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 
Observation-genetics-profile (i.e. Standard Profile for Genetics) 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 Society and LOINC The Standard Profile for Genetics 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).
Observation.component should be used in genetic profile for observations without sequence information while Observation.extension still be used for sequence information as component is only suitable for flat observations.
Here is a LOINC panel that could be supported by Observation.component, for example:
55232-3 Genetic analysis summary panel Blood or Tissue by Molecular genetics method
The usage of component is shown in example3-mutationlist-1/2/3/4.
Extensions added in genetics profile can be grouped into 4 categories:
| Profiles: | |
| Genetics | Describes how the observation resource is used to report structured genetic test results |
| Extensions: | |
| geneticsGenomeBuild | Genome Build : The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| geneticsChromosome | Chr : The chromosome containing the genetic finding. The value set binds to NCBI-Gene code system. |
| geneticsGenomicStart | GenomicStart : Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strand. |
| geneticsGenomicStop | GenomicStop : Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strand. |
| geneticsReferenceAllele | RefAllele : Nucleotide(s) from genomic start to genomic stop on the positive (+) strand of the genomic reference sequence. |
| geneticsObservedAllele | ObsAllele : Oserved nucleotides from genomic start to genomic stop on the positive (+) genomic strand. |
| geneticsTranscriptReferenceSequenceId | TransReferenceSeqID : Reference identifier for cDNA transcript, with version, from NCBI's RefSeq or ENSEMBL. |
| geneticsProteinReferenceSequenceId | ProteinReferenceSeq : Reference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL. |
| geneticsCIGAR | CIGAR : Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here |
| geneticsDNASequenceVariation | HGVSdnaVariant : cDNA variant following HGVS nomenclature on the given TranscriptReferenceSequenceId. |
| geneticsVariationId | VariantId : 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). |
| geneticsDNASequenceVariationType | DNAvariantType : Codified type for associated DNA Sequence Variation. DNA Sequence Variations use the HGVS notation which implies the DNA Sequence Variation Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience. LOINC Answer List values 48019-4 or Sequence Ontology vaues. |
| geneticsAminoAcidChange | HGVSproteinChange : Protein variant following HGVS nomenclature on the given ProteinReferenceSequenceId. |
| geneticsAminoAcidChangeType | ProteinChangeType : Type of variation expressed using Sequence Ontology or LOINC answer list 48006-1. |
| geneticsGene | Gene : Gene region 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. |
| geneticsDNARegionName | RegionName : Details of exonic location of variant (e.g. Exon 1). |
| geneticsAlleleName | AlleleName : Common name for variant or gene allele. |
| geneticsGenomicSourceClass | GenomicSource : Genomic source class means category of source of tissue sample used to determine the sequence. Here is the loinc answer List for Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6. |
| geneticsSpecies | Species : supports testing of human, viruses, and bacteria. |
| geneticsResult | Result : Results from genetic profile (e.g. One gene mutation with one type variation observed in a patient). It makes genetic profile support various genetic test(e.g. A genetic test reporting a list of gene mutations). |
| geneticsAssessedCondition | AssessedCondition : Used to denote condition context for genetic testing, which may influence reported variants and interpretation for large genomic testing panels e.g. lung cancer or familial breast cancer. |
| geneticsAllelicState | AllelicState : The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA. Here is the loinc answer List for Allelic state:1. Heteroplasmic (LA6703-8); 2. Homoplasmic (LA6704-6); 3. Homozygous (LA6705-3); 4. Heterozygous (LA6706-1); 5. Hemizygous (LA6707-9). |
| geneticsAllelicFrequency | AllelicFrequency : Allele frequencies. |
| geneticsCopyNumberEvent | CopyNumberEvent : Values: amplificaiton/deletion/LOH. |
| geneticsReadCoverage | ReadCoverage : Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. |
| Examples: | |
| Genetics Observation Example1 Somatic | Genetics Observation of Somatic Variant in Lung Cancer |
| Genetics Observation Example2 Germline | Genetics Observation of Germline BRCA1 Variant |
| Genetics Observation Example3 Mutation list | ABCB4 gene mutation analysis |
| Genetics Observation Example3-1 | ABCB4 gene mutation analysis - variant 1 |
| Genetics Observation Example3-2 | ABCB4 gene mutation analysis - variant 2 |
| Genetics Observation Example3-3 | ABCB4 gene mutation analysis - variant 3 |
| Genetics Observation Example3-4 | ABCB4 gene mutation analysis - variant 4 |
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 | |
| assessed-condition | reference | Condition assessed by genetic test | XML / JSON | |
| chromosome-genomicstart | string | Chromosome and Genomic Starting Position | XML / JSON | |
| condition-gene | string | HGNC gene symbol and assessed condition context | XML / JSON | |
| condition-gene-dnavariant | string | HGNC gene symbol HGVS DNA variant, and assessed condition context | 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 DSTU2 (v1.2.0-7447) generated on Fri, Dec 11, 2015 17:42+1100.
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