2015May core #1358 - Define source

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    • Type: Change Request
    • Resolution: Persuasive
    • Priority: Medium
    • FHIR Core (FHIR)
    • DSTU1 [deprecated]
    • Clinical Genomics
    • Observation
    • 4.20.21.1
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      Clarified what genomic source class means - source of tissue sample used to determine the sequence.

      Here is the loinc answer List for genomic source class:

      1. Germline LA6683-2

      2. Somatic LA6684-0

      3. Prenatal LA6685-7

      4. Likely Germline LA18194-3

      5. Likely Somatic LA18195-0

      6. Likely Prenatal LA18196-8

      7. Unknown Genomic Origin LA18197-6

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      Clarified what genomic source class means - source of tissue sample used to determine the sequence. Here is the loinc answer List for genomic source class: 1. Germline LA6683-2 2. Somatic LA6684-0 3. Prenatal LA6685-7 4. Likely Germline LA18194-3 5. Likely Somatic LA18195-0 6. Likely Prenatal LA18196-8 7. Unknown Genomic Origin LA18197-6
    • Gil Alterovitz/ Grant Wood
    • Clarification
    • Non-substantive
    • DSTU1 [deprecated]

      Existing Wording: The genomic class of the variant: Germline for inherited genome, somatic for cancer genome (e.g. DNA from tumor cells), and prenatal for fetal genome.

      Proposed Wording: Please define the term "source" and consistently adhere to it and its meaning.

      Comment:

      The description initially indicates "genomic class of the variant", which at first suggests variant type (such as silent, missense, nonsense, etc.). However, it then mentions "germline for inherited genome", which suggests that the distiction is whether a variant was one that was inherited or one that developed after a reproduction process which is inconsistent with the initially suggested idea. It then mentions "somatic", which suggests tissue source (such as somatic cell or germ cell), which is inconsistent with both of the two previously suggested ideas. It then mentions "cancer genome", which suggests either association with specific diseases or tissue source in terms of tumor cell, etc. type, both of which are inconsistent with all of the three previously suggested ideas (note that some genomic variants in a cancer cell could have been inherited and some variants could have arisen from somatic mutations). It then mentions "prenatal for fetal genome", which suggests either tissue source per body location, individual person source, or developmental stage, all three of which are inconsistent with all five of the previously suggested ideas. From this, it appears likely that multiple different ideas (possibly up to eight) are being inappropriatly conflated in this data element, and in any case the intended defintion needs to be stated for clarity, please.

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

              Created:
              Updated:
              Resolved: