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

4.33 Resource Sequence - Content

Clinical Genomics Work GroupMaturity Level: 0Compartments: Not linked to any defined compartments

Variation and Sequence data.

4.33.1 Overview

The Sequence resource is designed to describe a sequence variant or a sequence without variant information. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. Thus, the FHIR Sequence resource avoids large genomic payloads in a manner analogous to how the FHIR ImagingStudy resource references large images maintained in other systems. This resource 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).

4.33.1.1 Genetic Standards and Resources include:

4.33.2 Scope and Usage

This resource is designed to describe a sequence variation with clinical significance with information such as:

  • Name of the variation represented
  • Type of the variation
  • Gene region occupied by the variation
  • Name of the gene
  • Tissue source used to determine genotype of the variation

It is strongly encouraged to provide all available information in this resource 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.

4.33.3 Boundaries and Relationships

Focus of the resource is to provide data immediately relevant to clinical decision-making. Hence data such as precise read of DNA sequences and sequence alignment are not included; such data are nonetheless accessible through references to GA4GH (Global Alliance for Genomics and Health) API. The Sequence resource will be referenced by Observation to provide variant information. As clinical assessments/diagnosis of a patient are typically captured in the Condition resource or the ClinicalImpression resource, the Sequence resource can be referenced by the Condition resource to provide specific genetic data to support an assertions. This is analogous to how Condition references other resources, such as AllergyIntolerance, Procedure, and Questionnaire resources.

4.33.4 Resource Content

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceA Sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... variationID Σ0..*CodeableConceptIdentifier for variant and ClinVar, dbSNP or COSMIC identifier should be used
dbSNP (Example)
... referenceSeq Σ0..1CodeableConceptReference identifier. It must match the type in the Sequence.type field
ENSEMBL (Example)
... quantity Σ0..1QuantityQuantity of the sequence
... coordinate Σ0..*BackboneElementThe coordinate of the variant
.... chromosome Σ0..1CodeableConceptThe chromosome containing the genetic finding
.... start Σ0..1integer0-based start position (inclusive) of the sequence
.... end Σ0..1integer0-based end position (exclusive) of the sequence
.... genomeBuild Σ0..1CodeableConceptThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
... species Σ0..1CodeableConceptSupporting tests of human, viruses, and bacteria
... observedAllele Σ0..1stringNucleotide(s)/amino acids from start position of sequence to stop position of observed sequence
... referenceAllele Σ0..1stringNucleotide(s)/amino acids from start position of sequence to stop position of reference sequence
... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
... quality Σ0..*BackboneElementSequence Quality
.... start Σ0..1integer0-based start position (inclusive) of the sequence
.... end Σ0..1integer0-based end position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... platform Σ0..1CodeableConceptPlatform
... allelicState Σ0..1CodeableConceptThe level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
LOINC 53034-5 answerlist (Example)
... allelicFrequency Σ0..1decimalAllele frequencies
... copyNumberEvent Σ0..1CodeableConceptCopy Number Event: Values: amplificaiton / deletion / LOH
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... chip Σ0..1BackboneElementInformation of chip
.... chipId Σ0..1stringChip id
.... manufacturerId Σ0..1stringChip manufacturer id
.... version Σ0..1stringChip version
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... structure Σ0..1uriURI of the page containing information about the structure of the repository
.... variantId Σ0..1stringId of a GA4GH variant
.... readGroupSetId Σ0..1stringId of a GA4GH read group

