The CDISC Express framework is highly extensible. The system significantly speeds-up CDISC SDTM conversion, and has been successfully implemented for major biotechnology and pharmaceutical companies. Download for free


Conclusion: Today, it takes on average 10 to 15 years to develop a drug and costs near $1.2 billion. With only 2 of 10 marketed drugs returning revenues that match or exceed R&D costs, developing medical innovations has become more and more risky. Open source technologies are an innovative way to lower the cost of clinical trials and minimize risk, while ensuring the same level of quality as proprietary systems.

Ultimately, open source technologies increase the scope and variety of clinical trials, by enabling smaller institutions to pursue their clinical research that would otherwise be out-of-reach and beyond financial capacity. “We believe that an open-source approach has the best chance of ensuring that all kind of groups can be involved with the development of systems that have bearing on global public health”, explains Greg W. Fegan and Trudie A. Lang in their featured article Could an Open-Source Clinical Trial Data Management System Be What We Have All Been Looking For?

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A New Way to Collect Data: CDASH by Anayansi Gamboa

Apr 23, 2012 by     No Comments    Posted under: Best Practices, Best-Practices, Business Best Practices, CDISC, Clinical Data Management, Menu, Tips & Techniques

Clinical Data Interchange Standards Consortium

There is a general consensus that the old paper-based data management tools and processes were inefficient and should be optimized. Electronic Data Capture has transformed the process of clinical trials data collection from a paper-based Case Report Form (CRF) process (paper-based) to an electronic-based CRF process (edc process).

In an attempt to optimize the process of collecting and cleaning clinical data, the Clinical Data Interchange Standards Consortium (CDISC), has developed standards that span the research spectrum from preclinical through postmarketing studies, including regulatory submission. These standards primarily focus on definitions of electronic data, the mechanisms for transmitting them, and, to a limited degree, related documents, such as the protocol. Read more »

SAS : best place to work!

Apr 18, 2011 by     No Comments    Posted under: Business Best Practices

Once again, SAS has been elected as one of the 10 best places to work. A chance for me to evoke SAS history and the role of SAS programmers in companies.

SAS, as a language, was conceived in 1966 at North Carolina State University by a graduate student to address some complicated statistical analyses that he was working on. Later on, The SAS Institute was created in 1976, once they figured out, “Hey, maybe we can sell this and make some money?!”

Over the years, SAS has become an integrated system of software products used in biotech, financial, insurance, marketing, and retail industries, just to name a few. SAS is now used at more than 50,000 sites in over 100 countries, including 93 of the top 100 companies on the 2010 FORTUNE Global 500® list

SAS allows businesses to transform data about customers, performance, financials and more into information and predictive insight to support solid and coherent decisions.

I have been a SAS programmer in the health sector for the last 15 years. I have worked in several biotech companies and CROs. I now managed a team of SAS programmers at Clinovo.

From my experience as a SAS programmer and managing SAS programmers, I found out how important it is for a company to understand SAS programmers’ needs in terms of career and work content. SAS cannot be all taught. It comes with experience. You need to be at the right time at the right place.

Each programmer is different. Introvert, communicator,  extrovert, listener…each of us has his own personality and needs. It is a challenge for a company to identify SAS programmer profiles and provide them the right work experience that will uplift their skills and contribute to the company’s success.

Now, The Truth Behind Outsourcing Data Management and Biometrics to India!

Oct 13, 2010 by     No Comments    Posted under: Business Best Practices

Lessons learnt and the pitfalls to avoid

1. Select the right partner:

A decrease in quality is of course the first risk when outsourcing services. Only a handful of Indian outsourcing partners were able over the past few years to gain enough experience to develop genuine expertise.

Make sure to test their technical skills through detailed phone screenings and do not rely only on marketing materials that they may have fabricated from US competitors .

2. Get a technical project manager on staff as a liaison:

Communication overhead is difficult to handle due to time difference between the US and India.

To minimize the negative impact of the time differential, I recommend to have a technical project manager at your office starting their day at 2 PM (if you’re on the West Coast like we are) spending the afternoon with the US client or CRO and spending the rest of her time after dinner to assign and review work with the outsourced team in India until midnight or later. Read more »

Why Outsourcing Data Management and Biometrics to India?

Oct 1, 2010 by     No Comments    Posted under: Business Best Practices

At the turn of the millennium, IT outsourcing became very popular. India quickly became the main beneficiaries of this growing trend. Companies were indeed attracted by the rich pool of motivated English-speaking talent at a competitive price. Industry leaders like Bill Gates and Jack Welch were among the first to strike strategic alliances with Indian companies and opened a world class technology centre in Bangalore, India.

Outsourcing took a few years to reach the pharma industry. This is explained by the necessity to run clinical trials on the market the drug is developed for. However, the price of bringing a new drug to market costs on average $1 billion, the bulk of the cost being devoted to human clinical trials. To decrease rising costs, big pharmas started leveraging the Indian population for early phases of clinical trials. Although providing untested drugs to a developing country population creates ethical issues, this trend has continued accelerating.

In our business of supporting clinical trial data, outsourcing is even more recent. Read more »

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