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4.37 Resource Sequence - Content

Clinical Genomics

Work Group

Maturity Level: 0

Compartments: 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:

Variant Databases: dbSNP , ClinVar , and COSMIC
Reference Sequences: RefSeq and ENSEMBL

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.

Structure

Name	Flags	Card.	Type	Description & Constraints
Sequence	Σ		DomainResource	A Sequence
type	Σ	1..1	code	AA \| DNA \| RNA sequenceType (Example)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
quantity	Σ	0..1	Quantity	Quantity of the sequence
species	Σ	0..1	CodeableConcept	Supporting tests of human, viruses, and bacteria SNOMED CT Codes for species (Example)
referenceSeq	Σ	0..*	BackboneElement	Reference sequence
chromosome	Σ	0..1	CodeableConcept	The chromosome containing the genetic finding chromosome-human (Example)
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
referenceSeqId	Σ	1..1	CodeableConcept	Reference identifier ENSEMBL (Example)
referenceSeqPointer	Σ	0..1	Reference(Sequence)	A Pointer to another Sequence entity as refence sequence
referenceSeqString	Σ	0..1	string	A Reference Sequence string
windowStart	Σ	1..1	integer	0-based start position (inclusive) of the window on the reference sequence
windowEnd	Σ	1..1	integer	0-based end position (exclusive) of the window on the reference sequence
variation	Σ	0..1	BackboneElement	Variation info in this sequence
start	Σ	0..1	integer	0-based start position (inclusive) of the variation on the reference sequence
end	Σ	0..1	integer	0-based end position (exclusive) of the variation on the reference sequence
observedAllele	Σ	0..1	string	Nucleotide(s)/amino acids from start position to stop position of observed variation
referenceAllele	Σ	0..1	string	Nucleotide(s)/amino acids from start position to stop position of reference variation
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
quality	Σ	0..*	BackboneElement	Sequence Quality
start	Σ	0..1	integer	0-based start position (inclusive) of the sequence
end	Σ	0..1	integer	0-based end position (exclusive) of the sequence
score	Σ	0..1	Quantity	Quality score
method	Σ	0..1	string	Method for quality
allelicState	Σ	0..1	CodeableConcept	The 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	Σ	0..1	decimal	Allele frequencies
copyNumberEvent	Σ	0..1	CodeableConcept	Copy Number Event: Values: amplificaiton / deletion / LOH CopyNumberEvent (Example)
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Name of the repository
variantId	Σ	0..1	string	Id of the variant
readId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(Sequence)	Pointer to next atomic sequence
observedSeq	Σ	0..1	string	Observed Sequence
observation	Σ	0..1	Reference(Observation)	Observation-genetics
structureVariation	Σ	0..1	BackboneElement
precisionOfBoundaries	Σ	0..1	string	Precision of boundaries
reportedaCGHRatio	Σ	0..1	decimal	Structural Variant reported aCGH ratio
length	Σ	0..1	integer	Structural Variant Length
outer	Σ	0..1	BackboneElement
start	Σ	0..1	integer	Structural Variant Outer Start-End
end	Σ	0..1	integer	Structural Variant Outer Start-End
inner	Σ	0..1	BackboneElement
start	Σ	0..1	integer	Structural Variant Inner Start-End
end	Σ	0..1	integer	Structural Variant Inner Start-End
Documentation for this format

UML Diagram

XML Template

<Sequence xmlns="http://hl7.org/fhir"> 
 <!-- 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

