2.5 System/sample type

System (sample) type is the fourth part of the fully specified test name. It consists of two subparts; the first part names the System, the optional second part, delimited with a “^”, indicates the Super System source of the sample if it is not the patient, e.g., fetus, blood product unit, donor, etc.

We define different tests for the combination of Component (Analyte) and type of System (sample) that are commonly reported. In practice, laboratories include a relatively small range of sample types in their test names. Chemical tests commonly distinguish between serum, urine, blood, and cerebrospinal fluid. Microbiology cultures tend to distinguish between greater numbers of sources.

Example Systems are listed in Table 11. The complete set of active LOINC Systems is available in the LOINC Part File and can be identified because they contain a PartTypeName of SYSTEM.

Laboratories commonly build separate assays in their laboratory information systems (LIS’s) for serum, plasma, blood, urine, and cerebrospinal fluid. In addition, they may have a single test that includes all other body fluid specimens. The LOINC System Body fld is intended to reflect this distinction and represents body fluids other than serum, plasma, blood, urine, and cerebrospinal fluid. When LOINC terms with the System Body Fld are used, information about the specific specimen source or body fluid type should also be provided. Keep in mind that in many cases for tests that are run on pleural, peritoneal, synovial, and other types of fluid, LOINC has specific terms to represent these tests, and we encourage you to use the specific terms rather than the Body fld terms when possible.

We use XXX in the System to identify a material that is unknown or not specified — it could be solid or fluid, for example. XXX is also used in the System when the specimen or material is known but recorded elsewhere in the HL7/ASTM message. Yet, using XXX as a System can be problematic (see also Section 2.5.1 – Special issues related to XXX as a System below). XXX and Body fld are different in that Body fld represents a biologic fluid (other than serum, plasma, blood, urine, and cerebrospinal fluid, as stated above), whereas XXX can represent any material, biologic or nonbiologic, solid or fluid.

For many types of tests, the distinction between plasma and serum is irrelevant. When testing on serum or plasma is clinically equivalent, the System should be recorded as Ser/Plas, meaning “either Serum or Plasma”. Note that the use of a LOINC code with Ser/Plas as the System to report the result of a specific manufacturer’s assay does not imply that the given assay is approved for use with both serum and plasma specimens; it simply means that the results obtained from testing serum and plasma are clinically equivalent, independent of which assay was used. Sometimes the test can only be run on either plasma or serum; the Component will then be associated with either Ser or Plas in one observation. If the test can be run on either but the results are clinically different and standardized (a very rare circumstance), two separate tests will be defined in our file, one with a System Plas and one with a System Ser. The current LOINC database includes some Ser tests and some Plas tests that should really be Ser/Plas. As we determine that a Ser or Plas test really should have been designated Ser/Plas, we will change the designation.

As with Ser and Plas, when testing on various specimens is clinically equivalent and the system for the existing test(s) includes only one or a few of those systems, we will review such tests upon request and update them as appropriate to include the additional system(s). One such example is toxicology testing, in which at least a subset of tests (e.g., confirmatory) can be run on instruments that accept either Ser, Plas or Bld as the specimen, so we may update existing Ser/Plas or Bld terms to have the System Ser/Plas/Bld as appropriate.

If the test is run on a combination of specimens (such as a ratio of substance found in CSF and plasma), the sample types are joined with a “+”, for example: Plas+CSF, Ser+CSF, or Isolate+Ser.

Details about the exact source and collection method (e.g., blood drawn from the right arm and maintained on ice) are not a proper part of the test name and are reported in other parts of the message. For example, the SPM specimen segment of an HL7 message can be used to convey detailed information regarding the type of specimen, where and how it was collected, who collected it, and some basic characteristics of the specimen. Earlier versions of HL7 used OBR-17 as a field to report specimen source.

Table 11: Example Laboratory System/sample Types

These abbreviations are used in the laboratory LOINC codes. Systems in clinical LOINC terms are spelled out in full and should be easily understood.

2.5.1 Special issues related to XXX as a System

Increasingly we get requests, often from the public health context, for tests with XXX as the specimen. XXX is a valid LOINC specimen, and often needed in many cases. However, LOINC typically needs a term with a more specific specimen instead of, or in addition to the XXX. Recall that XXX can be used to represent any kind of specimen (insects, road kill, and ingested food) when the material is unknown or specified elsewhere in the HL7/ASTM message. LOINC already has some general specimen terms that are broad but more constrained than XXX, for example, Bld/Tiss and Body fld.

Use of XXX for the specimen can create problems. Firstly, the reference ranges for measures on a continuous scale change with specimen differences, and most systems depend upon the test code to get to the reference ranges. So using the same code for very different specimens can break the range checking in many systems. Of course the XXX specimen type is most commonly requested for microbiology tests used to identify micro-organisms by culture, DNA/RNA or specific antigens. In this case the nature of the specimen might not change the clinical implication for some organisms; we suspect that anthrax found anywhere in the body has the same implication. But it does make a big difference for some organisms that are natural inhabitants of the skin or digestive system, but not of the blood.

Thirdly, if there is no hint of the specimen in the test name, clinicians will have a more difficult time ordering common microbiology tests. They won’t be able to order urine culture and blood culture each with a single click, and laboratories will have a more difficult time managing these orders. This is especially true given the current state of many HL7 messages that only rarely use codes in the specimen field. (Granted, there is hope for the future.) Fourthly, and most importantly, there is the issue of approved use. Package inserts are very specific and limiting about the specimens for which the test kit is approved. We have had a recent request for a test with specimen of XXX whose package insert allowed its use only on Saliva. What do we do? Referral laboratories tend to define tests for class of specimens approved for use on the instruments/test kits they employ. We have received requests for terms with XXX, but the test is really only used for specimens from body parts that can “catch” STD.

So, the bottom line is that we won’t accept requests for tests with XXX specimens without a narrative description of the most common specimen and some sense of the range of specimens for which it is used. We will likely argue for either adding a distinct code for the dominantly common specimen (e.g. Stool for Entamoeba histolytica) or the specimen prescribed by the package insert, or for entertaining a new specimen code broader than those now available but narrower than XXX to accommodate a particular need, e.g. sterile body fluid, or Genital/anal/throat (for STD specimens). This will, of course, take time and discussion.

2.5.2 Super System (2nd subpart)

The second subpart of the System identifies a “super-system” when the source of the specimen is someone or something other than the patient and the result needs to be distinguished from the patient’s results because they will be stored together in the patient’s record. Examples of Super Systems include a blood product unit (BPU), a bone marrow donor, or a fetus. The Super System is also used when the clinical finding (history, physical) is about someone other than the patient and needs to be distinguished from the patient’s findings, for example, a history of diseases in a family member recorded in the patient’s chart. When the Super System is not included in a name, “patient” is the assumed default value.

For instance, an example of representing a coagulation study that uses measures on both patient and a control might be:

Coagulation reptilase induced:Time:Pt:PPP:Qn:Coag

Coagulation reptilase induced:Time:Pt:PPP^control:Qn:Coag

Blood banks often report red blood cell antigens for the patient and for each blood product pack assigned to that patient. So we have:

A Ag:PrThr:Pt:RBC:Ord:

A Ag:PrThr:Pt:RBC^BPU:Ord: