Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Behavior: Search Parameters

These define the properties by which a RESTful server can be searched. They can also be used for sorting and including related resources.

GenomicStudyFocusSearchParam

What the genomic study analysis is about, when it is not about the subject of record

GenomicStudyIdentifierSearchParam

Identifiers for the Study

GenomicStudyPatientSearchParam

Who the study is about

GenomicStudyStatusSearchParam

The status of the study

GenomicStudySubjectSearchParam

Who the study is about

MolecularDefinitionIdentifierSearchParam

The unique identity for a particular sequence

MolecularDefinitionMemberSearchParam

Reference to the state of the molecular member

MolecularDefinitionMoleculetypeSearchParam

Amino Acid Sequence/ DNA Sequence / RNA Sequence

MolecularDefinitionTopologySearchParam

The structural topology of the molecular entity (e.g., linear, circular)

MolecularDefinitionTypeSearchParam

Classification of the molecule into types other than those defined by moleculeType

Structures: Additional Resources

'Additional' resources that are not yet published in the FHIR core specification.

Genomic Study

A set of analyses performed to analyze and generate genomic data.

Molecular Definition

Definitional content for a molecular entity, such as a nucleotide or protein sequence.

Terminology: Value Sets

These define sets of codes used by systems conforming to this implementation guide.

Amino Acid 1-letter Ambiguous Symbols ValueSet

Single-letter symbols for amino acids including ambiguous symbols (A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z).

Amino Acid 1-letter Unambiguous Symbols ValueSet

Single-letter unambiguous symbols for the 20 common amino acids.

Amino Acid 3-letter Ambiguous Symbols ValueSet

Three-letter symbols for amino acids including ambiguous symbols (Ala, Asx, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr, Sec, Xaa, Glx).

Amino Acid 3-letter Unambiguous Symbols ValueSet

Three-letter unambiguous symbols for the 20 common amino acids.

Coordinate System Normalization Method ValueSet

The normalization method applied when placing a variant within a repetitive sequence region. The binding is extensible to allow new alignment conventions as they emerge.

Coordinate System Origin ValueSet

The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This binding is required because coordinate origin ambiguity directly causes errors in variant interpretation.

Genomic Study Change Type VS

The change type of the GenomicStudy analysis.

Genomic Study Data Format VS

The data formats relevant to Genomic Study analysis.

Genomic Study Method Type VS

The method type of the GenomicStudy analysis.

Genomic Study Region Type VS

The type or status of a set of genomic regions within a GenomicStudy analysis (studied, called, or uncalled).

Genomic Study Status VS

The status of the GenomicStudy.

Genomic Study Type VS

The type of the GenomicStudy.

HUGO Gene Nomenclature Committee Gene Names (HGNC)

This value set includes all HGNC Codes, which includes multiple code systems. The preferred system URL is http://www.genenames.org per the HL7 Terminology (THO) NamingSystem definition (https://terminology.hl7.org/NamingSystem-v3-hgnc.html). Gene IDs are used as CodeableConcepts, which must be sent with the HGNC gene ID including the prefix 'HGNC:' as the code and the HGNC 'gene symbol' as display. CAUTION: HGNC also indexes gene groups by numeric ID (without a prefix), and older systems may send HGNC gene IDs without the prefix, so care must be taken to confirm alignment. The genegroup code system is separately included to draw attention to this ambiguity and potential error.

Molecular Definition Literal Encoding VS

The encoding used in molecular definition literal representations.

Molecular Definition Molecule Type

The broad physical class of molecule represented by a MolecularDefinition resource instance: DNA, RNA, or amino acid (polypeptide). This ValueSet is used for the moleculeType element and is intentionally limited to top-level molecule classes to support consistent searching and profiling across systems. For finer-grained classification, use the type element bound to MolecularDefinitionType.

Molecular Definition Organism

The organism whose genome the genomeAssembly describes. Codes are drawn from the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy). The binding is extensible to accommodate any organism with a sequenced genome. Commonly used taxon IDs include 9606 (Homo sapiens) and 10090 (Mus musculus).

