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Does your assay happen to test for the galactomannan antigen, that is common across several fungi genus. Here’s the RELMA definition : Galactomannan is a polysaccharide cell wall component in certain species of fungi. The assay is used for the early diagnosis of invasive aspergillosis in immunocompromised patients undergoing hematopoietic stem cell transplantation and in patients with hematological malignancy. Other fungal sources galactomannan include Alternaria, Penicillium and Paecilomyces species, but these fungi are rarely seen in invasive disease.
This is the analyte I use in client mappings; there are several serum specimens available.
I was deferring to the HL7 CDA RMIM to define if there should be alphabetic strings or numeric code, pertaining to LOINC class. This was based on a premise that the reporting is taking place on assays with LOINC terms attached. It’s a “drill down” from the involved LOINC terms for each patient to have a table pull of the associated CLASS field in the LOINC database.
As for the second question, each LOINC term only has one class assigned it in the database. In our experience the LOINC-assigned class serves as a baseline of organization, but it does not mimic the real world laboratory workstations/departments (which I am aligning with the “lab specialty” term being used). For example, the PULM class blood gas measurements are often performed in a medical laboratory setting, rather than the pulmonary department. However, a medical laboratory will provide a variety of assays (described in their electronic Directory of Services [eDOS]) and these cross many LOINC classes.
Perhaps I am not understanding the context of the word ‘CLASS’ in the original question.
Not being familiar with Italian laws, but realizing HL7 CDA has the RMIM to identify source material; wouldn’t the HL7 CDA RMIM prescribe the format definition for the related lab specialty class? It seems the alpha character format of the CLASS field within the LOINC database (DRUGDOSE, DRUG/TOX, MOLPATH.MUT, etc) that is easily retrievable by the computer.
Thanks for helping educate me,
Your question brought three scenarios to mind. Two of the scenarios have to do with answers encoded to SNOMED CT. Any of the microbiology LOINC terms with PRID property, such as 81655-3 Respiratory pathogens DNA and RNA identified in Respiratory specimen by NAA with probe detection, have an example answer lists containing types of organisms found, and each of them would have a SNOMED CT term. Example answers for 81655-3 are No organism(s) detected, Influenza A (H3N2), Adenovirus, Parechovirus, and much more. If more than one organism’s DNA is found, there are more than one SNOMED CT term in the answer.
The second scenario is of post coordination of phrased answers. LOINC term 36903-3 is testing for Chlamydia trachomatis & Neisseria gonorrhoeae DNA; example answers here are phrases: Chlamydia trachomatis detected; Chlamydia trachomatis not detected. Multiple SNOMED CT terms would need to be used for the organism and the qualifier.
The third scenario pertains to the composition of the LOINC Parts to a single LOINC term. Translating each LOINC Part to its SNOMED CT counterpart brings up a post coordinated expression, of which there’s been two subset file releases for public review in recent years. More explanation of post coordinated expressions can be found at https://confluence.ihtsdotools.org/display/DOCSTART/7.+SNOMED+CT+Expressions
With an abundance of possibilities, I’m not sure there’s an easy answer to your second question “what does that mean about the result.” Clinically, I wouldn’t be able to speculate. Theoretically in format, I would say it means the result has complexity.
Have a great day, Hope this helps
While not being certain what you’re asking your database/use case to achieve, I would recommend you let the loinc.csv class (ALLERGY, CHEM, etc) and classtype field starnd for themselves (1,2,3,4). Are you able to link the loinc table to your database fields and cross-check that way?
Let me know what outcome you’re trying to derive, and I’ll try to help further.
All the best,
Hope all is well with you and yours. From the LOINC terms referenced, you have a molecular genetic assay for F10 gene targeted mutation analysis. I checked https://loinc.org/submissions/queue/ and didn’t find F10 or Factor X in the search. A literature reference search found https://www.ncbi.nlm.nih.gov/gene/2159 ; and http://www.omim.org/entry/613872 .
It seems totally suited for your next submission!
All the best,
Pam Banning2018-06-22 at 13:01 in reply to: use of 'sequencing' method for molecular genetic test #22478
It’s been my experience if you propose the specific genes where sequencing is being offered, Regenstrief does consider them. In June 2018 LOINC User’s Manual, section 220.127.116.11 calls out that sequencing as a particular method that will be called out. I know there are people within LabCorp, Quest Diagnostics, Mayo Medical Labs, and ARUP responsible for submissions from their test compendiums. We just never know where in their queues the sequencing assays reside. If you need any assistance in getting started on a submission, I’m happy to help direct.
