Does the system “body fluid” really exclude peritoneal, synovial, and pleural fluid?
Many hospitals/EHRs report certain fluid tests (e.g. nucleated cell count in a body fluid) using the same code, regardless of whether the body fluid is pleural, peritoneal, etc. They identify the type of fluid in a separate value. (This is similar to the way some report ABG and VBG values using the same codes, using a ‘specimen type’ value to distinguish between the two.)
I had always assumed the codes in the system “body fluid” represented these unspecified fluid type codes, but upon looking at any body fluid code, the part description for “body fld” states:
The LOINC "Body fld" System represents any body fluid that does not already have its own named System in LOINC, such as cochlear fluid or chyle. "Body fld" is not a high-level concept that includes all body fluids.
As both pleural and peritoneal fluid have their own LOINC system, per this definition, they are excluded from "Body fluid".
I feel that the “body fluid” system actually IS commonly being used to represent all body fluids (at least body fluids that aren’t blood or urine). The rank of the various “body fluid” labs strongly argue against these values representing things like cochlear fluid / chyle. If we shouldn’t be using body fluid codes for unspecified fluids, which codes should we use?
I appreciate your asking this. I hadn’t realized there was an “exclusion” statement in the User’s Guide, or we would have had a conversation earlier. LOINC development keeps in mind there are multiple ways to build a database and express specimens. I agree that sites can built one body fluid type data element for an observation, and have an accompanying specimen type field that delineates which specimen was used. A site that had a more granular build, with multiple LIS elements for different specimens of the same analyte, would be using the specific pericardial, peritoneal system LOINCs. Whenever we provided LOINC services for a client, we would explain that we’d never ask them to rebuild their database in order to map to LOINC. There’s something there for everyone.
In the past three years, there’s been more emphasis for the IVD vendors to provide the LOINCs, which is “upstream” from the healthcare/hospital provider systems and their LIS. I’ll bring the Body Fluid statement in the User’s Guide up to Regenstrief and Lab LOINC committee for clarification.
The Lab LOINC committee met this morning (9/17) and agreed there needed to be editing to the Part Description of Body Fluid, and to the User’s Guide. You’ll find these edits in the anticipated December release 2020. You may proceed with using body fluid LOINC codes, and are requested to provide supporting information of the actual specimen, either in an accompanying OBX of the Specimen Source, or in the SPM segment of the HL7 message. Most LIS’s we’ve worked with have the additional result field stating the specimen (going into HL7 OBX from there).
Question related to this topic: Some labs have tests dedicated to fluid coming from cysts: pancreatic cyst, ovarian cyst, or unspecified cyst. For instance carcinoembryonic antigen on fluid from ovarian kyst.
Is there any value more specific than “Body fluid” for representing this kind of specimen?
Hello Francois! LOINC’s intent is not to be the sole source of all possible information, including source and methodology. It is intended to work alongside other standards.
Two thoughts from the specimen arena: 1. A lot of work has been performed on a Specimen Cross Mapping table through the American Public Health Laboratories’ Lab Community of Practice workgroup. This table incorporates other portions of the HL7 message format to provide additional information. This is augmentary to the LOINC specimen attribute of Body Fluid. You can find some information on it at https://www.cdc.gov/labhit/paper/2016-standardization-of-laboratory-test-coding---phi-conference.pdf If you are interested in seeing the latest release of the Specimen CMT, I will locate that for you.
The LOINC term 31208-2 Specimen source identified is the most commonly used LOINC term. This demonstrates laboratories using one additional field to portray more information about the specimen used in this assay.
If your site is not using HL7 or a laboratory information system, the above options may not help record a specimen such as “fluid from an ovarian cyst”.
Hello Francois! LOINC’s intent is not to be the sole source of all possible information, including source and methodology. It is intended to work alongside other standards.
