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LOINC Clinical Committee

April 28, 2026

Stanley M. Huff, MD

Eza Hafeza, MD

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Topics

• Jim Case is planning to retire at the end of 2026!
• Priorities for the LOINC Ontology
• HL7 Clinical Genomics Topics
• Modeling “Risk of” calculations and evaluations

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LOINC Ontology: What do we want to add in the next version?

• High priority clinical observations
• Binding of value sets (answer lists) to nominal LOINCs
• Document ontology
• Survey instruments
• Radiology concepts
• Calculations (these really don’t fit in the lab model)
• More lab
• Genetics
• Other?

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General approach to human genetic test results�

https://build.fhir.org/ig/HL7/genomics-reporting/

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HL7 Genomics Reporting Implementation Guide

• A guiding principle from the IG

“[strategy] avoids pre-coordinating the type of variant, medication, or other information into the Observation.code as this makes it easier to leverage industry standard terminologies for genomic information (e.g., HGVS) and avoids needing to duplicate this information into observation coding systems such as LOINC.”�

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Avoiding combinatorial explosion

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Interface A (variable representation, rheumatologist view)

OBX|1|CE|4821-5^HLA-B27^LN|1|60373001^Detected^SNI|

(this approach causes creation of a LOINC code for each HLA type)

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Interface B (value representation, transplant, or paternity view)

OBX|1|CE|4694-6^HLA-TYPE^LN|1|34453005^B27^SNI|

(this allows reuse of the HLA Type as the value of the result)�

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Pre coordinated Cystic Fibrosis Gene and VariantTests

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Genetic Testing Options (simplified FHIR)

Observation

code: (38456-0 ) CFTR gene

c.3849+10kbC>T [Detection] in

Blood or Tissue by Molecular

genetics method

value: Detected

(SCTID: 260373001)

Observation

component {

code: (48018-6): Gene studied [ID]

value: (HGNC:1884) CFTR gene

c.3849+10kbC>T"

system (66746-9): Blood

(SCTID: 119297000)

method: (85069-3): Molecular genetics

(SCTID 708068002)

value: Detected

(SCTID: 260373001)

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Option #1

Option #2 - Preferred

Genotype Example - preferred

<Observation xmlns="http://hl7.org/fhir">

…

<component>

<code>

<coding>

<system value="http://loinc.org"/>

<code value="48018-6"/>

<display value="Gene studied [ID]"/>

</coding>

</code>

<valueCodeableConcept>

<coding>

<system value="http://www.genenames.org"/>

<code value="HGNC:4932"/>

<display value="HLA-B"/>

</coding>

</valueCodeableConcept>

</component>

</Observation>

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Variant Study Result - preferred

…

<component>

<code>

<coding>

<system value="http://loinc.org"/>

<code value="48018-6"/>

<display value=” Gene studied [ID]"/>

</coding>

</code>

<valueCodeableConcept>

<coding>

<system value="http://www.genenames.org"/>

<code value="HGNC:262"/>

<display value="CYP2C19"/>

</coding>

</valueCodeableConcept>

</component>

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HGNC Database

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LOINC codes to support the Genomics Reporting Implementation Guide

https://build.fhir.org/ig/HL7/genomics-reporting/general.html

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FHIR Genomics Reporting IG:�overview of the IG artifacts

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Subtypes of Genomic Findings

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LOINC codes for reporting genetic test results

We (LOINC) are investigating whether there are data elements in the genetic result exchange FHIR profiles that should have LOINC codes. The FHIR profiles are:

• General Genomic Reporting
• Variant Reporting
• Cytogenomic Reporting
• Pharmacogenomic Reporting
• Somatic Reporting
• Histocompatibility and Immunogenetic Reporting

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Some Existing Genetic LOINC Codes

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LOINC codes to support Molecular Definition Implementation Guide for Molecular Data Types

https://build.fhir.org/ig/HL7/cg-incubator/branches/main/en/StructureDefinition-MolecularDefinition.html

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LOINC codes for Molecular Definitions

• We (LOINC) are investigating whether there are data elements in the Molecular Definitions IG that should have LOINC codes.

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Profiles on the Molecular Definition Resource

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Example LOINC candidate concepts

• moleculeType: (e.g., DNA, RNA, polypeptide)
• moleculeSubtype: (e.g., mRNA, genomic_DNA, lncRNA)
• strand orientation type: (e.g., forward, reverse)
• coordinate system origin type: (e.g., sequence-start, cds-start, feature-start, feature-end)
• coordinate system type: (e.g., 0-based interval counting, 0-based character counting, 1-based character counting)
• normalization method (e.g., left-shift, right-shift, and fully-justified)
• focus concept type: (e.g., allele state, context state, reference state, alternative state)
• location (cytobandLocation)

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The cytobandLocation element

• The cytobandLocation element defines a genomic location based on cytogenetic banding within a specific reference genome assembly
• Chromosome number: (e.g., 1-22, X, Y).
• Arm: "p" for the short arm or "q" for the long arm.
• Band/Sub-band: A series of numbers separated by dots indicating the band, sub-band, and sub-sub-band (e.g., 2p16.3). 
• It contains a mandatory genomeAssembly element which details the reference genome used and includes
• an optional organism (species) specified as a CodeableConcept
• optional elements for the assembly build number, accession identifier, and a description

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Genome Assembly Example - Chr7, GRCh38.p14

• Chr7: The gene or sequence is located on Chromosome 7.
• GRCh38: This is the main human reference genome assembly (Genome Reference Consortium Human Build 38), released in 2013-2014, which acts as the current, standard "map" of the human genome.
• .p14 (Patch 14): This indicates the 14th minor, non-coordinate-changing update to the GRCh38 assembly, released on February 3, 2022.
• Meaning of the Patch (p14): Patches are added to improve the assembly without changing the main chromosome coordinates.

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LOINC codes for “Risk of …”

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Profile of existing “risk of” codes

• 277 – “Risk of” concepts (excluding panels, docs)
• 109 Ordinal Risk
• 99 Quantitative Risk
• 35 Narrative Risk
• 34 Nominal (coded) Risk
• 82 “Risk of” genetic conditions – likely to increase
• Kind of property: Find, Imp, Likelihood
• Wide variety of methods and calculations
• Relative risk – patient divided by control group

Conclusion – We are at “risk of” combinatorial explosion! (pun intended!)

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Possible approach – post coordination

Quantitative Risk Model {

- condition/diagnosis (from SNOMED CT)

- probability

- formula

- literature reference (not sent in messages)

- other stuff…?

}

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Make formal models based on “property”

Make similar models for:

• Quantitative risk
• Ordinal risk
• Nominal risk
• Narrative risk
• Relative risk

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Proposal

• We make formal post coordinated models for the different kinds of risk
• We maintain LOINC codes and value sets for the data elements used in post coordination
• We encourage people to implement a post coordinated solution
• We continue to make pre coordinated “risk of” concepts when needed

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Thank you for attending!

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Reference Slides

© Regenstrief Institute, Inc.

2025 LOINC CONFERENCE

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