Genotype describes combinations of genomic variations that together are associated with a particular phenotype - i.e., a specific physical, behavioral, or risk-associated difference associated with the organism whose specimen was tested. Genotype is used to convey corresponding haplotypes or variations at a particular locus. Many genotypes are expressed as simple strings, and can be conveyed in valueCodeableConcept.text. In some cases, genotypes are sufficiently standardized to be conveyed as codes in valueCodeableConcept.code.

For HLA, KIR, and other genes in the immunogenomics domain, the National Marrow Donor Program (NMDP) led a community effort to define the Genotype List String (GL String) grammar, described here. Notably, the GL String uses '+' as a delimiter between alleles in a genotype. It also has delimiters for ambiguous genotypes, allele lists, and haplotypes.

For Pharmacogenomics, implementers SHOULD send coded haplotypes, and for genotypes (diplotypes) MAY use a simple, human readable grammar of:

[HGNC gene symbol], followed by white space, followed by a slash ('/') delimited list of haplotype names].

Here are some examples that are standardized, note that there are examples which still lack standardization today.

• Coded HLA (glstring)
  

  {
    "valueCodeableConcept": {
      "coding": [{
        "system": "http://glstring.org",
        "version": "1.0",
        "code": "#hla#3.23#HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01"
      }]
    }
  }
          

• PGx Genotype (textually represents the CYP2C9 *2C haplotype (or 'star allele') on one chromosome and the CYP2C9 *1A haplotype on the homologous chromosome)
  

  {
    "valueCodeableConcept": {
      "text": "CYP2C9 *2C/*1A"
    }
  }
          

For both genotypes and haplotypes, reporting the structured variant data is optional. However, implementers SHOULD when possible. For example, sending PGX star-alleles without variant-level information is not best practice as it is both potentially ambiguous and can preclude future utility of the report.