doco Documentation for this format

UML Diagram

Sequence (DomainResource)Amino acid / cDNA transcript / RNA variationtype : code [1..1] « Type if a sequence -- DNA, RNA, or amino acid sequence (Strength=Example)sequenceType?? »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)variationID : CodeableConcept [0..*] « Variant ID (Strength=Example)dbSNP?? »Reference identifier for cDNA transcript/protein, with version, from NCBI's RefSeq or ENSEMBL. This reference sequence identifier must match the type in the Sequence.type fieldreferenceSeq : CodeableConcept [0..1] « Reference identifier (Strength=Example)ENSEMBL?? »Quantity of the sequencequantity : Quantity [0..1]The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteriaspecies : CodeableConcept [0..1]Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strandobservedAllele : string [0..1]Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strandreferenceAllele : string [0..1]Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)cigar : string [0..1]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 DNAallelicState : CodeableConcept [0..1] « LOINC answer list for AllelicState (Strength=Example)LOINC 53034-5 answerlist?? »Allele frequenciesallelicFrequency : decimal [0..1]Values: amplificaiton / deletion / LOHcopyNumberEvent : CodeableConcept [0..1]Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]CoordinateThe chromosome containing the genetic finding. The value set will be 1-22, X, Y when the species is human without chromosome abnormality. Otherwise, NCBI-Gene code system should be usedchromosome : CodeableConcept [0..1]Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strandstart : integer [0..1]Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strandend : integer [0..1]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 usedgenomeBuild : CodeableConcept [0..1]Quality0-based start position (inclusive) of the sequencestart : integer [0..1]0-based end position (exclusive) of the sequenceend : integer [0..1]Quality scorescore : Quantity [0..1]Platformplatform : CodeableConcept [0..1]ChipChip idchipId : string [0..1]Chip manufacturer idmanufacturerId : string [0..1]Chip versionversion : string [0..1]RepositoryURI of a GA4GH repository which contains further details about the genetics dataurl : uri [0..1]URI of a GA4GH repository which contains further details about the genetics dataname : string [0..1]URI of the page containing information about the structure of the repositorystructure : uri [0..1]Id of the GA4GH call set that matches identity of patient. A CallSet in GA4GH represents an individualvariantId : string [0..1]Id of the GA4GH read group from which details about the sequence can be found. A read group in GA4GH represents a set of DNA reads processed the same way by the sequencerreadGroupSetId : string [0..1]The coordinate of the variantcoordinate[0..*]Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processingquality[0..*]Information of chipchip[0..1]External repositoryrepository[0..*]

XML Template

<Sequence xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <type value="[code]"/><!-- 1..1 AA | DNA | RNA -->
 <variationID><!-- 0..* CodeableConcept Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used --></variationID>
 <referenceSeq><!-- 0..1 CodeableConcept Reference identifier.  It must match the type in the Sequence.type field --></referenceSeq>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <coordinate>  <!-- 0..* The coordinate of the variant -->
  <chromosome><!-- 0..1 CodeableConcept The chromosome containing the genetic finding --></chromosome>
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the sequence -->
  <genomeBuild><!-- 0..1 CodeableConcept The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' --></genomeBuild>
 </coordinate>
 <species><!-- 0..1 CodeableConcept Supporting tests of human, viruses, and bacteria --></species>
 <observedAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence -->
 <referenceAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence -->
 <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
 <quality>  <!-- 0..* Sequence Quality -->
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the sequence -->
  <score><!-- 0..1 Quantity Quality score --></score>
  <platform><!-- 0..1 CodeableConcept Platform --></platform>
 </quality>
 <allelicState><!-- 0..1 CodeableConcept The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous --></allelicState>
 <allelicFrequency value="[decimal]"/><!-- 0..1 Allele frequencies -->
 <copyNumberEvent><!-- 0..1 CodeableConcept Copy Number Event: Values: amplificaiton / deletion / LOH --></copyNumberEvent>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <chip>  <!-- 0..1 Information of chip -->
  <chipId value="[string]"/><!-- 0..1 Chip id -->
  <manufacturerId value="[string]"/><!-- 0..1 Chip manufacturer id -->
  <version value="[string]"/><!-- 0..1 Chip version -->
 </chip>
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <structure value="[uri]"/><!-- 0..1 URI of the page containing information about the structure of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of a GA4GH variant -->
  <readGroupSetId value="[string]"/><!-- 0..1 Id of a GA4GH read group -->
 </repository>
</Sequence>

