Do Biomarker Exchange Standards Exist?

Last week I was part of a very interesting email exchange on the topic of biomarker exchange standards. The correspondents were Sandor Szalma of Johnson & Johnson, who is heading up the embryonic working group on this subject, and James McGurk, director of informatics at Daiichi Sankyo Pharma Development. Because for every person brave enough to ask a question there are often many others silently asking it, I thought I’d provide the exchange in full. We welcome further questions on this topic; please leave a comment.

James McGurk: I think Sandor Szalma’s presentations about biomarker data exchange have been extremely good and stimulated much-needed discussion.  It is clear that this is a pressing need in both drug discovery and development.  Since I spent many years in discovery informatics before moving to development I am familiar with the different approaches these organizations have regarding the exchange and use of data. One thing that has puzzled me about this entire discussion is this:  It appears that we are, primarily, discussing exchange of experimental results: subject/patient/organism phenotype data, laboratory tests, genetic and genomics results, bio-images, etc. If that is the case I am wondering why we are focusing on data exchange standards. These types of results are routinely exchanged as part of development projects. Standards organizations such as CDISC and HL7 have deep experience developing and maintaining operational systems precisely for this purpose. And although the exchange standards are far from perfect, most or all of the key elements and infrastructure are already in place and in widespread use. It seems to me we run the risk of trying to solve problems that have already been solved.  I think it would behoove us to explore whether these existing systems might be fit-for-purpose.  If they are not an exact fit, it is possible that slight modifications will allow them to serve.

I recognize, based on my experiences in discovery informatics, that most discovery organizations have internally developed data management systems which can be very idiosyncratic.  This means that data exchange with outside collaborators of vendors can be quite difficult.  As biomarker work is increasingly outsourced even in discovery, this may become untenable.  Organizations will have to move to adopt more generic data models.  This has been the path in development for the past decade. Unless (as is certainly possible) I do not understand fully what others mean by “biomarkers” I think we might benefit from consideration of paths other than the creation de novo of another standard.  I certainly can see the need to develop systems to integrate different data types into a “biomarker signature”, the creation of controlled vocabularies for metadata which might work as part of existing standards, or the development of other meta-standards. At this point, though, I think it’s important to clarify whether or not biomarkers are different enough from the types of data we routinely manage and exchange that they require their own set of standards.

Sandor Szalma: To address several of your points above. Indeed, the various experimental results are routinely exchanged between organizations, but how this exchange occurs varies from organization to organization. Since pharma is now more focused on managing large amounts of parallel collaborations, managing all of these data without standards is a problem. Yes, certain organizations have taken on standards development, but data outside of clinical trials safety/efficacy and not directly involved in health care currently do not have an appropriate organization trying to standardize. So this is an opportunity. Even if, as you state, exchange standards for some of these are in place, that has not been my experience within Janssen and it seems that many people share this experience with me in other pharmas, too. It is possible that is solved, just that solution is not widely known/adopted. Part of this workstream’s task is to explore the existing standard space and perhaps find a way to bootstrap this project by simple modification of existing standards if they indeed exist or are available. We do not intend to create a new standard where there is already an existing one or where a simple modification could do the job. It is not “standards for standards’ sake” but a much more utilitarian approach–we have a business problem and we need is solved (yesterday).

As you state in your last sentence, a key first step would be to determine if biomarker data is different enough from other data we know how to manage and exchange. I’m not aware of the existence of a generic data exchange standard supporting biological assays–of which biomarkers are a special case. Am I wrong on this point? Do you know of such a standard?

Posted in Pistoia Alliance Blog.

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