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Variant Reporting

This section provides guidance on reporting genetic tests that involve sequencing the DNA, RNA or amino acid chains of the specimen. This includes direct sequencing, shotgun sequencing, array-based variant testing and other mechanisms.

Currently, there is one profile used to model most variant information. In future versions of this implementation guide, HL7 may subdivide Variant into multiple sub-profiles with more specific purpose.

Diagram showing the sequencing profiles

Figure 1: Sequencing Profiles

(Profile links: Variant )

The core of the typical report is a list of identified variants – each with many possible attributes. The variant profile allows a full description of the variant found using properties from a variety of testing approaches and allowing for a variety of descriptive mechanisms. An individual variant may be defined and described by multiple attributes delivered as component values. Most of these components are optional, but labs are encouraged to populate what properties they know. The underlying clinical concept behind each component is mapped to a specific LOINC code. Clinicians are accustomed to receiving descriptive information such as the HVGS genomic and amino acid expression, the type of variant (e.g. deletion) and the reference sequence. The identifiers to online databases can be easily consumed by CDS systems.

Note that there are two coordinate systems one can use when referencing positions within a molecular sequence. In particular, information from HGVS is 1-based, with special rules for consideration that can be less than straight forward when switching between insertions and deletions. For clarity and consistency, one must take care not to mix coordinate systems within the same resource instance. If HGVS is used within a resource instance, the rest of the instance should also be 1-based so as not to mix coordinate systems. Below is a picture that could explain the difference between the two systems:

image coordinate system description

The Variant profile can reference other Variant observations via hasMember when there is a need to represent a named grouping of variants that has a specified clinical effect or phenotype but is not a recognized Haplotype or Genotype. An example would be a compound heterozygote, or other types of findings as in the Complex Variant Type component which uses this LOINC code.