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A Sequence resource stores data about a patient's DNA or RNA sequences.
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Sequence |
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Field Name |
Field Type |
Cardinality |
Description |
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genomeBuild1 |
string |
1 |
Assembly of the sequence |
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type2 |
code |
1 |
Type of the sequence. One of dna, rna, or aa. |
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quantity2 |
quantity |
0..1 |
Quantity of sequence presented in the sample |
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referenceSeq2
|
string |
0..1 |
Reference of the sequence (IUPAC format) |
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observedSeq2
|
string |
1 |
Read string for the sequence (IUPAC format) |
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cigar1 |
string |
0..1 |
CIGAR string for the sequence |
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source2 |
0..1 |
Source of the sequence. |
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source.sample |
code |
0..1 |
Type of the sample of the sequence. One of prenatal, somatic, or germline. |
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source.lab |
Resource (Procedure) |
0..1 |
Procedure in which the sequence is determined. |
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chromosome1 |
string |
1 |
Chromosome of the sequence. The chromosome containing the genetic finding. e.g. "1" for chromosome 1 |
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startPosition1 (GenomicStart) |
integer |
1 |
Start of the sequence. 0-based |
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endPosition1 (GenomicStop) |
integer |
1 |
End of the sequence |
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species1 |
CodeableConcept |
1 |
Species identifier (NCBI taxonomy) |
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patient |
Resource (Patient) |
1 |
Genetic lab’s patient ID for this sequence |
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1 Adopted from SMART into the HL7 Clinical Genomics Standard Profile for Genetics. Where elements were constrained for integration into the observation profile which is limited to genetic information, the FHIR DSTU2 name is in parenthesis.
2 Sequence and Sequencing Lab Resources are undergoing HL7 review for inclusion in FHIR DSTU3.
3 These components are inherited from the FHIR Observation resource.
4 These components focus on HL7 standard reporting findings based on traditional genetic testing technologies.
Gets a Sequence
HTTP Request: GET /Sequence/{Id}
Parameters:
Id - ID of Sequence to get
Permission Scope: user/Sequence.read or patient/Sequence.read
Request Body: None
Response Body: If successful, returns the requested Sequence resource
Updates a Sequence
HTTP Request: PUT /Sequence/{Id}
Parameters:
Id - ID of Sequence to update
Permission Scope: user/Sequence.write or patient/Sequence.write
Request Body: Sequence Resource with updated values
Response Body: None
Searches for a Sequence
HTTP Request: GET /Sequence
Parameters:
Coordinate - Coordinate of sequence (Chromosome:Start-End format)
Source - Source of sequence
Patient - Patient sequence is coming from
Type - Type of sequence
Permission Scope: User/Sequence.read or Patient/Sequence.read
Request Body: None
Response: If successful, returns the Sequences that match the search parameters