STU 3 Candidate
This page is part of the FHIR Specification (v1.4.0: STU 3 Ballot 3). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions 
. Page versions: R4B R4 R3
Observation-genetics-profile extends Observation resource to enable reporting of structured genetic test results. In addition, the genetics profile contextualizes well established standards from the field of clinical genetics into the standards of healthcare (e.g. HGNC - HUGO Gene Nomenclature Committee's international standard for gene names, symbols, and identifiers).
, ClinVar , and COSMIC and ENSEMBL - Human Genee Nomenclature Committee nomenclature from the Human Genome Variantion SocietyThe Observation-genetics profile supports reporting of a DNA variant at the genomic, cDNA, and protein change level. In addition, a condition context may be provided, as AssessedCondition. For large genomic tests, a condition may be used as an input into the analytic pipeline to aid in the identification of clinically relevant variants related to the test order. It is strongly encouraged to provide all available information in this profile for any reported variants, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize variants over time or across sources. However, these data should not be used to dynamically correct/change variant representations for clinical use outside of the laboratory, due to insufficient information.
Implementers should be aware that semantic equivalency of results of genetic variants cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.
This FHIR genomics work is based on work of the HL7 Clinical Genomics Workgroup and modeled based on the Domain Analysis Model and SMART on FHIR Genomics as published in JAMIA 2015 (http://jamia.oxfordjournals.org/content/early/2015/07/21/jamia.ocv045.long).
The HL7 Clinical Genomics Work Group emphasizes the importance of transmitting structured genetic findings within the clinical, translational, and research environments fully integrated with other clinical data, in order to drive outcomes analysis, operational decision making, discovery research, and public health reporting. The standard doesn't currently cover the reporting of clinically relevant negative or wild type results within genetic data portion of the message.
Here is the document of HL7 Version 3 Domain Analysis Model where the examples used in genetics profile are from (Page 5).
Extension - geneticsInterpretation points to an Observation entity. In this Observation entity, Observation.component is used for recording clinical interpretations for variation.
Here is a LOINC panel that could be supported by Observation.component:
| LOINC # | Component | Description/Comments |
|---|---|---|
| 51963-7 | Medication Assessed | A coded medication accessed in a pharmacogenetic test (recommend RxNorm). |
| 51964-5 | Drug Efficacy Analysis Overall Interpretation | Overall predicted phenotype for drug efficacy for all DNA Sequence Variations identified in a single case. LOINC Answer List values can be seen in table below. |
| 51967-8 | Genetic disease assessed | A coded disease which is associated with the region of DNA covered by the genetic test (recommend SNOMED). |
| 51969-4 | Genetic analysis summary report | Narrative report in disease diagnostic-based format, which is used for pharmacogenomic reporting as well and disease risk or diagnosis. These reports currently follow the same formatting recommendations. |
| 51971-0 | Drug metabolism analysis overall interpretation | Overall predicted phenotype for drug metabolism for all DNA Sequence Variations identified in a single case. LOINC Answer List values can be seen in table below. |
| 53039-4 | Genetic Disease Analysis Overall Carrier Interpretation | Carrier Identification interpretation of all identified DNA Sequence Variations along with any known clinical information for the benefit of aiding clinicians in understanding the results overall. LOINC Answer List values can be seen in table below. |
| LOINC Code | Sequence | Answer text | LOINC answer code |
|---|---|---|---|
| 51964-5 | 1 | Responsive | LA6677-4 |
| 2 | Resistant | LA6676-6 | |
| 3 | Negative | LA6577-6 | |
| 4 | Inconclusive | LA9663-1 | |
| 5 | Failure | LA9664-9 | |
| 51971-0 | 1 | Ultrarapid metabolizer | LA10315-2 |
| 2 | Extensive metabolizer | LA10316-0 | |
| 3 | Intermediate metabolizer | LA10317-8 | |
| 4 | Poor metabolizer | LA9657-3 | |
| 5 | Inconclusive | LA9663-1 | |
| 53039-4 | 1 | Carrier | LA10314-5 |
| 2 | Negative | LA6577-6 | |
| 3 | Inconclusive | LA9663-1 | |
| 4 | Failure | LA9664-9 |
In addition, in this Observation entity, Observation.related is used to link itself with Observation-genetics profile. Observation.related.type is 'derived-from' as it provides clinical interpretation for variation recoreded in Observation-genetics entity.
| Profiles: | |
| ObservationForGenetics | Describes how the observation resource is used to report structured genetic test results |
| Extensions: | |
| observation-geneticsTranscriptReferenceSequenceId | Transcript Reference Sequence Identifier : This field carries the ID for the transcribed reference sequence that part of the genetic reference sequence that is converted to Messenger RNA. |
| observation-geneticsProteinReferenceSequenceId | Protein Reference Sequence : Reference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL. |
| observation-geneticsDNASequenceVariation | DNA Sequence Variation : Human Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing. Reference Sequence id used for HGVS naming must be anotated. |
| observation-geneticsDNAVariationId | Variant Id : Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC). |
| observation-geneticsDNASequenceVariationType | DNA Variant Type : Codified type for associated DNA Sequence Variation. DNA Sequence Variations use the HGVS notation which implies the DNA Sequence Variation Type. |
| observation-geneticsAminoAcidChange | Amino Acid Change : Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference Sequence id used for HGVS naming must be anotated. |
| observation-geneticsAminoAcidChangeType | Amino Acid Change Type : Codified type for associated Amino Acid Change. |
| observation-geneticsGene | Gene Identifier : Gene in which the sequence is found. Currently values from HGNC are supported. Other systems or genes not defined in HGNC (e.g. BCR-ABL fusion gene) can be added by using local extension. |
| observation-geneticsDNARegionName | DNA Region Name : A human readable name for the region of interest. Typically Exon #, Intron # or other. NOTE: This is not standardized and is mainly for convenience and display purposes. |
| observation-geneticsAlleleName | AlleleName : Common name for variant or gene allele. |
| observation-geneticsGenomicSourceClass | Genomic Source Class : Source of sample used to determine the sequence in sequencing lab -- germline, somatic, prenatal. |
| observation-geneticsSequence | Sequence : Refer to the Sequence resource, representing genetics data. |
| observation-geneticsInterpretation | Clinical Interpretations for the Variant : Clinical Interpretations for the Variant. It's a reference to an Observation resource. |
Search parameters defined by this package. See Searching for more information about searching in REST, messaging, and services.
| Name | Type | Description | Paths | Source |
| amino-acid-change | string | HGVS Protein Change | XML / JSON | |
| dna-variant | string | HGVS DNA variant | XML / JSON | |
| gene-amino-acid-change | string | HGNC gene symbol and HGVS Protein change | XML / JSON | |
| gene-dnavariant | string | HGNC gene symbol and HGVS DNA Variant | XML / JSON | |
| gene-identifier | token | HGNC gene symbol and identifier | XML / JSON |
© HL7.org 2011+. FHIR STU3 Candidate (v1.4.0-8139) generated on Thu, Mar 31, 2016 08:09+1100. QA Page
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