LOINC Property - Likelihood and associated LOINC terms

2025-Sep-08

Hi all,

We are looking for feedback related to this LOINC part and associated LOINC terms.

RELMA defines this property as following: “Risk is the probability (chance) of a certain event happening, such as developing a particular disease or inheriting a specific mutation. Risk can be represented as a fraction or a percent. For example, a 1 in 1,000 chance can be represented as 1/1,000 or 0.1%.”

Example LOINC terms that are using this property:

LOINC_NUM	LONG_COMMON_NAME	COMPONENT	PROPERTY	TIME_ASPCT	SYSTEM	SCALE_TYP	METHOD_TYP
43995-0	Trisomy 21 risk [Likelihood] in Fetus	Trisomy 21 risk	Likelihood	Pt	^Fetus	Qn
49090-4	Fetal Trisomy 21 risk [Likelihood] Based on maternal age	Trisomy 21 risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age
73970-6	Fetal Trisomy 21 risk [Likelihood] based on Plasma cell-free DNA by Dosage of chromosome-specific cfDNA	Trisomy 21 risk	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA
75561-1	Fetal Trisomy 21 risk [Likelihood] based on Plasma cell-free+WBC DNA by Dosage of chromosome-specific cfDNA	Trisomy 21 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA
75563-7	Fetal Trisomy 21 risk [Likelihood] based on Plasma cell-free+WBC DNA by Dosage of chromosome-specific cfDNA Narrative	Trisomy 21 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA

For creating post coordinated expression for the examples noted above, our proposal is to:

Create new component concept as following:
7894007 | Karyotype morphology (morphologic abnormality)
78989007 | Trisomy (morphologic abnormality)
NEW | Trisomy 21 (morphologic abnormality)
Create a new property as following
New | Likelihood (property) (qualifier value)

Other attributes (including method) will be mapped as specified in the LOINC terms.

Best Regards,

Farzaneh

CC: Suzanne Santamaria

Comments

Farzaneh Ashrafi

Aug 21, 2017

Summary of discussions in OIMP call, August 2017 (To be continued in the next OIMP call):

Likelihood as a property is similar to presence.

Can we consider it as "level of risk" (Also see: 30207005 | Risk of (contextual qualifier) (qualifier value))? No: although many of the LOINC terms are related to risk, there are a few (e.g. Sex) that don't indicate "risk". They are related to a prognosis.

A side note: Swapna noted that use of prior in some of the LOINC components is to differentiate the method (maternal age or population risk vs. a quantitative technique). The following two terms refer to the same component, but the method id different:

75568-6	Fetal Monosomy X prior risk [Likelihood] Based on maternal age Narrative	Monosomy X prior risk	Likelihood	Pt	^Fetus	Nar	Based on maternal age
75569-4	Fetal Monosomy X risk [Likelihood] based on Plasma cell-free+WBC DNA by Dosage of chromosome-specific cfDNA Narrative	Monosomy X risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA

(edited)

Jim Case

Mar 1, 2018

I do not agree that likelihood is the same as presence. Presence is a binary construct (there or not there) whereas likelihood is the probability that something will be there. Likelihood is a potential (outcome of a probability model) as opposed to an absolute. Even with a high risk, there is still a chance that the manifestation does not occur.

One can generate a likelihood from a large set of presence absence occurrences, but that would be the only relationship between them.

(edited)

Farzaneh Ashrafi

Oct 13, 2017

List of LOINC terms:

LOINC_NUM	COMPONENT	PROPERTY	TIME_ASPCT	SYSTEM	SCALE_TYP	METHOD_TYP	CLASS
79423-0	Cardiovascular disease 10Y risk	Likelihood	Pt	^Patient	Qn	ACC-AHA Pooled Cohort.Goff 2013	CARD.RISK
85624-5	Kidney failure 2Y risk	Likelihood	Pt	^Patient	Qn	KFRE	CHEM
85625-2	Kidney failure 5Y risk	Likelihood	Pt	^Patient	Qn	KFRE	CHEM
48803-1	Neural tube defect risk	Likelihood	Pt	^Fetus	Qn		CHEM
49091-2	Neural tube defect risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	CHEM
49838-6	Neural tube defect risk	Likelihood	Pt	^Population	Qn		CHEM
48671-2	Prostate cancer risk	Likelihood	Pt	^Patient	Qn	Estimated	CHEM
58769-1	Trisomy 13 risk	Likelihood	Pt	^Fetus	Qn		CHEM
43994-3	Trisomy 18 risk	Likelihood	Pt	^Fetus	Qn		CHEM
47223-3	Trisomy 18 risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	CHEM
67816-9	Trisomy 18+Trisomy 13 risk	Likelihood	Pt	^Fetus	Qn		CHEM
43995-0	Trisomy 21 risk	Likelihood	Pt	^Fetus	Qn		CHEM
49090-4	Trisomy 21 risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	CHEM
47222-5	Trisomy 21 risk based on maternal age + Alpha-1-Fetoprotein + Choriogonadotropin + Estriol.unconjugated	Likelihood	Pt	^Fetus	Qn		CHEM
49030-0	Trisomy 21 risk based on maternal age + Pregnancy associated plasma protein A + Choriogonadotropin + Nuchal translucency	Likelihood	Pt	^Fetus	Qn		CHEM
49059-9	Trisomy 21+Trisomy 18 risk	Likelihood	Pt	^Fetus	Qn		CHEM
77351-5	Probability of suspected pulmonary embolism prior to imaging	Likelihood	Pt	^Patient	Ord		H&P.HX
75586-8	Angelman syndrome prior risk	Likelihood	Pt	^Fetus	Qn	Based on general population risk	MOLPATH
75587-6	Angelman syndrome prior risk	Likelihood	Pt	^Fetus	Nar	Based on general population risk	MOLPATH
75588-4	Angelman syndrome risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH
75589-2	Angelman syndrome risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH
73821-1	Chromosome X & Y aneuploidy risk	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH
75566-0	Monosomy X prior risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	MOLPATH
75568-6	Monosomy X prior risk	Likelihood	Pt	^Fetus	Nar	Based on maternal age	MOLPATH
75567-8	Monosomy X risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH
75569-4	Monosomy X risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH
75668-4	Sex	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH
75598-3	1p36 deletion prior risk	Likelihood	Pt	^Fetus	Qn	Based on general population risk	MOLPATH.DEL
75599-1	1p36 deletion prior risk	Likelihood	Pt	^Fetus	Nar	Based on general population risk	MOLPATH.DEL
75600-7	1p36 deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75601-5	1p36 deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75574-4	22q11.2 deletion prior risk	Likelihood	Pt	^Fetus	Qn	Based on general population risk	MOLPATH.DEL
75575-1	22q11.2 deletion prior risk	Likelihood	Pt	^Fetus	Nar	Based on general population risk	MOLPATH.DEL
75576-9	22q11.2 deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75577-7	22q11.2 deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75592-6	5p deletion prior risk	Likelihood	Pt	^Fetus	Qn	Based on general population risk	MOLPATH.DEL
75593-4	5p deletion prior risk	Likelihood	Pt	^Fetus	Nar	Based on general population risk	MOLPATH.DEL
75594-2	5p deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75595-9	5p deletion risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75580-1	Prader-Willi syndrome prior risk	Likelihood	Pt	^Fetus	Qn	Based on general population risk	MOLPATH.DEL
75581-9	Prader-Willi syndrome prior risk	Likelihood	Pt	^Fetus	Nar	Based on general population risk	MOLPATH.DEL
75582-7	Prader-Willi syndrome risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75583-5	Prader-Willi syndrome risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.DEL
75546-2	Trisomy 13 prior risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	MOLPATH.TRISOMY
75550-4	Trisomy 13 prior risk	Likelihood	Pt	^Fetus	Nar	Based on maternal age	MOLPATH.TRISOMY
73969-8	Trisomy 13 risk	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75548-8	Trisomy 13 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75551-2	Trisomy 13 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75554-6	Trisomy 18 prior risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	MOLPATH.TRISOMY
75556-1	Trisomy 18 prior risk	Likelihood	Pt	^Fetus	Nar	Based on maternal age	MOLPATH.TRISOMY
73968-0	Trisomy 18 risk	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75555-3	Trisomy 18 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75557-9	Trisomy 18 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75562-9	Trisomy 21 prior risk	Likelihood	Pt	^Fetus	Nar	Based on maternal age	MOLPATH.TRISOMY
75560-3	Trisomy 21 prior risk	Likelihood	Pt	^Fetus	Qn	Based on maternal age	MOLPATH.TRISOMY
73970-6	Trisomy 21 risk	Likelihood	Pt	Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75563-7	Trisomy 21 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Nar	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY
75561-1	Trisomy 21 risk	Likelihood	Pt	WBC.DNA+Plas.cfDNA	Qn	Dosage of chromosome specific cf DNA	MOLPATH.TRISOMY

Farzaneh Ashrafi

Oct 17, 2017

OIMP meeting in Bratislava:

Likelihood as a new property:
- Likelihood and relationship to Presence
- - p=1 → Present, p=0 → Absent
- Likelihood and relationship to dispositions
- - p>0 → there is a (pre-)dispostion to X (?)
Probability of Disease rather or karyotypic morphologic abnormality?
Modelling:
- | Observable | :
- - | Property type | = | Likelihood |, // Likelihood has a precise definition in statistics!
  - | Inheres in | = | Fetus |,
  - Technique | = | estimation of.. |
  - | Component| = | 737542000 | Trisomy 21 (morphologic abnormality) |
  - Or
- - | Towards | = | 41040004 | Complete trisomy 21 syndrome (disorder) | // Not in range