Molecular Definition Representation Code

Example codes for representing a molecular entity by accession identifier. Codes are drawn from molecular sequence databases registered in HL7 terminology: NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq) and LRG (http://www.lrg-sequence.org). This binding is example strength — implementations are not constrained to these systems and may use any appropriate molecular sequence identifier system.

Molecular Definition Representation Focus VS

The domain concept that is the focus of the representation in a MolecularDefinition.

Molecular Definition Strand

The strand orientation of a sequenceLocation. 'Forward' corresponds to the plus/sense/Watson strand (5' to 3' in the standard reference orientation); 'reverse' corresponds to the minus/antisense/Crick strand (3' to 5' in the standard reference orientation).

Molecular Definition Topology

The structural topology of a molecular entity as defined by the MolecularDefinition resource. Includes linear, circular, linear-discontiguous (gapped), and branched forms.

Molecular Definition Type

Domain-semantic subtype classifications for a MolecularDefinition resource instance, providing greater specificity than the moleculeType element. For example, an instance with moleculeType 'rna' may have a type of 'mrna' or 'mirna'. This ValueSet is an enumerated, curated set of locally-defined codes covering clinically relevant DNA and RNA subtypes. The binding is extensible: implementers may use codes from other systems when no suitable code exists in this set.

Nucleotide DNA 1-letter Ambiguous Symbols ValueSet

Single-letter ambiguous symbols for DNA residues including all IUPAC codes (G, A, T, C, R, Y, M, K, S, W, H, B, V, D, N).

Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet

Single-letter unambiguous symbols for DNA residues, including N for any nucleotide (G, A, T, C, N).

Nucleotide DNA 1-letter Unambiguous Symbols ValueSet

Single-letter unambiguous symbols for DNA residues (G, A, T, C).

Nucleotide RNA 1-letter Unambiguous Symbols ValueSet

Single-letter unambiguous symbols for RNA residues (G, A, U, C).

Terminology: Code Systems

These define new code systems used by systems conforming to this implementation guide.

Amino Acid Symbols

Single-letter and three-letter symbols for amino acids based on IUPAC nomenclature, including unambiguous and ambiguous symbols.

Coordinate System Normalization Method CodeSystem

The normalization method applied when a variant can be placed at multiple equivalent positions within a repetitive sequence region. Different community standards (VCF, HGVS, VOCA/GA4GH) apply different alignment conventions, and recording which was used is necessary for lossless round-tripping of variant representations across systems. No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group.

Coordinate System Origin CodeSystem

The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This identifies the conceptual anchor point on the molecule where numbering begins, independent of whether numbering is 0-based or 1-based (which is captured in coordinateSystem.system). No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group.

Genomic Study Change Type

The change type relevant to GenomicStudy analysis.

Genomic Study Data Format

The data format relevant to genomics. These formats and relevant codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute.

Genomic Study Method Type

The method type of the GenomicStudy analysis. These method types and relevant codes were pulled from National Library of Medicine-Genetic Testing Registry (NCBI-GTR) values of describing different testing methods on various levels: major method category, method category, and primary methodology

Genomic Study Region Type

The type or status of a set of genomic regions within a GenomicStudy analysis, indicating the relationship of those regions to the analysis outcome.

Genomic Study Status

The status of the GenomicStudy.

Genomic Study Type

The type relevant to GenomicStudy.

Molecular Definition Literal Encoding

Codes for the encoding used in molecular definition literal representations, based on IUPAC standards for nucleotide and amino acid sequences.

Molecular Definition Molecule Type CodeSystem

The broad physical class of molecule represented by a MolecularDefinition resource instance: DNA, RNA, or amino acid (polypeptide). Codes are intentionally limited to top-level molecule classes to support consistent searching and profiling across systems. For finer-grained classification, use the type element bound to MolecularDefinitionType.

Molecular Definition Representation Focus

The domain concept that is the focus of the representation in a MolecularDefinition. This element is used to disambiguate the representations of different alleles or states at a given location.

Molecular Definition Strand CodeSystem

The strand orientation of a sequenceLocation. Orientation of molecular sequences, indicating directionality for nucleotides (5' to 3' or 3' to 5') or amino acids (N to C terminus).

