STU 3 Candidate

This page is part of the FHIR Specification (v1.4.0: STU 3 Ballot 3). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

4.37 Resource Sequence - Content

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

Variation and Sequence data.

4.37.1 Scope and Usage

The Sequence resource is designed to describe an atomic sequence which contains more than one bases but has at most one variation. Atomic sequences can be connected by link element and they will lead to sequence graph. By this method, a sequence can be reported. 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).

4.37.1.1 Genetic Standards and Resources include:

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.

4.37.2 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.

4.37.3 Resource Content

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceA Sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... quantity Σ0..1QuantityQuantity of the sequence
... species Σ0..1CodeableConceptSupporting tests of human, viruses, and bacteria
SNOMED CT Codes for species (Example)
... referenceSeq Σ0..*BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptThe chromosome containing the genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ1..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... windowStart Σ1..1integer0-based start position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integer0-based end position (exclusive) of the window on the reference sequence
... variation Σ0..1BackboneElementVariation info in this sequence
.... start Σ0..1integer0-based start position (inclusive) of the variation on the reference sequence
.... end Σ0..1integer0-based end position (exclusive) of the variation on the reference sequence
.... observedAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of observed variation
.... referenceAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of reference variation
.... 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
.... method Σ0..1stringMethod for quality
... 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
CopyNumberEvent (Example)
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... variantId Σ0..1stringId of the variant
.... readId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... observedSeq Σ0..1stringObserved Sequence
... observation Σ0..1Reference(Observation)Observation-genetics
... structureVariation Σ0..1BackboneElement
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Outer Start-End
..... end Σ0..1integerStructural Variant Outer Start-End
.... inner Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Inner Start-End
..... end Σ0..1integerStructural Variant Inner Start-End

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?? »The patient, or group of patients whose sequencing results are described by this resourcepatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »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] « Species of the organism from which the sequence was extracted (Strength=Example)SNOMED CT Codes for species?? »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] « Copy Number Event (Strength=Example)CopyNumberEvent?? »Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]Pointer to next atomic sequence which at most contains one variationpointer : Reference [0..*] « Sequence »Observed SequenceobservedSeq : string [0..1]Analysis of the sequenceobservation : Reference [0..1] « Observation »ReferenceSeqThe 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] « Chromosome number for human (Strength=Example)chromosome-human?? »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 : string [0..1]Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_� identifies reference sequence for genes, “NM_� for messenger RNA transcripts, and “NP_� for amino acid sequencesreferenceSeqId : CodeableConcept [1..1] « Reference identifier (Strength=Example)ENSEMBL?? »A Pointer to another Sequence entity as refence sequencereferenceSeqPointer : Reference [0..1] « Sequence »A Reference Sequence stringreferenceSeqString : string [0..1]0-based start position (inclusive) of the window on the reference sequencewindowStart : integer [1..1]0-based end position (exclusive) of the window on the reference sequencewindowEnd : integer [1..1]Variation0-based start position (inclusive) of the variation on the reference sequencestart : integer [0..1]0-based end position (exclusive) of the variation on the reference sequenceend : integer [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]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]Method for qualitymethod : string [0..1]RepositoryURI of an external repository which contains further details about the genetics dataurl : uri [0..1]URI of an external repository which contains further details about the genetics dataname : string [0..1]Id of the variation in this external repositoryvariantId : string [0..1]Id of the read in this external repositoryreadId : string [0..1]StructureVariationPrecision of boundariesprecisionOfBoundaries : string [0..1]Structural Variant reported aCGH ratioreportedaCGHRatio : decimal [0..1]Structural Variant Lengthlength : integer [0..1]OuterStructural Variant Outer Start-Endstart : integer [0..1]Structural Variant Outer Start-Endend : integer [0..1]InnerStructural Variant Inner Start-Endstart : integer [0..1]Structural Variant Inner Start-Endend : integer [0..1]Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) referenceSeq[0..*]Variation info in this sequencevariation[0..1]Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processingquality[0..*]Configurations of the external repositoryrepository[0..*]Structural variant outerouter[0..1]Structural variant innerinner[0..1]Structural variantstructureVariation[0..1]

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 -->
 <patient><!-- 0..1 Reference(Patient) Who and/or what this is about --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <species><!-- 0..1 CodeableConcept Supporting tests of human, viruses, and bacteria --></species>
 <referenceSeq>  <!-- 0..* Reference sequence -->
  <chromosome><!-- 0..1 CodeableConcept The chromosome containing the genetic finding --></chromosome>
  <genomeBuild value="[string]"/><!-- 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' -->
  <referenceSeqId><!-- 1..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(Sequence) A Pointer to another Sequence entity as refence sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A Reference Sequence string -->
  <windowStart value="[integer]"/><!-- 1..1 0-based start position (inclusive) of the window on the  reference sequence -->
  <windowEnd value="[integer]"/><!-- 1..1 0-based end position (exclusive) of the window on the reference sequence -->
 </referenceSeq>
 <variation>  <!-- 0..1 Variation info in this sequence -->
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the variation on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the variation on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position to stop position of observed variation -->
  <referenceAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position to stop position of reference variation -->
  <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
 </variation>
 <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>
  <method value="[string]"/><!-- 0..1 Method for quality -->
 </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 -->
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of the variant -->
  <readId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(Sequence) Pointer to next atomic sequence --></pointer>
 <observedSeq value="[string]"/><!-- 0..1 Observed Sequence -->
 <observation><!-- 0..1 Reference(Observation) Observation-genetics --></observation>
 <structureVariation> 
  <precisionOfBoundaries value="[string]"/><!-- 0..1 Precision of boundaries -->
  <reportedaCGHRatio value="[decimal]"/><!-- 0..1 Structural Variant reported aCGH ratio -->
  <length value="[integer]"/><!-- 0..1 Structural Variant Length -->
  <outer> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
  </outer>
  <inner> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
  </inner>
 </structureVariation>
</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
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "quantity" : { Quantity }, // Quantity of the sequence
  "species" : { CodeableConcept }, // Supporting tests of human, viruses, and bacteria
  "referenceSeq" : [{ // Reference sequence
    "chromosome" : { CodeableConcept }, // The chromosome containing the genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "referenceSeqId" : { CodeableConcept }, // R!  Reference identifier
    "referenceSeqPointer" : { Reference(Sequence) }, // A Pointer to another Sequence entity as refence sequence
    "referenceSeqString" : "<string>", // A Reference Sequence string
    "windowStart" : <integer>, // R!  0-based start position (inclusive) of the window on the  reference sequence
    "windowEnd" : <integer> // R!  0-based end position (exclusive) of the window on the reference sequence
  }],
  "variation" : { // Variation info in this sequence
    "start" : <integer>, // 0-based start position (inclusive) of the variation on the  reference sequence
    "end" : <integer>, // 0-based end position (exclusive) of the variation on the reference sequence
    "observedAllele" : "<string>", // Nucleotide(s)/amino acids from start position to stop position of observed variation
    "referenceAllele" : "<string>", // Nucleotide(s)/amino acids from start position to stop position of reference variation
    "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
    "method" : "<string>" // Method for quality
  }],
  "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
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "variantId" : "<string>", // Id of the variant
    "readId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(Sequence) }], // Pointer to next atomic sequence
  "observedSeq" : "<string>", // Observed Sequence
  "observation" : { Reference(Observation) }, // Observation-genetics
  "structureVariation" : { // 
    "precisionOfBoundaries" : "<string>", // Precision of boundaries
    "reportedaCGHRatio" : <decimal>, // Structural Variant reported aCGH ratio
    "length" : <integer>, // Structural Variant Length
    "outer" : { // 
      "start" : <integer>, // Structural Variant Outer Start-End
      "end" : <integer> // Structural Variant Outer Start-End
    },
    "inner" : { // 
      "start" : <integer>, // Structural Variant Inner Start-End
      "end" : <integer> // Structural Variant Inner Start-End
    }
  }
}

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceA Sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... quantity Σ0..1QuantityQuantity of the sequence
... species Σ0..1CodeableConceptSupporting tests of human, viruses, and bacteria
SNOMED CT Codes for species (Example)
... referenceSeq Σ0..*BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptThe chromosome containing the genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ1..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... windowStart Σ1..1integer0-based start position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integer0-based end position (exclusive) of the window on the reference sequence
... variation Σ0..1BackboneElementVariation info in this sequence
.... start Σ0..1integer0-based start position (inclusive) of the variation on the reference sequence
.... end Σ0..1integer0-based end position (exclusive) of the variation on the reference sequence
.... observedAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of observed variation
.... referenceAllele Σ0..1stringNucleotide(s)/amino acids from start position to stop position of reference variation
.... 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
.... method Σ0..1stringMethod for quality
... 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
CopyNumberEvent (Example)
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... variantId Σ0..1stringId of the variant
.... readId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... observedSeq Σ0..1stringObserved Sequence
... observation Σ0..1Reference(Observation)Observation-genetics
... structureVariation Σ0..1BackboneElement
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Outer Start-End
..... end Σ0..1integerStructural Variant Outer Start-End
.... inner Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Inner Start-End
..... end Σ0..1integerStructural Variant Inner Start-End

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?? »The patient, or group of patients whose sequencing results are described by this resourcepatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »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] « Species of the organism from which the sequence was extracted (Strength=Example)SNOMED CT Codes for species?? »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] « Copy Number Event (Strength=Example)CopyNumberEvent?? »Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]Pointer to next atomic sequence which at most contains one variationpointer : Reference [0..*] « Sequence »Observed SequenceobservedSeq : string [0..1]Analysis of the sequenceobservation : Reference [0..1] « Observation »ReferenceSeqThe 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] « Chromosome number for human (Strength=Example)chromosome-human?? »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 : string [0..1]Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_� identifies reference sequence for genes, “NM_� for messenger RNA transcripts, and “NP_� for amino acid sequencesreferenceSeqId : CodeableConcept [1..1] « Reference identifier (Strength=Example)ENSEMBL?? »A Pointer to another Sequence entity as refence sequencereferenceSeqPointer : Reference [0..1] « Sequence »A Reference Sequence stringreferenceSeqString : string [0..1]0-based start position (inclusive) of the window on the reference sequencewindowStart : integer [1..1]0-based end position (exclusive) of the window on the reference sequencewindowEnd : integer [1..1]Variation0-based start position (inclusive) of the variation on the reference sequencestart : integer [0..1]0-based end position (exclusive) of the variation on the reference sequenceend : integer [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]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]Method for qualitymethod : string [0..1]RepositoryURI of an external repository which contains further details about the genetics dataurl : uri [0..1]URI of an external repository which contains further details about the genetics dataname : string [0..1]Id of the variation in this external repositoryvariantId : string [0..1]Id of the read in this external repositoryreadId : string [0..1]StructureVariationPrecision of boundariesprecisionOfBoundaries : string [0..1]Structural Variant reported aCGH ratioreportedaCGHRatio : decimal [0..1]Structural Variant Lengthlength : integer [0..1]OuterStructural Variant Outer Start-Endstart : integer [0..1]Structural Variant Outer Start-Endend : integer [0..1]InnerStructural Variant Inner Start-Endstart : integer [0..1]Structural Variant Inner Start-Endend : integer [0..1]Reference Sequence. It can be described in two ways. One is provide the unique identifier of reference sequence submitted to NCBI. The start and end position of window on reference sequence should be defined. The other way is using genome build, chromosome number,and also the start, end position of window (this method is specifically for DNA reference sequence) referenceSeq[0..*]Variation info in this sequencevariation[0..1]Quality for sequence quality vary by platform reflecting differences in sequencing chemistry and digital processingquality[0..*]Configurations of the external repositoryrepository[0..*]Structural variant outerouter[0..1]Structural variant innerinner[0..1]Structural variantstructureVariation[0..1]