JSON Template

{doco
  "resourceType" : "Sequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "type" : "<code>", // R!  AA | DNA | RNA
  "variationID" : [{ CodeableConcept }], // Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used
  "referenceSeq" : { CodeableConcept }, // Reference identifier.  It must match the type in the Sequence.type field
  "quantity" : { Quantity }, // Quantity of the sequence
  "coordinate" : [{ // The coordinate of the variant
    "chromosome" : { CodeableConcept }, // The chromosome containing the genetic finding
    "start" : <integer>, // 0-based start position (inclusive) of the sequence
    "end" : <integer>, // 0-based end position (exclusive) of the sequence
    "genomeBuild" : { CodeableConcept } // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
  }],
  "species" : { CodeableConcept }, // Supporting tests of human, viruses, and bacteria
  "observedAllele" : "<string>", // Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence
  "referenceAllele" : "<string>", // Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence
  "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
  "quality" : [{ // Sequence Quality
    "start" : <integer>, // 0-based start position (inclusive) of the sequence
    "end" : <integer>, // 0-based end position (exclusive) of the sequence
    "score" : { Quantity }, // Quality score
    "platform" : { CodeableConcept } // Platform
  }],
  "allelicState" : { CodeableConcept }, // The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
  "allelicFrequency" : <decimal>, // Allele frequencies
  "copyNumberEvent" : { CodeableConcept }, // Copy Number Event: Values: amplificaiton / deletion / LOH
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "chip" : { // Information of chip
    "chipId" : "<string>", // Chip id
    "manufacturerId" : "<string>", // Chip manufacturer id
    "version" : "<string>" // Chip version
  },
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "structure" : "<uri>", // URI of the page containing information about the structure of the repository
    "variantId" : "<string>", // Id of a GA4GH variant
    "readGroupSetId" : "<string>" // Id of a GA4GH read group
  }]
}

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceA Sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... variationID Σ0..*CodeableConceptIdentifier for variant and ClinVar, dbSNP or COSMIC identifier should be used
dbSNP (Example)
... referenceSeq Σ0..1CodeableConceptReference identifier. It must match the type in the Sequence.type field
ENSEMBL (Example)
... quantity Σ0..1QuantityQuantity of the sequence
... coordinate Σ0..*BackboneElementThe coordinate of the variant
.... chromosome Σ0..1CodeableConceptThe chromosome containing the genetic finding
.... start Σ0..1integer0-based start position (inclusive) of the sequence
.... end Σ0..1integer0-based end position (exclusive) of the sequence
.... genomeBuild Σ0..1CodeableConceptThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
... species Σ0..1CodeableConceptSupporting tests of human, viruses, and bacteria
... observedAllele Σ0..1stringNucleotide(s)/amino acids from start position of sequence to stop position of observed sequence
... referenceAllele Σ0..1stringNucleotide(s)/amino acids from start position of sequence to stop position of reference sequence
... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
... quality Σ0..*BackboneElementSequence Quality
.... start Σ0..1integer0-based start position (inclusive) of the sequence
.... end Σ0..1integer0-based end position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... platform Σ0..1CodeableConceptPlatform
... allelicState Σ0..1CodeableConceptThe level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
LOINC 53034-5 answerlist (Example)
... allelicFrequency Σ0..1decimalAllele frequencies
... copyNumberEvent Σ0..1CodeableConceptCopy Number Event: Values: amplificaiton / deletion / LOH
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... chip Σ0..1BackboneElementInformation of chip
.... chipId Σ0..1stringChip id
.... manufacturerId Σ0..1stringChip manufacturer id
.... version Σ0..1stringChip version
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... structure Σ0..1uriURI of the page containing information about the structure of the repository
.... variantId Σ0..1stringId of a GA4GH variant
.... readGroupSetId Σ0..1stringId of a GA4GH read group

doco Documentation for this format

UML Diagram

Sequence (DomainResource)Amino acid / cDNA transcript / RNA variationtype : code [1..1] « Type if a sequence -- DNA, RNA, or amino acid sequence (Strength=Example)sequenceType?? »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)variationID : CodeableConcept [0..*] « Variant ID (Strength=Example)dbSNP?? »Reference identifier for cDNA transcript/protein, with version, from NCBI's RefSeq or ENSEMBL. This reference sequence identifier must match the type in the Sequence.type fieldreferenceSeq : CodeableConcept [0..1] « Reference identifier (Strength=Example)ENSEMBL?? »Quantity of the sequencequantity : Quantity [0..1]The organism from which sample of the sequence was extracted. Supporting tests of human, viruses, and bacteriaspecies : CodeableConcept [0..1]Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strandobservedAllele : string [0..1]Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strandreferenceAllele : string [0..1]Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)cigar : string [0..1]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 DNAallelicState : CodeableConcept [0..1] « LOINC answer list for AllelicState (Strength=Example)LOINC 53034-5 answerlist?? »Allele frequenciesallelicFrequency : decimal [0..1]Values: amplificaiton / deletion / LOHcopyNumberEvent : CodeableConcept [0..1]Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]CoordinateThe chromosome containing the genetic finding. The value set will be 1-22, X, Y when the species is human without chromosome abnormality. Otherwise, NCBI-Gene code system should be usedchromosome : CodeableConcept [0..1]Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strandstart : integer [0..1]Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strandend : integer [0..1]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 usedgenomeBuild : CodeableConcept [0..1]Quality0-based start position (inclusive) of the sequencestart : integer [0..1]0-based end position (exclusive) of the sequenceend : integer [0..1]Quality scorescore : Quantity [0..1]Platformplatform : CodeableConcept [0..1]ChipChip idchipId : string [0..1]Chip manufacturer idmanufacturerId : string [0..1]Chip versionversion : string [0..1]RepositoryURI of a GA4GH repository which contains further details about the genetics dataurl : uri [0..1]URI of a GA4GH repository which contains further details about the genetics dataname : string [0..1]URI of the page containing information about the structure of the repositorystructure : uri [0..1]Id of the GA4GH call set that matches identity of patient. A CallSet in GA4GH represents an individualvariantId : string [0..1]Id of the GA4GH read group from which details about the sequence can be found. A read group in GA4GH represents a set of DNA reads processed the same way by the sequencerreadGroupSetId : string [0..1]The coordinate of the variantcoordinate[0..*]Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processingquality[0..*]Information of chipchip[0..1]External repositoryrepository[0..*]

XML Template

<Sequence xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <type value="[code]"/><!-- 1..1 AA | DNA | RNA -->
 <variationID><!-- 0..* CodeableConcept Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used --></variationID>
 <referenceSeq><!-- 0..1 CodeableConcept Reference identifier.  It must match the type in the Sequence.type field --></referenceSeq>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <coordinate>  <!-- 0..* The coordinate of the variant -->
  <chromosome><!-- 0..1 CodeableConcept The chromosome containing the genetic finding --></chromosome>
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the sequence -->
  <genomeBuild><!-- 0..1 CodeableConcept The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' --></genomeBuild>
 </coordinate>
 <species><!-- 0..1 CodeableConcept Supporting tests of human, viruses, and bacteria --></species>
 <observedAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence -->
 <referenceAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence -->
 <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
 <quality>  <!-- 0..* Sequence Quality -->
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the sequence -->
  <score><!-- 0..1 Quantity Quality score --></score>
  <platform><!-- 0..1 CodeableConcept Platform --></platform>
 </quality>
 <allelicState><!-- 0..1 CodeableConcept The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous --></allelicState>
 <allelicFrequency value="[decimal]"/><!-- 0..1 Allele frequencies -->
 <copyNumberEvent><!-- 0..1 CodeableConcept Copy Number Event: Values: amplificaiton / deletion / LOH --></copyNumberEvent>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <chip>  <!-- 0..1 Information of chip -->
  <chipId value="[string]"/><!-- 0..1 Chip id -->
  <manufacturerId value="[string]"/><!-- 0..1 Chip manufacturer id -->
  <version value="[string]"/><!-- 0..1 Chip version -->
 </chip>
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <structure value="[uri]"/><!-- 0..1 URI of the page containing information about the structure of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of a GA4GH variant -->
  <readGroupSetId value="[string]"/><!-- 0..1 Id of a GA4GH read group -->
 </repository>
</Sequence>

