Saturday, June 6, 2015

FDA starts embracing LOINC

Two friendly colleagues from pharma companies pointed me to very recent FDA publications about LOINC, the worldwide coding system for laboratory test codes in healthcare.
The first is the "Study Standards Resources" mentioning LOINC as a standard used by the FDA (better "was", as the mentioning was removed a few days later). The second, a few days later, is however much more important. It is an article in the Federal Register titled "Electronic Study Data Submissions; Data Standards; Support for the Logical Observation Identifiers names and codes".

You might want to read it before continueing reading this blog entry.

I have been "fighting" several years now for having LOINC recognized as the identifying coding system for lab tests in SDTM submissions. CDISC however developed its own coding system for lab tests, which is inconsistent and does not allow to uniquely identify tests. My formal request to put the further development of CDISC-CT-Lab codes (LBTESTCD/LBTEST) onto hold, and gradually move to LOINC, did however not make me many friends in the CDISC Controlled TerminologyTeam, at the contrary.

In their newest Federal Register publication, the FDA requests comments on their initiative, especially about "the Agency recognizes that the high level of granularity inherent in LOINC has presented coding challenges and that these challenges have led to the creation of subsets of LOINC to help facilitate coding" with the specific question:

"Should FDA identify a LOINC subset for its use case?"

I think this is a good idea. LOINC has over 72,000 test codes. LOINC itself already published a "top 2000+ LOINC codes", i.e. a list of the 2,000 most used codes. Also in Austria, where the use of LOINC coding is mandatory for use in the national electronic health record system (ELGA), a subset has been published which should preferentially be used. And then we have the very old "LOINC codes for common CDISC tests", which has unfortunately not been maintained in the last years.

Important is that such a subset needs to be a "recommendation", otherwise people will start "pushing" tests with codes that are not into the list, into one of the test codes that is in the list, thus essentially falsifying the information. If the FDA would recommend the 2000+ list, or would pick up the old CDISC list again (and modernize it), this would be a very wise step, as e.g. the 2000+ list covers  98% of all the tests done in hospitals (and probably also in research).

There is however no technical limitation to allowing the full LOINC list of test codes, as there are now RESTful Web Services available for looking up test codes and their meaning. You can find the complete list here.The National Library of Medicine even has a  LOINC web service with very detailed information about many of the test which is queried using the LOINC code. This web service, and other CDISC-CT web services, have already been implemented in the "Smart Dataset-XML Viewer", a software tool for inspecting SDTM submissions in Dataset-XML format. They can also be implemented easily in any modern software tool, including the ones used by the FDA.

The FDA starting embracing LOINC (does CDISC soon follow?) is a major step forward. I have been "fighting" several years for this, so you can imagine that my weekend is now already perfect ...


  1. This is really good news!

    Concerning the LOINC subset, I didn't get the idea. Every LOINC code is curated by a team of experts, so there seems to be a need for every entry. Why a limitation? Will somebody try to learn all the codes so life would be easier with 2000? Should ICD-10 also be limited to the 2000 most popular diseases?

  2. I mostly agree with you...
    I presume that at the FDA, they are afraight that reviewers need to know/understand all >72,000 codes. Using things like web services (or an FDA-own database) there is however no such need. Question is whether the FDA reviewers all (will) have the technical means to have fast LOINC-lookups.
    So their request for a subset is more on the psychological level I think, i.e. not fraightening their own reviewers... So if we can get them "over the bridge" by using a subset, and then convince them that the whole LOINC can be used, this would make things go forward.
    Subsets only make sense in (hospital) labs when mapping local codes to LOINC codes.