Clarification on comments re Biomarker.name

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CLOSED - Need clarification on comments re Biomarker.name (row 22)

Current Definitions

Biomarker

DEFINITION: A measurable and quantifiable biological parameter which serves as index for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc. [Source: adapted from MESH]

EXAMPLE(S): Specific enzyme concentration, Specific hormone concentration, Specific gene phenotype distribution in a population, Presence of biological substances

OTHER NAME(S):

NOTE(S):

Biomarker.name

DEFINITION: The textual identifier for the biomarker as provided by the assigning source.

EXAMPLE(S): G48V, L10I, K20R, M36I, A71V, V82T

OTHER NAME(S):

NOTE(S):

Ballot Comment

examples all list variants using old standard for amino acid nomenclature. Recommend adding p. and moving it from biomarker to common name or alias, because the biomarker definition specifies a known association between genotype and phenotype. That is, even for variants of unknown significance the alias representation should be listed.

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need clarification - is this saying we should add "p." before or after the example values and change the attribute name from "name" to "commonName" or "alias"? The reasoning for the apparent name change is not clear, can submitter explain or rephrase?

Outstanding Questions

  • What should the example value be?
  • What should the attribute name be?
  • Can the rationale be clarified?

Responses

Lauren Becnel: For protein examples, they are suggesting that you prepend each example with p. p.G48V says that there is a change at the 48th position in a protein from aa G to V. For non-protein examples, you would not use the p. All of your examples look like proteins, which again raises the question about scope & if it’s limited to genomics or inclusive other other CLIA-certified omics tests. See http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5755

DISCUSSION 20160223 (TYPE: EX): add "p." to all example values since currently they are all proteins, other values can be added later when the scope question Lauren raises is addressed, but at least our extant values will be accurate.

UPDATES DONE IN THE MODEL


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