2nd DSTU Draft For Comment

This page is part of the FHIR Specification (v0.4.0: DSTU 2 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

Standard Profile for Genetics (Conformance Package)

Ullman-Cullere, Mollie Mollie H Ullman-Cullere 2014-12-07T16:43:16Z 2014-12-07T23:19:00Z 12.00 7740 20115 240 75 False False /div /@xsi:schemaLocation /div/#id /div/h2 /div/p/#id /div/p /div/p/a /div/p/a/@href /div/ul/li http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 Observation-genetics-profile extends Observation 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). http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 This profile supports the reporting of genetic findings in a platform independent manner. At the current time, the laboratory may only have information for a portion of the fields depending on the testing platform. As tools, software and testing platforms mature, the laboratory will be able to report the unambiguous and computer-friendly genomic coordinates, while also reporting the cDNA and/or amino acid (protein) change preferred by clinicians. Unfortunately, for some testing platforms, the exact nucleotide change is not included in the output and only the allele name is available. HL7 is working with other external stakeholders to promote reporting of unambiguous findings. http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 Organizations using the Observation-Genetics-Profile should refer to the HL7 Clinical Genomics Domain Analysis Model for background context, use of LOINC or other coding systems, use cases, and details of best practices. http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 1 Scope and Usage 1 http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context 2 The extension of the observation resource for genetic reporting should be considered in the context of the HL7 Clinical Genomics Domain Analysis Model. http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context http://www.w3.org/1999/xhtml ../../schema/fhir-xhtml.xsd 2 Background and Context

© HL7.org 2011+. FHIR DSTU (v0.4.0-4167) generated on Mon, Feb 23, 2015 09:21+1100.
Links: What's a DSTU? | Version History | Compare to DSTU1 | | Propose a change

Profiles:
Genetics	Describes how the observation resource is used to report structured genetic test results : Standard Profile for Genetics
Extensions:
ProfilegeneticsGenomeBuild	The Genome Build used for reference, with version number if used. : The Genome Build used for reference. Version number must be included if a versioned release of a primary build was used.
ProfilegeneticsChromosome	The chromosome containing the variant. : The chromosome containing the genetic finding.
ProfilegeneticsGenomicReferenceSequenceIdentifier	The genomic reference sequence identifier. : The genomic reference sequence identifier is included, to support testing using alternative reference sequences.
ProfilegeneticsGenomicStart	Nucleotide location start : Nucleotide location for start of genomic finding.
ProfilegeneticsGenomicStop	Nucleotide location end : Nucleotide location for end of genomic finding.
ProfilegeneticsReferenceAllele	Nucleotides at location on reference sequence. Use '-' for insertions. : Nucleotide(s) from genomic start to genomic stop on reference sequence. Use '-' for insertions.
ProfilegeneticsObservedAllele	Oserved nucleotides at genomic location. Use '-' for delections. : Oserved nucleotides from genomic start to genomic stop. Use '-' for delections.
ProfilegeneticsGeneIdentifier	HGNC gene symbol and identifier. : HGNC gene symbol and identifier from HUGO Gene Nomenclature Committee at: http://www.genenames.org/.
ProfilegeneticsTranscriptReferenceSequenseIdentifier	Reference identifier for cDNA transcript, with version. : Reference identifier for cDNA transcript, with version, from NCBI's RefSeq or ENSEMBL.
ProfilegeneticsDNASequenceVariationIdentifier	cDNA variant following HGVS nomenclature and identifiers. : cDNA variant following HGVS nomenclature and identifiers to internal and external systems if known (e.g. ClinVar identifier).
ProfilegeneticsDNARegionName	Exonic location of variant. : Details of exonic location of variant (e.g. Exon 1).
ProfilegeneticsDNASequenceVariationType	Type of variation expressed using Sequence Ontology or LOINC codes. : 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.
ProfilegeneticsProteinReferenceSequenceIndentifier	Reference identifier for protein transcript, with version. : Reference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL.
ProfilegeneticsAminoAcidChange	Protein variant following HGVS nomenclature and identifiers. : Protein variant following HGVS nomenclature and identifiers to internal and external systems if known.
ProfilegeneticsAminoAcidChangeType	Type of protien variation expressed using Sequence Ontology or LOINC codes. : Type of variation expressed using Sequence Ontology or LOINC answer list 48006-1.
ProfilegeneticsAlleleName	Common name : Common name for variant or gene allele.
ProfilegeneticsGenomicSourceClass	Genomic source of the variant : The genomic class of the variant: Germline for inherited genome, somatic for cancer genome (e.g. DNA from tumor cells), and prenatal for fetal genome. Associated with LOINC answer list: 48002-0.
ProfilegeneticsAllelicState	Variant allelic state : The level of occurrence of a single DNA Sequence Variation. Heterozygous:Variation present in one of the two genes of homologous chromosomes, while Homozygous means that it is present in both genes. Hemizygous: Variation exists in the only single copy of a gene in a non-homologous chromosome (i.e. male X and Y chromosome). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic: Variation is present in all of the copies of mitochondrial DNA. LOINC Answer List values 53034-5.