Interpretation

This message intends to represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory.

Data model

Field Type Status Description
id string required Arbitrary identifier
resolution_status Resolution_status required The current status of work on the case
phenopacket_or_family Phenopacket or Family element required The subject of this interpretation
diagnosis Diagnosis repeated One or more diagnoses, if made
meta_data See MetaData required Metadata about this interpretation

Example

 {
 "id": "SOLVERD:0000123456",
 "resolutionStatus": "SOLVED",
 "phenopacket": {
   "id": "SOLVERD:0000234567",
   "subject": {
     "id": "SOLVERD:0000345678",
     "dateOfBirth": "1998-01-01T00:00:00Z",
     "sex": "MALE"
   },
   "phenotypicFeatures": [{
     "type": {
       "id": "HP:0001159",
       "label": "Syndactyly"
     },
     "classOfOnset": {
       "id": "HP:0003577",
       "label": "Congenital onset"
     }
   }, {
     "type": {
       "id": "HP:0002090",
       "label": "Pneumonia"
     },
     "classOfOnset": {
       "id": "HP:0011463",
       "label": "Childhood onset"
     }
   }, {
     "type": {
       "id": "HP:0000028",
       "label": "Cryptorchidism"
     },
     "classOfOnset": {
       "id": "HP:0003577",
       "label": "Congenital onset"
     }
   }, {
     "type": {
       "id": "HP:0011109",
       "label": "Chronic sinusitis"
     },
     "severity": {
       "id": "HP:0012828",
       "label": "Severe"
     },
     "classOfOnset": {
       "id": "HP:0003581",
       "label": "Adult onset"
     }
   }],
   "variants": [{
     "hgvsAllele": {
       "hgvs": "NM_001361.4:c.403C\u003eT"
     },
     "zygosity": {
       "id": "GENO:0000135",
       "label": "heterozygous"
     }
   }, {
     "hgvsAllele": {
       "hgvs": "NM_001361.4:c.454G\u003eA"
     },
     "zygosity": {
       "id": "GENO:0000135",
       "label": "heterozygous"
     }
   }, {
     "hgvsAllele": {
       "hgvs": "NM_001369.2:c.12599dupA"
     },
     "zygosity": {
       "id": "GENO:0000136",
       "label": "homozygous"
     }
   }]
 },
 "diagnosis": [{
   "disease": {
     "term": {
       "id": "OMIM:263750",
       "label": "Miller syndrome"
     }
   },
   "genomicInterpretations": [{
     "status": "CAUSATIVE",
     "gene": {
       "id": "HGNC:2867",
       "symbol": "DHODH"
     }
   }]
 }]
}

id

The id has the same interpretation as the id element in the Individual element.

Resolution_status

The interpretation has a ResolutionStatus that refers to the status of the attempted diagnosis.

Data model

Name Description
UNKNOWN No information is available about the diagnosis
SOLVED The interpretation is considered to be a definitive diagnosis
UNSOLVED No definitive diagnosis was found
IN_PROGRESS No diagnosis has been found to date but additional differential diagnostic work is in progress.

Example

{
   "resolutionStatus": "SOLVED"
}

phenopacket_or_family

This element refers to the Phenopacket or Family element for whom the interpretation is being made.

diagnosis

This refers to the diagnosis (or if applicable to the diagnoses) made. See Diagnosis, below.

meta_data

This element contains structured definitions of the resources and ontologies used within the phenopacket. See MetaData for further information.

Diagnosis

The diagnosis element is meant to refer to the disease that is infered to be present in the individual or family being analyzed. The diagnosis can be made by means of an analysis of the phenotypic or the genomic findings or both. The element is optional because if the resolution_status is UNSOLVED then there is no diagnosis.

Data elements

Field Type Status Description
disease Disease required The diagnosed condition
genomic_interpretations GenomicInterpretation repeated The genomic elements assessed as being responsible for the disease or empty

Example

{
   "disease": {
     "term": {
       "id": "OMIM:263750",
       "label": "Miller syndrome"
     }
   },
   "genomicInterpretations": [{
     "status": "CAUSATIVE",
     "gene": {
       "id": "HGNC:2867",
       "symbol": "DHODH"
     }
   }]
}

The genomic_interpretations should be used if the genetic findings were used to help make the diagnosis, but can be omitted if genetic/genomic analysis was not contributory or were not performed.

GenomicInterpretation

A statement about the contribution of a genomic element towards the observed phenotype. Note that this does not intend to encode any knowledge or results of specific computations.

Data model
Field Type Status Example
status GenomicInterpretation Status required How the call of this GenomicInterpretation was interpreted
call Gene or Variant required The gene or variant contributing to the diagnosis

Example

{
  "status": "CAUSATIVE",
  "gene": {
    "id": "HGNC:2867",
    "symbol": "DHODH"
  }
}

A gene can be listed as CAUSATIVE. Alternatively, or additionally, a variant may be listed as CAUSATIVE. Note that the intended semantics is different from the ACMG interpretation of sequence variants, which classifies variants with respect to their pathogenicity. The Interpretation element classifies variants as being responsible or not for the phenotypic and disease observations in the proband. A variant can be pathogenic according to the ACMG guidelines but not be causative for the particular disease being investigated (for instance, a heterozygous variant associated with an autosomal recessive disease may be found in a proband with causative variants in another gene).

GenomicInterpretation Status

An enumeration describing the status of a GenomicInterpretation

Data model

Name Description
UNKNOWN It is not known how this genomic element contributes to the diagnosis
REJECTED The genomic element has been investigated and ruled-out
CANDIDATE The genomic element is under investigation
CAUSATIVE The genomic element has been judged to be contributing to the diagnosis

Example

{
  "status": "CAUSATIVE"
}