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SequenceConsensusSequenceBlock[edit | edit source]

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[edit | edit source]

STU3

Profile Details[edit | edit source]

Profiled Resource(s)[edit | edit source]

Constraints to be Applied[edit | edit source]

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[edit | edit source]

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

  • Clinical genomics specific extensions.

Example Scenarios[edit | edit source]

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

Scope of coverage[edit | edit source]

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

Realm[edit | edit source]

Clinical genomics.

Ownership[edit | edit source]

Owning committee name[edit | edit source]

Clinical Genomics

Contributing or Reviewing Work Groups[edit | edit source]

  • None

Expected implementations[edit | edit source]

gForge Users[edit | edit source]

  • Gil Alterovitz
  • Gaston Fiore

FHIR Profile Development Project Insight ID[edit | edit source]

1110

Plans[edit | edit source]

Timelines[edit | edit source]

  • July 2016

Balloting Requirements[edit | edit source]

  • Ballot with next FHIR DSTU or Normative Edition

Desired Ballot Date

  • End 2016