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 -->
 <patient><!-- 0..1 Reference(Patient) Who and/or what this is about --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <species><!-- 0..1 CodeableConcept Supporting tests of human, viruses, and bacteria --></species>
 <referenceSeq>  <!-- 0..* Reference sequence -->
  <chromosome><!-- 0..1 CodeableConcept The chromosome containing the genetic finding --></chromosome>
  <genomeBuild value="[string]"/><!-- 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' -->
  <referenceSeqId><!-- 1..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(Sequence) A Pointer to another Sequence entity as refence sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A Reference Sequence string -->
  <windowStart value="[integer]"/><!-- 1..1 0-based start position (inclusive) of the window on the  reference sequence -->
  <windowEnd value="[integer]"/><!-- 1..1 0-based end position (exclusive) of the window on the reference sequence -->
 </referenceSeq>
 <variation>  <!-- 0..1 Variation info in this sequence -->
  <start value="[integer]"/><!-- 0..1 0-based start position (inclusive) of the variation on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 0-based end position (exclusive) of the variation on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position to stop position of observed variation -->
  <referenceAllele value="[string]"/><!-- 0..1 Nucleotide(s)/amino acids from start position to stop position of reference variation -->
  <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
 </variation>
 <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>
  <method value="[string]"/><!-- 0..1 Method for quality -->
 </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 -->
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of the variant -->
  <readId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(Sequence) Pointer to next atomic sequence --></pointer>
 <observedSeq value="[string]"/><!-- 0..1 Observed Sequence -->
 <observation><!-- 0..1 Reference(Observation) Observation-genetics --></observation>
 <structureVariation> 
  <precisionOfBoundaries value="[string]"/><!-- 0..1 Precision of boundaries -->
  <reportedaCGHRatio value="[decimal]"/><!-- 0..1 Structural Variant reported aCGH ratio -->
  <length value="[integer]"/><!-- 0..1 Structural Variant Length -->
  <outer> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
  </outer>
  <inner> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
  </inner>
 </structureVariation>
</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
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "quantity" : { Quantity }, // Quantity of the sequence
  "species" : { CodeableConcept }, // Supporting tests of human, viruses, and bacteria
  "referenceSeq" : [{ // Reference sequence
    "chromosome" : { CodeableConcept }, // The chromosome containing the genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "referenceSeqId" : { CodeableConcept }, // R!  Reference identifier
    "referenceSeqPointer" : { Reference(Sequence) }, // A Pointer to another Sequence entity as refence sequence
    "referenceSeqString" : "<string>", // A Reference Sequence string
    "windowStart" : <integer>, // R!  0-based start position (inclusive) of the window on the  reference sequence
    "windowEnd" : <integer> // R!  0-based end position (exclusive) of the window on the reference sequence
  }],
  "variation" : { // Variation info in this sequence
    "start" : <integer>, // 0-based start position (inclusive) of the variation on the  reference sequence
    "end" : <integer>, // 0-based end position (exclusive) of the variation on the reference sequence
    "observedAllele" : "<string>", // Nucleotide(s)/amino acids from start position to stop position of observed variation
    "referenceAllele" : "<string>", // Nucleotide(s)/amino acids from start position to stop position of reference variation
    "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
    "method" : "<string>" // Method for quality
  }],
  "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
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "variantId" : "<string>", // Id of the variant
    "readId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(Sequence) }], // Pointer to next atomic sequence
  "observedSeq" : "<string>", // Observed Sequence
  "observation" : { Reference(Observation) }, // Observation-genetics
  "structureVariation" : { // 
    "precisionOfBoundaries" : "<string>", // Precision of boundaries
    "reportedaCGHRatio" : <decimal>, // Structural Variant reported aCGH ratio
    "length" : <integer>, // Structural Variant Length
    "outer" : { // 
      "start" : <integer>, // Structural Variant Outer Start-End
      "end" : <integer> // Structural Variant Outer Start-End
    },
    "inner" : { // 
      "start" : <integer>, // Structural Variant Inner Start-End
      "end" : <integer> // Structural Variant Inner Start-End
    }
  }
}

 

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

4.37.3.1 Terminology Bindings

PathDefinitionTypeReference
Sequence.type Type if a sequence -- DNA, RNA, or amino acid sequenceExamplesequenceType
Sequence.species Species of the organism from which the sequence was extractedExampleSNOMED CT Codes for species
Sequence.referenceSeq.chromosome Chromosome number for humanExamplechromosome-human
Sequence.referenceSeq.referenceSeqId Reference identifierExampleENSEMBL
Sequence.allelicState LOINC answer list for AllelicStateExampleLOINC 53034-5 answerlist
Sequence.copyNumberEvent Copy Number EventExampleCopyNumberEvent

4.37.4 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.referenceSeq.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.variation.end
patientreferenceThe subject that the observation is aboutSequence.patient
(Patient)
speciestokenThe organism from which sample of the sequence was extracted.Sequence.species
startnumberStart position (0-based inclusive) of the sequenceSequence.variation.start
typetokenThe type of the variant: Amino acid / cDNA transcript / RNA variation.Sequence.type