Discussion needed on change from display names on 84413-4 - 2018-May Genomics #31

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    • Type: Change Request
    • Resolution: Not Persuasive with Modification
    • Priority: Medium
    • Genomics Reporting (FHIR)
    • STU3
    • Clinical Genomics
    • (profiles) [deprecated]
    • Hide

      Not Persuasive with Mod: Keep as CodeableConcept, add the following text to the IG near the discussion of Genotype:

      Genotype is used to convey corresponding haplotypes or variations at a particular locus - for instance, [1] "TPMT *1/*3A" represents the TPMT *1 haplotype (or 'star allele') on one chromosome and the TPMT *3A haplotype on the homologous chromosome; [2] "A/C" represents a heterozygous "A" and a heterozygous "C" at SNP rs1142345. Many genotypes are expressed as simple strings, and can be conveyed in genotype.valueCodeableConcept.text. In some cases, genotypes are sufficiently standardized to be conveyed as codes (in genotype.valueCodeableConcept.code).

      For HLA, KIR, and other genes in the immunogenetics 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, we define here a simple grammar of [HGNC gene symbol followed by white space followed by a slash ('/') delimited list of haplotype codes], where the codeSystem is set to the codeSystem of the haplotypes (e.g. Pharmvar).

      Here's some examples:

      Text only:

      <valueCodeableConcept>

      <text>A/C at SNP rs1142345</text>

      </valueCodeableConcept>

      Coded HLA

      <valueCodeableConcept>

      <coding>

      <system value="http://glstring.org"/>

      <version value="1.0"/>

      <code value="[hla|3.23]HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01"/>

      </coding>

      </valueCodeableConcept>

      Coded PGx

      <valueCodeableConcept>

      <coding>

      <system value="https://www.pharmvar.org/"/>

      <code value=value="CYP2C9 *1A/*1A"/>

      </coding>

      </valueCodeableConcept>

      Show
      Not Persuasive with Mod: Keep as CodeableConcept, add the following text to the IG near the discussion of Genotype: Genotype is used to convey corresponding haplotypes or variations at a particular locus - for instance, [1] "TPMT *1/*3A" represents the TPMT *1 haplotype (or 'star allele') on one chromosome and the TPMT *3A haplotype on the homologous chromosome; [2] "A/C" represents a heterozygous "A" and a heterozygous "C" at SNP rs1142345 . Many genotypes are expressed as simple strings, and can be conveyed in genotype.valueCodeableConcept.text. In some cases, genotypes are sufficiently standardized to be conveyed as codes (in genotype.valueCodeableConcept.code). For HLA, KIR, and other genes in the immunogenetics 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, we define here a simple grammar of [HGNC gene symbol followed by white space followed by a slash ('/') delimited list of haplotype codes] , where the codeSystem is set to the codeSystem of the haplotypes (e.g. Pharmvar). Here's some examples: Text only: <valueCodeableConcept> <text>A/C at SNP rs1142345</text> </valueCodeableConcept> Coded HLA <valueCodeableConcept> <coding> <system value=" http://glstring.org"/ > <version value="1.0"/> <code value=" [hla|3.23] HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01"/> </coding> </valueCodeableConcept> Coded PGx <valueCodeableConcept> <coding> <system value=" https://www.pharmvar.org/ "/> <code value=value="CYP2C9 *1A/*1A"/> </coding> </valueCodeableConcept>
    • Bob D / Patrick: 17-0-0
    • Correction
    • Non-substantive

      Existing Wording: Figure 5: Genotype 84413-4

      Proposed Wording: Genotype Display Name 84413-4

      Comment:

      I understand why you want to shorten, but the change could mislead. These are not solid codes for genotype or haplotype. Would like to find a way to link from the figure (or content below them) to the LOINC code, description and answer list. Have linked to the answer list in the change document but these early tables are a bit more digestable. Lets talk.

      Summary:

      Discussion needed on change from display names on 84413-4

            Assignee:
            Unassigned
            Reporter:
            clemmcdonald
            Watchers:
            2 Start watching this issue

              Created:
              Updated:
              Resolved: