Connectathon 11 Snapshot

This page is part of the FHIR Specification (v1.2.0: STU 3 Draft). 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

4.28.13 Observation for Genetics

4.28.13.1 Overview

4.28.13.2 Scope and Usage

4.28.13.3 Content

Profiles:
ObservationForGeneticsDescribes how the observation resource is used to report structured genetic test results
Extensions:
observation-geneticsSequenceSequence :

Refer to the Sequence resource, representing genetics data.

observation-geneticsSourceGenomicSourceClass :

Genomic source class means category of source of tissue sample used to determine the sequence: Germline / Somatic / Prenatal / Likely Germline / Likely Somatic / Likely Prenatal / Unknown Genomic Origin.

observation-geneticsVariationHGVSObservedVariantHGVS :

Observed Amino acid / cDNA /RNA variant following HGVS nomenclature.

observation-geneticsVariationTypeVariationType :

Type of variation expressed using Sequence Ontology or LOINC answer list: Wild type / Deletion / Duplication / Insertion / Insertion or Deletion / Inversion / Substitution.

observation-geneticsGeneGene :

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-geneticsRegionRegion :

Gene region at which the region is mapped (e.g. "exon19").

observation-geneticsAminoAcidVariationPredictedAminoAcidChange :

HGVS nomenclature for predicted amino acid change.

Examples:
Genetics Observation -1

Genetics Observation of Somatic Variant in Lung Cancer

Genetics Observation -2

BRACAnalysis -1

Genetics Observation -3

BRACAnalysis -2

Genetics Observation -4

Allele with multiple variants

Genetics Observation -5

Further analysis for a variant - using related element

Genetics Observation -6-1

Genetics Observation for BRCA1 c.181T>G

Genetics Observation -6-2

Genetics Observation for BRCA1 c.181T>A

Genetics Observation -6-3

Genetics Observation for BRCA1 n.342T>G

Genetics Observation -7

PCR genetics observation