Draft of Clinical Genomics extension to the FHIR Observation for reporting of a DNA variant.
Scope of Release 1: Does not include interpretation. Constrained to a DNA variant type which is supported by HGVS nomenclature. Testing platforms supported
include NGS, Sanger Sequencing, and testing kits.
Due date extended to December 4, 2015
Therefore, consider extending to support HLA typing, CNV, and Translocations
Analysis of FHIR extensions stemming from Gil’s work: http://smartgenomics.wikispaces.com/GeneticObservation
Similar to genetic disease or medication assessed
Out of Scope for release 1
Equal to sequence variation
In Scope – Needs further definition
Need to extend to support unambiguous definition of a variant (if available) and additional
extension for cross testing platform support

traitAssesed - Target trait being studied

variant - HGVS identifier of an variant
being associated with the phenotype
studied
o
genotype - Reference to a Sequence
resource indicating the patient's genotype
on a variant
Need further definition
o
interpretation - Interpretation of a variant's
effect on the patient's phenotype
Out of scope for release 1
o
comment - A comment of the variant's
effect
Unstructured data for variant effect
Out of scope for release 1
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Suggested – preliminary draft
Suggested Name
(names in bold come from previous
HL7 CG standards)
Constraints
Definition
GenomeBuild.version

Genomic Reference Sequence Identifier 

Chromosome



GenomicReferenceSequence.version
o
o
o
Genomic start
o
o
o
Genomic stop
o
o
o
Reference allele
Observed allele
Gene
cDNAReferenceSequence.version
cDNASequenceVariation using HGVS
Nomenclature
Exon
Gene Identifier
Transcript Reference Sequence Identifier
DNA Sequence Variation Identifier
HGNC
NCBI or EBI
HGVS
DNA Region Name
cDNAChangeType
DNA Sequence Variation Type
Consider linking to SO
Ontology terms
Consider linking to SO
Ontology terms
NCBI or EBI
HGVS
RNAReferenceSequence.version
AASequenceVariation using HGVS
Nomenclature
AAChangeType
CommonVariantSynonym
Genomic source class
Amino Acid Change
Amino Acid Change Type
Allele Name
Genomic source class
Consider linking to SO
Ontology terms
(germline, somatic,
prenatal, unknown
genomic origin, likely
germline, likely somatic,
likely fetal)
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Allelic State
Allelic State
Heteroplasmic,
Homoplasmic,
Homozygous,
Heterozygous,
Hemizygous
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