Molecular Definition Topology CodeSystem

The structural topology of a molecular entity as defined by the MolecularDefinition resource. Includes linear, circular, linear-discontiguous (gapped), and branched forms.

Molecular Definition Type CodeSystem

Domain-semantic subtype classifications for a MolecularDefinition resource instance, providing greater specificity than the moleculeType element. For example, an instance with moleculeType 'rna' may have a type of 'mrna' or 'mirna'. This CodeSystem is an enumerated, curated set covering clinically relevant DNA and RNA subtypes. The binding on this CodeSystem is extensible: implementers may use codes from other systems when no suitable code exists here.

NCBI Taxonomy (fragment)

A fragment of the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) containing taxon IDs referenced by examples and profiles in this IG. Numeric taxon IDs are used as codes; scientific names are used as display text. This fragment covers commonly used research organisms and representative clinical viral pathogens. Add entries here as new examples reference additional taxon IDs.

Nucleotide DNA Symbols

Single-letter symbols for DNA residues based on IUPAC nomenclature, including unambiguous, ambiguous, and N symbols.

Nucleotide RNA Symbols

Single-letter unambiguous symbols for RNA residues based on IUPAC nomenclature.

Example: Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.

Genomic Study Example

Genomic Study Example

Genomic Study Lung Mass Example

Genomic Study Lung Mass Example

Genomic Study PGx Example

Genomic Study PGx Example

Genomic Study Somatic Study Example

Genomic Study Somatic Study Example

Genomic Study Trio Example

Genomic Study Trio Example

Molecular Definition Allele 1

Molecular Definition Allele 1

Molecular Definition Allele 2

Molecular Definition Allele 2

Molecular Definition Allele 3

Molecular Definition Allele 3

Molecular Definition Allele 4

Molecular Definition Allele 4

Molecular Definition Allele 5

Molecular Definition Allele 5

Molecular Definition Allele 6

Molecular Definition Allele 6

Molecular Definition Allele 7

Molecular Definition Allele 7

Molecular Definition Allele Sliced 1

Molecular Definition Allele Sliced 1

Molecular Definition Allele Sliced CYP2C19 1016

Molecular Definition Allele Sliced CYP2C19 1016

Molecular Definition Allele Sliced CYP2C19 661

Molecular Definition Allele Sliced CYP2C19 661

Molecular Definition Allele Sliced CYP2C19 Literal Only

Molecular Definition Allele Sliced CYP2C19 Literal Only

Molecular Definition Allele Sliced HLA00381

Molecular Definition Allele Sliced HLA00381

Molecular Definition Allele Sliced PGx Variant 1011

Molecular Definition Allele Sliced PGx Variant 1011

Molecular Definition Example

Molecular Definition Example

Molecular Definition Genomic CYP2C19 Accession

Molecular Definition Genomic CYP2C19 Accession

Molecular Definition Genotype 1

Molecular Definition Genotype 1

Molecular Definition Haplotype 1

Molecular Definition Haplotype 1

Molecular Definition Haplotype 2

Molecular Definition Haplotype 2

Molecular Definition Replaced Sequence

Molecular Definition Replaced Sequence

Molecular Definition Replacement Sequence

Molecular Definition Replacement Sequence

Molecular Definition Sequence 0 2B Concatenated

Molecular Definition Sequence 0 2B Concatenated

Molecular Definition Sequence 1

Molecular Definition Sequence 1

Molecular Definition Sequence 1 2B Concatenated

Molecular Definition Sequence 1 2B Concatenated

Molecular Definition Sequence 2 2B Concatenated

Molecular Definition Sequence 2 2B Concatenated

Molecular Definition Sequence A

Molecular Definition Sequence A

Molecular Definition Sequence A AA IUPAC

Molecular Definition Sequence A AA IUPAC

Molecular Definition Sequence A DNA IUPAC

Molecular Definition Sequence A DNA IUPAC