Two thoughts from the specimen arena: 1. A lot of work has been performed on a Specimen Cross Mapping table through the American Public Health Laboratories’ Lab Community of Practice workgroup. This table incorporates other portions of the HL7 message format to provide additional information. This is augmentary to the LOINC specimen attribute of Body Fluid. You can find some information on it at https://www.cdc.gov/labhit/paper/2016-standardization-of-laboratory-test-coding---phi-conference.pdf If you are interested in seeing the latest release of the Specimen CMT, I will locate that for you.
The LOINC term 31208-2 Specimen source identified is the most commonly used LOINC term. This demonstrates laboratories using one additional field to portray more information about the specimen used in this assay.
If your site is not using HL7 or a laboratory information system, the above options may not help record a specimen such as “fluid from an ovarian cyst”.
Thank you Pam, my best wishes to you for this new year.
I’m fully aware of the articulation of LOINC with HL7 standards V2, CDA and FHIR, and have a precise view of the SPM segment, of the former specimen CMET in V3, and of the Specimen resource in FHIR, being the initiator of the SpecimenDefinition resource. I’ve set in place the ongoing French translation of LOINC 10 years ago, and collaborated on several occasions with Daniel Vreeman in the past.
In my example of a European lab performing CEA on various body fluids, the ultimate goal is to have unambiguous order messages as well as CDA lab reports. The lab would like to have, beside the ‘CEA on Body fluid’ LOINC code (12515-3), another code with a meaning ‘CEA on a body fluid obtained by puncture from a cyst or an organ’. That would require the presence of such a SYSTEM, somewhat less generic than Body fluid.
Hence my question: Is there, among the more than 2,800 existing SYSTEM parts, a value approaching what I’m looking for.
In any case, I’m very much interested in the latest release of the CMT. Could you please point me to it?
We have a colleague and friend in common! Riki Merrick is the lead of our Lab Community of Practice, and I understand you are her IHE PaLM co-chair. She started emailing responses with you, but for the sake of the Forum, I’ll insert a link to the Specimen Cross Mapping table and a note of current development.
The latest version of the specimenCMT is on Manjula's (CDC) computer in a dB format - we are working through the good old spreadsheet that has outstanding questions on the LabMCoP calls on Thursdays, COVID permitting. That spreadsheet is on the APHL sharepoint site:
This concept can feed SPM-4, however it would make sense to me to have this specimen type also coded in the SYSTEM axis of LOINC, so as to be able to create LOINC terms for tests performed on this kind of specimen, more precise than Body fluid.
In addition to “Body fld”, we also have a System “Asp”, which represents the fluid withdrawn during an aspiration procedure from an abnormal collection of fluid, such as from an abscess or cyst. “Asp” is used for abnormal fluid collections that are aspirated, while “Body fld” is used for named body fluids, such as synovial fluid or peritoneal fluid, that are not inherently pathologic.
I have a related question. Since the specimen type of Body Fluid has been relaxed to include named body fluids, can I apply this same logic to Tissue?
I’m currently working on a test from a reference lab, else I’d request a new XXX specimen LOINC. They send specimen in a separate observation. The reference lab provides no LOINCs for this test.
Accepted specimens for this test in 2015 when we assigned a LOINC in our system were blood, bone marrow, or extracted RNA. We took some liberty with “tissue” and assigned a LOINC of Bld/Tiss, reasoning that extracted RNA and bone marrow are both tissue – and it would be silly to ask for Bld/Bone mar/Ext RNA.
Now the reference lab is removing extracted RNA as an acceptable specimen, leaving just Bld/Bone mar. Since the LOINC documentation still says we can’t include named systems in a broader category, our fudged “tissue” system is now too much of a stretch.
So, do I have to remove the LOINC altogether, or can I use a Bld/Tiss LOINC when the accepted specimen is Bld/Bone mar?
…or will you allow me to request a new LOINC of XXX specimen for another lab’s test?
…been reading 2.73 documentation. It seems you’re being more strict with xxx specimen than I have been.
I find hope for my sanity in section 3.9.4.1. Does this section mean I can use a Bld/Tiss LOINC for Bld/Bone mar in a genetic test and that we LOINCed the test correctly the first time? If it helps, the two LOINCs we’ve assigned for the observations are 70291-0 and 72210-8.