JSON Template

{doco
  "resourceType" : "Sequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "type" : "<code>", // R!  AA | DNA | RNA
  "variationID" : [{ CodeableConcept }], // Identifier for variant and ClinVar, dbSNP or COSMIC identifier should be used
  "referenceSeq" : { CodeableConcept }, // Reference identifier.  It must match the type in the Sequence.type field
  "quantity" : { Quantity }, // Quantity of the sequence
  "coordinate" : [{ // The coordinate of the variant
    "chromosome" : { CodeableConcept }, // The chromosome containing the genetic finding
    "start" : <integer>, // 0-based start position (inclusive) of the sequence
    "end" : <integer>, // 0-based end position (exclusive) of the sequence
    "genomeBuild" : { CodeableConcept } // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
  }],
  "species" : { CodeableConcept }, // Supporting tests of human, viruses, and bacteria
  "observedAllele" : "<string>", // Nucleotide(s)/amino acids from start position of sequence to stop position of observed sequence
  "referenceAllele" : "<string>", // Nucleotide(s)/amino acids from start position of sequence to stop position of reference sequence
  "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
  "quality" : [{ // Sequence Quality
    "start" : <integer>, // 0-based start position (inclusive) of the sequence
    "end" : <integer>, // 0-based end position (exclusive) of the sequence
    "score" : { Quantity }, // Quality score
    "platform" : { CodeableConcept } // Platform
  }],
  "allelicState" : { CodeableConcept }, // The level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
  "allelicFrequency" : <decimal>, // Allele frequencies
  "copyNumberEvent" : { CodeableConcept }, // Copy Number Event: Values: amplificaiton / deletion / LOH
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "chip" : { // Information of chip
    "chipId" : "<string>", // Chip id
    "manufacturerId" : "<string>", // Chip manufacturer id
    "version" : "<string>" // Chip version
  },
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "structure" : "<uri>", // URI of the page containing information about the structure of the repository
    "variantId" : "<string>", // Id of a GA4GH variant
    "readGroupSetId" : "<string>" // Id of a GA4GH read group
  }]
}

 

Alternate definitions: Schema/Schematron, Resource Profile (XML, JSON), Questionnaire

4.33.4.1 Terminology Bindings

PathDefinitionTypeReference
Sequence.type Type if a sequence -- DNA, RNA, or amino acid sequenceExamplesequenceType
Sequence.variationID Variant IDExampledbSNP
Sequence.referenceSeq Reference identifierExampleENSEMBL
Sequence.allelicState LOINC answer list for AllelicStateExampleLOINC 53034-5 answerlist

4.33.5 Search Parameters

Search parameters for this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

NameTypeDescriptionPaths
chromosometokenChromosome of the sequenceSequence.coordinate.chromosome
coordinatecompositeGenomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
endnumberEnd position (0-based exclusive) of the sequenceSequence.coordinate.end
speciestokenThe organism from which sample of the sequence was extracted.Sequence.species
startnumberStart position (0-based inclusive) of the sequenceSequence.coordinate.start
typetokenThe type of the variant: Amino acid / cDNA transcript / RNA variation.Sequence.type
variationidtokenIdentifier for variantSequence.variationID