FHIR R4 MolecularSequence Library

Overview

This asset is a component of MuleSoft Accelerator for Healthcare.

MuleSoft Accelerator for Healthcare enables healthcare providers to unlock critical patient data to build a patient 360 within Salesforce Health Cloud, faster and easier than ever before. The solution includes pre-built APIs, connectors, integration templates, and prescriptive end-to-end reference architecture to bring patient demographics information and COVID-19 test results from any EHR into Health Cloud using HL7 V2 or FHIR standards.

The solution also provides a library of United States Core Data for Interoperability (USCDI) and FHIR R4 resources to help healthcare developers adhere to interoperability needs and jumpstart the development of healthcare digital transformation initiatives.

Use case covered

The Clinical Genomics committee  has identified overlaps and redundancies between content in the MolecularSequence resource and content in Observation profiles in the evolving Implementation Guide for Clinical Genomics Reporting found here . The committee is considering options for modifying the resource and anticipates potential changes being brought forward in an upcoming ballot.

The MolecularSequence resource is designed to describe an atomic sequence which contains the alignment sequencing test result and multiple variations. 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 MolecularSequence resource avoids large genomic payloads in a manner analogous to how the FHIR ImagingStudy resource references large images maintained in other systems. For use cases, details on how this resource interact with other Clinical Genomics resources or profiles, please refer to implementation guidance document here.

Genetic Standards and Resources include:

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

This resource is designed to describe sequence variations with clinical significance with information such as:

• Name of the variation represented
• Type of the variation
• Gene region occupied by the variation
• Tissue source used to determine genotype of the variation
• Quality of the result

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.

This library is used by FHIR R4 MolecularSequence API.

More information about FHIR R4 MolecularSequence specification can be found here.