Molecular Definition Sequence AF1961831 URL

Molecular Definition Sequence AF1961831 URL

Molecular Definition Sequence C

Molecular Definition Sequence C

Molecular Definition Sequence CGG

Molecular Definition Sequence CGG

Molecular Definition Sequence CYP2C19 Accession

Molecular Definition Sequence CYP2C19 Accession

Molecular Definition Sequence CYP2C19 Attached

Molecular Definition Sequence CYP2C19 Attached

Molecular Definition Sequence CYP2C19 Concatenated Regions

Molecular Definition Sequence CYP2C19 Concatenated Regions

Molecular Definition Sequence CYP2C19 Downstream Region

Molecular Definition Sequence CYP2C19 Downstream Region

Molecular Definition Sequence CYP2C19 Gene Region

Molecular Definition Sequence CYP2C19 Gene Region

Molecular Definition Sequence CYP2C19 URL

Molecular Definition Sequence CYP2C19 URL

Molecular Definition Sequence CYP2C19 Upstream Region

Molecular Definition Sequence CYP2C19 Upstream Region

Molecular Definition Sequence FMR1

Molecular Definition Sequence FMR1

Molecular Definition Sequence FMR1 CGG 20x Edited Referenced

Molecular Definition Sequence FMR1 CGG 20x Edited Referenced

Molecular Definition Sequence FMR1 CGG 20x Repeat

Molecular Definition Sequence FMR1 CGG 20x Repeat

Molecular Definition Sequence G

Molecular Definition Sequence G

Molecular Definition Sequence GGC

Molecular Definition Sequence GGC

Molecular Definition Sequence HLA000011

Molecular Definition Sequence HLA000011

Molecular Definition Sequence LRG584

Molecular Definition Sequence LRG584

Molecular Definition Sequence MSH2

Molecular Definition Sequence MSH2

Molecular Definition Sequence NC00001010 URL

Molecular Definition Sequence NC00001010 URL

Molecular Definition Sequence NM0007694 URL

Molecular Definition Sequence NM0007694 URL

Molecular Definition Sequence Repeat

Molecular Definition Sequence Repeat

Molecular Definition Sequence T

Molecular Definition Sequence T

Molecular Definition Starting Sequence 2B Extracted

Molecular Definition Starting Sequence 2B Extracted

Molecular Definition Starting Sequence 2B Relative

Molecular Definition Starting Sequence 2B Relative

Molecular Definition Variation 1

Molecular Definition Variation 1

Molecular Definition Variation CYP2C19 1015 SPDI

Molecular Definition Variation CYP2C19 1015 SPDI

Molecular Definition Variation CYP2C19 1015 VRS

Molecular Definition Variation CYP2C19 1015 VRS

Molecular Definition Variation CYP2C19 1016 VCF

Molecular Definition Variation CYP2C19 1016 VCF

Molecular Definition Variation CYP2C19 661

Molecular Definition Variation CYP2C19 661

Molecular Definition Variation CYP2C19 991 HGVS

Molecular Definition Variation CYP2C19 991 HGVS

Molecular Definition Variation PGx Variant 1011

Molecular Definition Variation PGx Variant 1011

Molecular Definition Variation PGx Variant 1012

Molecular Definition Variation PGx Variant 1012

Molecular Definition Variation PGx Variant 1013

Molecular Definition Variation PGx Variant 1013

Molecular Definition Variation PGx Variant 1014

Molecular Definition Variation PGx Variant 1014

Molecular Definition Variation PGx Variant 1015

Molecular Definition Variation PGx Variant 1015

Molecular Definition Variation PGx Variant 1016

Molecular Definition Variation PGx Variant 1016

Molecular Definition Variation PGx Variant 1017

Molecular Definition Variation PGx Variant 1017

Molecular Definition Variation PGx Variant 1018

Molecular Definition Variation PGx Variant 1018

Molecular Definition Variation PGx Variant 1019

Molecular Definition Variation PGx Variant 1019

Molecular Definition Variation PGx Variant 1020

Molecular Definition Variation PGx Variant 1020

Molecular Definition Variation PGx Variant 1021

Molecular Definition Variation PGx Variant 1021

Other

These are resources that are used within this implementation guide that do not fit into one of the other categories.