Your test message came through; all is well At first glance, there is one panel established, 53775-3, with three required elements (53776-1 is an interpretation element of IgM and total). Might it be suitable for your use?
I’m unaware of any table Regenstrief provides in this manner. The UCUM documents are descriptions and instructions on translation local unit displays to the standard UCUM format. There are example UCUM tied with terms in RELMA (and therefore extrapolation is possible). In early, early LOINC days, 3M had internally used synonyms of properties to our units of measure domain. Everyone’s foundation has matured with time, and toolsets along with them.
Sorry to not help you more specifically.
email@example.com at 21:49 in reply to: Choosing between using on outside vendor to do mapping versus doing it yourself #18592
Once you have a good handle on the actual scope (number of terms; orders and results?; departments, etc), the benefactors internally (who will become your enablers if there are barriers), the projects competing for your resources and the desired timeline, it’s probably a good time to start a vendor search. Be sure and know your company’s contracting process, because that time needs to be included, as well as search time. 3M Health Information has stored on the Documents section of the LOINC website a sample project plan (internal or external). I have recently updated it, if you’d like a copy email me.
Hope this helps,
[Moderator’s note: the file to which Pam refers is available for download.]
- This reply was modified 1 year ago by Tim Briscoe. Reason: Added link to download
Hello, please review the LOINC User’s Guide section 2.3 for the formal description. I like to think of this attribute as keeping numeric values in distinct aggregates (apples and apples vs apples and oranges). A value of 25 could be 25 mg/dL, 25 mmol/L, 25 IU/L; these are all very different in concentration basis. Having distinct LOINC codes allows the computers to recognize these are not to be placed on the same reference line, nor trend them together.
Hope this helps!
- This reply was modified 1 year ago by Pam Banning. Reason: grammar
Use the first tab, labeled Search, instead of the second tab, Mapping Screen. You’ll have everything you need. If you need the style of the mapping search window, you can just type over the LMOF without incident.
Have a happy and safe 4th of July.
I don’t know how I missed this, very sorry for the delay. Regenstrief has asked for feedback on a particular LOINC Order Panel through the Contact Us page under submissions. I have already turned in feedback on Electrolytes and Arterial Blood gases. They have not been addressed as yet.
3M Health Information Systems
Hello, 3M staffers found this for your consideration:
From the <span style=”text-decoration: underline;”>Manual of Clinical Microbiology, 8<sup>th</sup> Edition, 2003 pg. 1158-1159 </span>:
“Methods that are commonly used to test rapidly growing aerobic and facultative anaerobic bacteria are, for a variety of reasons, unsuitable for testing most mycobacterial species. For example, the conventional disk diffusion method is not suitable for testing slowly growing mycobacteria because the drug diffuses throughout the medium before growth of the mycobacteria is significantly affected. The methods generally accepted for determining the antimicrobial susceptibility of mycobacteria are based on the growth of the microorganisms on solid or in liquid medium containing a specified concentration of a single drug.”
“Based on the current NCCLS guidelines, a rapid susceptibility testing method should be used in conjunction with rapid methods of primary culture and identification to allow the earliest possible detection of resistance.”
Sorry for the ancient reference but it should suffice because organism growth rates still determine the testing method. Generally, all susceptibility methods are used based on CLSI (formerly NCCLS) guidelines to which the public and IHTSDO do not have access. They are a purchased set of guidelines. The Mayo reference below is the best I can find as it actually references the CLSI guidelines.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197070/ Mtb testing, 2011 reference
There are rapid methods for susceptibility testing on Mtbc (a slow-growing organism) now also based on other reading so if we ever get AFB drugs for mapping, it behooves us to ask the method of testing.
Pam & Elva
We use Annotation Comment 48767-8 for such a comment. The definition reads “This is an observation code indicating that a particular observation represents a free text annotation comment that can be appended to some other observation such as a lab result.”
We like this better than the Service Comment series, because they can be used for a different intent in the receiving system than in your sending system, and the note could get misinterpreted. Both sides using 48767-8 would understand that this is additional information.
Hope this helps,
Pam Banning, firstname.lastname@example.org