3.9.4.1 Specimens in molecular genetics
Blood is the most common specimen for molecular pathology studies. Leukocytes, bone marrow, tumors, products of
conception and forensic specimens also contain DNA and are important specimens. The System (specimen) used in
the LOINC name for genetic testing will usually be Bld/Tiss since the distinction between these two specimens is
rarely important to the result of a molecular pathology test. We have split this further to accommodate fetal
specimens (Tiss^fetus). Other specimens include amniotic fluid, CVS, bone marrow, fixed tissue, and CSF.
The breakout of pericardial, synovial, peritoneal fluids from a generic body fluid has always been intended as offerings to help match with a local LIS set up. Some sites use the same result field for all body fluids; they would be using the LOINC for that analyte with an XXX system. The premise has been that if lumping all body fluid types into one result field, there would be a separate result field identifying the Fluid Type or Specimen Type. Other sites have implemented separate laboratory result fields for the different body fluid types; they would be using the specific system LOINCs. The separate field for system wouldn’t be necessary in the latter.
As far as the question of you submitting for another lab…the preference is definitely for the laboratory performing the assay to submit for a new LOINC term. They have more performance information for Regenstrief ‘behind the scenes’.
When discussing molecular genetics and specimens, I include a stance of perspective: are we speaking of the patient or possibly a tumor or (as the User’s Guide denotes) a fetus.
For the specific LOINCs you’ve provided - have you read both the term and part descriptions on the Details page? Does that change any part of your question?
Without knowing any more of the assay/reference lab/etc I dare not speculate on correctness. I will state the chosen LOINCs follow the specimen identification just as 3.9.4.1 denotes.
Yes, 3M includes Bone Marrow in with Tissue on molecular assays.
Earlier in the two+ decades of performing this work, we wouldn’t ask someone to build their LIS differently. The LOINC database had options to cover different builds. With the hindsight now comes hints to end users for a more thoughtful way to build the LIS for metadata use.
Yes, 3M includes Bone Marrow in with Tissue on molecular assays.
Earlier in the two+ decades of performing this work, we wouldn’t ask someone to build their LIS differently. The LOINC database had options to cover different builds. With the hindsight now comes hints to end users for a more thoughtful way to build the LIS for metadata use.
Bld/Tiss LOINCs can be used for Bld/Marrow/Fluids or other “tissue” types when a single lab result or order is built and not separate results for each type of specimen or source.
The challenge with building laboratory tests (orders or results) within a LIS or EHR is there is some practicality with builds which unfortunately means build patterns are not the same for every lab test. Where a single order or result is used across multiple specimens and/or sources and a single orderable and/or resultable can be built, then these LOINCs can be used to encode them.
This pattern is fairly common in microbiology, pathology, genomics and molecular testing to name a few. Let’s say you have a “Wound Culture.” One can build precoordinated terms in the EHR and LIS with every single specimen site (each anatomic site that can be swabbed for said culture) that can have a wound culture. There would be 250+ terms and would require as many specific LOINCs. As you may see such “combinatorial explosion” as terminologists call it, would not be very practical for lab builds and maintenance, nor LOINC codes and maintenance. Furthermore, clinicians already are burdened and I’ve heard some complain that searching for test orders or results is already too long or requires too many clicks.
Thus the more practical approach of having a single “specimen-less” lab order and results is taken with builds. An Ask at Order Entry (AOE) question of “Specimen Source?” is often included in the requirements for the order so the person collecting the specimen can respond. As Pam indicated, this is the most common LOINC as it’s utilized in so many panel orders as an AOE, but it is also reported as a test result with these panels too.
You see this pattern repeat for GC Culture where the source can be male or female genitalia, other types of cultures, many genetics tests, especially for cancer markers/genes where tissue may be submitted from many different “sources,” etc. In fact, with genetic testing, there are many more “generic” LOINCs such as “gene mutations found” that involve more short answer responses. This approach has been taken over precoordinated terms with every combination of gene with “mutations found,” which would lead to combinatorial explosion.
