Representing Patient Family Health History

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Type Standard / Implementation Specification Standards Process Maturity Implementation Maturity Adoption Level Federally required Cost Test Tool Availability
Standard for observations
Final
Production
Rating 3
No
Free
N/A
Standard for observation values
Final
Production
Rating 3
Yes
Free
N/A
Limitations, Dependencies, and Preconditions for Consideration
Applicable Value Set(s) and Starter Set(s)
  • Some details around family genomic health history may not be captured by SNOMED CT®.
  • For clinical genomics purposes, the Human Phenotype Ontology (HPO) developed by Robinson, et al. and uses information from the Online Mendelian Inheritance in Man to generate its terms. It is popular within the genomics community, and is used by some organizations to describe "phenotypic abnormalities".
  • See LOINC projects in the Interoperability Proving Ground.
  • For more information about observations and observation values, see Appendix II for an informational resource developed by the Health IT Standards Committee. 

Diagnosis and Conditions:

  • Problem Type 2.16.840.1.113883.3.88.12.3221.7.2 (LOINC® code system)
  • Problem urn:oid:2.16.840.1.113883.3.88.12.3221.7.4 (SNOMED CT® code system)

For genomic data:

  • Gene Identifier: HGNC Value Set (2.16.840.1.113883.4.642.2.468)
  • Transcript Reference Sequence Identifier: NCBI vocabulary
  • DNA Sequence Variation Identifier: NCBI vocabulary
  • DNA Sequence Variation: HGVS nomenclature (2.16.840.1.113883.4.642.2.392)

For family relationships and roles:

Comment

Need code system for family…

Need code system for family relationships, SNOMED CT and HL7 V3 Personal Relationship have good value sets for this.

NCBI genomic data resources

NCBI resources for sequences, including RefSeq, dbVar, and dbSNP,  can be found here:

https://www.ncbi.nlm.nih.gov/guide/all/

Are the value sets in ISA accounting for the decisions and imple

  • Personal Relationship Role Type”  Personal Relationship Role Type urn:oid:2.16.840.1.113883.1.11.19563
  • There is a discrepancy between this value set and FHIR 4.0.  More generally are the value sets in ISA accounting for the decisions and implementations being made with FHIR?
    • Definition:          
      • A relationship between two people characterizing their "familial" relationship
      • OID:       2.16.840.1.113883.1.11.19579 (for OID based terminology systems)
    • Title:      V3 Value SetFamilyMember
    • Name:  v3.FamilyMember
    • Defining URL:     http://terminology.hl7.org/ValueSet/v3-FamilyMember

Standard for observation…

Standard for observation values: should probably be Standard for observation values that are represented as codes (won't apply if they are free text or numbers).

Many of the details of Family Genomic History are not capturable by SNOMED CT. They will require the code systems provided by NCBI such as ClinVar, dbSNP, etc.

This is a greatly exaggerated assessment in the CMS Assessments. A large provider of IHE interfaces see SNOMED CT codes for 5% or fewer variables with multiple choice answers. Most are either text and/or local codes. 

feedback

Consider adding the following info to starter set

OMOP common data model is using SNOMED CT concepts (descendants of SNOMED CT term 125677006 (http://snomed.info/id/125677006))  to standardize family relationships (reference: https://github.com/OHDSI/CommonDataModel/wiki/FACT_RELATIONSHIP#conventions  ).