Thursday, February 25, 2016

Phil's webinar on LOINC and CDISC

Today, I attended an excellent "CDISC members only Webinar" given by Phil Pochon (Covance) on LOINC and it's use in CDISC.
Phil is an early contributor to CDISC (considerably longer than I am), and very well known for the development of the CDISC Lab Standard and his contributions to SDTM.

So Phil is one of the people I highly respect.

Phil explained the concepts of LOINC very well and especially the differences with the CDISC controlled terminology for lab tests and results.

Also he answered the questions that were posed extremely  well, giving his opinion about how LOINC should be used in combination with CDISC standards (there isn't a CDISC policy on this yet).

In this blog, I want to extend on some of the questions that were posed and on which I have a different opinion (Phil knows that).

There were several questions about how to map information from local labs (such as local lab test codes) to LOINC. Phil gave some suggestions about looking at the units used, the method provided (if any), and so on.
My opinion about this is: "don't": if the lab cannot provide you the LOINC code with the test result, don't try to derive it. Even when "LBLOINC" would become "expected" in SDTM in the future, I would suggest not to try to derive it (SDTM is about captured data, not about derived data). Reason is that such a derivation may lead to disaster, also because the reviewer at the FDA cannot see whether the given LOINC code comes from the instrument that did the measurement, or was "guessed" by the person that created the SDTM files. This is a serious data quality issue.

There was a short discussion about whether labs should provide the LOINC code together with each test result for each measurement. My opinion about that is that if your lab cannot provide LOINC codes, you should not work with that lab anymore. Also, sponsors and CROs should have a statement in their data transfer agreements with labs that the latter should not only deliver "a" LOINC code with each result, but should deliver "the correct" LOINC code with each result.

Phil also answered a question about having LOINC codes specified for lab test in the protocol. He stated that this is a long-term goal. I would however state that sponsors should start doing this now. Even if not all labs can always provide what (LOINC code) is described in the protocol, giving the (expected/preferred/suggested) LOINC code in the protocol would immediately increase data quality, as the bandwith of what is finally delivered would surely become smaller. For example, for "glucose in urine", there is a multitude of lab test, ranging from quantitative to ordinal to qualitative, each with a different LOINC code. It is impossible to bring all these results to a single "standardized value" (this is required by SDTM). Providing the (expected/preferred/suggested) LOINC code in the protocol and passing this information to the labs would at least reduce the breadth of different tests that were actually done, making the mapping to SDTM considerably easier, and at the same time improving data quality considerably.

An interesting question was whether LBLOINC applies to LBORRES (original result) or to LBSTRES(C/N) (standardized result). I checked it in the SDTM and it is not specified there. It still states "Dictionary-derived LOINC code for LBTEST", which is a disaster definition as LBLOINC should be taken from the data transfer itself, and not be derived (probably leading to disaster.)
If I understood it well, Phil suggested to apply it to the "standardized" result. For example, if I obtain the glucose value in "moles/l" (e.g. LOINC code 22705-8) but standardize on "mg/dL", this would mean that I need to (automatically?) transform this LOINC code into the alternative on in "mg/dL" which is (I think) 5792-7.
In my opinion, one should not do this, but use the LOINC code that was delivered by the lab, so on the original result. Why? Let me take an example: Suppose one of the labs has delivered the value as "ordinal", so using values like +1, +2, etc.. (LOINC code 25428-4). How can I ever standardize these to a concentration? If I can, I guess this is highly arbitrary, and thus leads to another decrease in data quality. So I would propose that LBLOINC is always given as the value that is provided by the lab (so original results) and that that is clearly explained in the SDTM-IG.

Another interesting discussion was on the use of UCUM unit notation. According to Phil, most of the lab units published by the CDISC team in the past are identical with or very similar to the UCUM notation. My experience is different. What was very interesting is that Phil told that when they (the CDISC-CT team) receive a "new term request" for a lab unit, they first look into UCUM to see whether there is one there, and if so, take that one. I am very glad about that!
But Phil also told that they get many requests for new unit terms that do not fit into the UCUM system (like arbitrary units for some special tests), so that they then develop their own one.
Personally, I think they shouldn't. If a unit term is so special that it does not fit with UCUM, and also cannot be handled by so-called "UCUM annotations" (CDISC should standardize on the annotations, not on the units), then I wonder whether the requested term is good and generic enough to be standardized on at all. After all, the [UNIT] codelist is extensible.

My personal opinion is still that CDISC should stop the development of lab test (code) terminology and steadily move to LOINC completely. For example, it is my opinion that it should now already be allowed to simply put the LOINC code in LBTESTCD (maybe with an "L" in front, as test codes are still not allowed to start with a number, a rule stemming from the punchcard era...).