{
  "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

Name	Flags	Card.	Type	Description & Constraints
Sequence	Σ		DomainResource	A Sequence
type	Σ	1..1	code	AA \| DNA \| RNA sequenceType (Example)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
quantity	Σ	0..1	Quantity	Quantity of the sequence
species	Σ	0..1	CodeableConcept	Supporting tests of human, viruses, and bacteria SNOMED CT Codes for species (Example)
referenceSeq	Σ	0..*	BackboneElement	Reference sequence
chromosome	Σ	0..1	CodeableConcept	The chromosome containing the genetic finding chromosome-human (Example)
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
referenceSeqId	Σ	1..1	CodeableConcept	Reference identifier ENSEMBL (Example)
referenceSeqPointer	Σ	0..1	Reference(Sequence)	A Pointer to another Sequence entity as refence sequence
referenceSeqString	Σ	0..1	string	A Reference Sequence string
windowStart	Σ	1..1	integer	0-based start position (inclusive) of the window on the reference sequence
windowEnd	Σ	1..1	integer	0-based end position (exclusive) of the window on the reference sequence
variation	Σ	0..1	BackboneElement	Variation info in this sequence
start	Σ	0..1	integer	0-based start position (inclusive) of the variation on the reference sequence
end	Σ	0..1	integer	0-based end position (exclusive) of the variation on the reference sequence
observedAllele	Σ	0..1	string	Nucleotide(s)/amino acids from start position to stop position of observed variation
referenceAllele	Σ	0..1	string	Nucleotide(s)/amino acids from start position to stop position of reference variation
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
quality	Σ	0..*	BackboneElement	Sequence Quality
start	Σ	0..1	integer	0-based start position (inclusive) of the sequence
end	Σ	0..1	integer	0-based end position (exclusive) of the sequence
score	Σ	0..1	Quantity	Quality score
method	Σ	0..1	string	Method for quality
allelicState	Σ	0..1	CodeableConcept	The 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	Σ	0..1	decimal	Allele frequencies
copyNumberEvent	Σ	0..1	CodeableConcept	Copy Number Event: Values: amplificaiton / deletion / LOH CopyNumberEvent (Example)
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Name of the repository
variantId	Σ	0..1	string	Id of the variant
readId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(Sequence)	Pointer to next atomic sequence
observedSeq	Σ	0..1	string	Observed Sequence
observation	Σ	0..1	Reference(Observation)	Observation-genetics
structureVariation	Σ	0..1	BackboneElement
precisionOfBoundaries	Σ	0..1	string	Precision of boundaries
reportedaCGHRatio	Σ	0..1	decimal	Structural Variant reported aCGH ratio
length	Σ	0..1	integer	Structural Variant Length
outer	Σ	0..1	BackboneElement
start	Σ	0..1	integer	Structural Variant Outer Start-End
end	Σ	0..1	integer	Structural Variant Outer Start-End
inner	Σ	0..1	BackboneElement
start	Σ	0..1	integer	Structural Variant Inner Start-End
end	Σ	0..1	integer	Structural Variant Inner Start-End
Documentation for this format

UML Diagram

XML Template

<Sequence xmlns="http://hl7.org/fhir"> 
 <!-- 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

{
  "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

Path	Definition	Type	Reference
Sequence.type	Type if a sequence -- DNA, RNA, or amino acid sequence	Example	sequenceType
Sequence.species	Species of the organism from which the sequence was extracted	Example	SNOMED CT Codes for species
Sequence.referenceSeq.chromosome	Chromosome number for human	Example	chromosome-human
Sequence.referenceSeq.referenceSeqId	Reference identifier	Example	ENSEMBL
Sequence.allelicState	LOINC answer list for AllelicState	Example	LOINC 53034-5 answerlist
Sequence.copyNumberEvent	Copy Number Event	Example	CopyNumberEvent

Path

Definition

Type

Reference

Sequence.type

Type if a sequence -- DNA, RNA, or amino acid sequence

Example

sequenceType

Sequence.species

Species of the organism from which the sequence was extracted

Example

SNOMED CT Codes for species

Sequence.referenceSeq.chromosome

Chromosome number for human

Example

chromosome-human

Sequence.referenceSeq.referenceSeqId

Reference identifier

Example

ENSEMBL

Sequence.allelicState

LOINC answer list for AllelicState

Example

LOINC 53034-5 answerlist

Sequence.copyNumberEvent

Copy Number Event

Example

CopyNumberEvent

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.

Name	Type	Description	Paths
chromosome	token	Chromosome of the sequence	Sequence.referenceSeq.chromosome
coordinate	composite	Genomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
end	number	End position (0-based exclusive) of the sequence	Sequence.variation.end
patient	reference	The subject that the observation is about	Sequence.patient (Patient)
species	token	The organism from which sample of the sequence was extracted.	Sequence.species
start	number	Start position (0-based inclusive) of the sequence	Sequence.variation.start
type	token	The type of the variant: Amino acid / cDNA transcript / RNA variation.	Sequence.type