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10.1.15 10.1.16 Observation-genetics

Orders and Observations Work Group Maturity Level : N/A Standards Status : Informative

The material on this page is currently undergoing work to be refactored or potentially removed in a future release as further analysis is done as part of the Genomics Reporting Implementation Guide .

10.1.15.1 10.1.16.1 Overview

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).

For use cases, details on how this resource interact with other Clinical Genomics resources or profiles, please refer to implementation guidance document here .

10.1.15.1.1 10.1.16.1.1 Genetic Standards and Resources include:

10.1.15.2 10.1.16.2 Scope and Usage

The 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).

10.1.15.3 10.1.16.3 Interpretation

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 Codes
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 Answer Lists
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.

10.1.15.4 10.1.16.4 Content

Profiles :
Observation-Genetics Describes how the observation resource is used to report structured genetic test results
Extensions :
observation-geneticsGene Gene :

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).

observation-geneticsDNARegionName DNARegionName :

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. LOINC Code: ( 47999-8 ).

observation-geneticsCopyNumberEvent CopyNumberEvent :

A variation that increases or decreases the copy number of a given region ( SO:0001019 ). Values: amplification/deletion/LOH.

observation-geneticsGenomicSourceClass GenomicSourceClass :

Source of sample used to determine the sequence in sequencing lab -- germline, somatic, prenatal. LOINC Code: ( 48002-0 ).

observation-geneticsInterpretation Interpretation :

Clinical Interpretations for variant. It's a reference to an Observation resource.

observation-geneticsVariant Variant :

Variant information.

observation-geneticsAminoAcidChange AminoAcidChange :

AminoAcidChange information.

observation-geneticsAllele Allele :

Allele information.

observation-geneticsAncestry Ancestry :

Ancestry information.

observation-geneticsPhaseSet PhaseSet :

Phase set information.

Examples :
Genetics 1

Genetics example 1

Genetics 2

Genetics example 2

Genetics 3

Genetics example 3

Genetics 4

Genetics example 4

Genetics 5

Genetics example 5

Diplotype(with Haplotypes Ref)

Example of diplotype data (with haplotypes observation as reference)

Haplotype

Example of haplotype data that is basis of a diplotype data

Haplotype-2

Example of another haplotype data that is basis of a diplotype data

Phenotype

Example of phenotype data

TPMT-diplotype

Example of a TPMT diplotype that link to two TPMT haplotype observations

TPMT-haplotype-one

Example of a TPMT haplotype observation

TPMT-haplotype-two

Example of another TPMT haplotype observation

Breast Cancer genetic test

Example of breast cancer genetic observation

10.1.15.5 10.1.16.5 Search Parameters

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