SequenceConsensusSequenceBlock FHIR Profile Proposal

SequenceConsensusSequenceBlock

Describes consensus sequence block used in HLA typing report.

This profile was created to attempt to satisfy the requirements for a specific use case: HLA genotyping by NGS methods. It is based on the principles of the Minimum Information for ReportIng Next generation sequence Genotyping (MIRING) as described in Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25. A technical implementation of MIRING was developed in the Histomimmungenetics Markup Language (HML) and published in Hum Immunol. 2015 Dec;76(12):963-74. doi: 10.1016/j.humimm.2015.08.001. Epub 2015 Aug 28. The schema for HML may be found in http://schemas.nmdp.org/

We are using MIRING and HML to inform how FHIR profile(s) may be developed. In this case, a Consensus Sequence is composed of one or more Consensus Sequence Blocks. Metadata about each block is important, but not yet captured in the Sequence Resource, or other profiles. These include: phase set, expected copy number, block continuity, and strand. This profile extends the Sequence Resource to add these elements.

Profile balloting plans

STU3

Profile Details

Profiled Resource(s)

• Sequence

Constraints to be Applied

The following constraints are applied to the Sequence resource as necessary:

• Constrain the cardinality of the data elements within the resource.
• Constrain the mustSupport attribute of the data elements within the resource.
• Define searchParameters as necessary for the resource.
• Constrain vocabularies for the resources as applicable.

Extensions to be Applied

The following extensions are applied to the Sequence resource as appropriate:

• Clinical genomics specific extensions.

Example Scenarios

• Query Examples for each resource.
• Query Result Examples for each resource.

Scope of coverage

• Subject: patient
• Disciplines: Patient Care, Clinical Research, Public Health
• Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc.

Realm

Clinical genomics.

Ownership

Owning committee name

Clinical Genomics

Contributing or Reviewing Work Groups

• None

gForge Users

• Gil Alterovitz
• Gaston Fiore

FHIR Profile Development Project Insight ID

1110

Plans

Timelines

• July 2016

Balloting Requirements

• Ballot with next FHIR DSTU or Normative Edition

Desired Ballot Date

• End 2016