CNVAnalysis-called

CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

De Novo Child Patient

De Novo Child Patient

De Novo Encounter

De Novo Encounter

De Novo Father Patient

De Novo Father Patient

De Novo Father Related Person

De Novo Father Related Person

De Novo Mother Patient

De Novo Mother Patient

De Novo Mother Related Person

De Novo Mother Related Person

De Novo Specimen 1

De Novo Specimen 1

De Novo Specimen 2

De Novo Specimen 2

De Novo Specimen 3

De Novo Specimen 3

Denovo Mutation Example Group

[markdown]

Father Patient

Father Patient

Father Specimen

Father Specimen

Genomic Encounter

Genomic Encounter

Genomic Patient

Genomic Patient

Genomic Service Request

Genomic Service Request

Genomic Service Request 2

Genomic Service Request 2

Genomic Service Request 3

Genomic Service Request 3

Genomic Service Request 4

Genomic Service Request 4

Genomic Service Request Father

Genomic Service Request Father

Genomic Service Request Mother

Genomic Service Request Mother

Genomic Service Request Proband

Genomic Service Request Proband

Genomic Specimen

Genomic Specimen

Genomic Study Examples List

Genomic Study Examples List

Genomic Study Operations List

Genomic Study Operations List

Molecular Definition Examples List

Molecular Definition Examples List

Molecular Definition Operations List

Molecular Definition Operations List

Mother Patient

Mother Patient

Mother Specimen

Mother Specimen

NGS Sequencing Device

NGS Sequencing Device

Normal Specimen

Normal Specimen

PGx Patient

PGx Patient

PGx Service Request

PGx Service Request

PGx Specimen

PGx Specimen

Practitioner 01

Practitioner 01

Practitioner 02

Practitioner 02

Proband Patient

Proband Patient

Proband Specimen

Proband Specimen

SimpleVariantAnalysis-called

SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

Somatic Patient

Somatic Patient

Somatic Service Request

Somatic Service Request

Triodenovo Software Device

Triodenovo Software Device

Tumor Specimen

Tumor Specimen

WES-FullSequencedRegion-GRCh38

WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

example-genomicFile-af1961831-url

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. Homo sapiens MHC class I antigen (HLA-B) gene

example-genomicFile-cyp2c19-accession

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. CYP2C19 gene sequence

example-genomicFile-cyp2c19-attached

CYP2C19 gene sequence

example-genomicFile-cyp2c19-url

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline. CYP2C19 gene sequence

example-genomicFile-hla00001

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

example-genomicFile-mw7162561

A sample Document Reference instance representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds.

example-genomicFile-ng0083843

A sample Document Reference instance representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10.

example-genomicFile-nm0002513

A sample Document Reference instance representing Homo sapiens mutS homolog 2 (MSH2), transcript variant 1, mRNA.

example-genomicFile-nm0007694

(CYP2C19), mRNA

example-genomicFile-nm0020245

A sample Document Reference instance representing Homo sapiens FMRP translational regulator 1 (FMR1), transcript variant ISO1, mRNA.

example-genomicfile-nc00001010-url

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicBEDfile

A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

genomicFile1

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFile2

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFile3

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFile4

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFileFather

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFileGroupAsSubject

Combined VCF file of a Proband and Parents that may be used as input or output of a genomic analysis pipeline.

genomicFileMother

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicFileProband

A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

genomicVCFfile

A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.

genomicVCFfile-cnv

genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.

genomicVCFfile-simple

genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.

pgxVCFfile

VCF file containing PGX variant calls for CYP2C19, CYP2C9, and VKORC1

somaticCalledRegions

BED file describing regions that passed coverage and quality thresholds in the tumor/normal DNA analysis

somaticFusionFile

VCF file containing gene fusions and transcript variants identified from tumor RNA sequencing

somaticRNAstudiedRegions

BED file describing studied regions for RNA sequencing (fusion and transcript variant detection)

somaticVCFfile

VCF file containing somatic variants identified from tumor/normal paired DNA sequencing