extrinsic genotype [GENO_0000524]

A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. An extrinsic genotype describes variation in the ‘expression level’ of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. The ‘extrinsic genotype’ concept is contrasted with the more familiar notion of an ‘intrinsic genotype’, describing variation in the inherent genomic sequence (i.e. ‘allelic state’). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model ‘extrinsic’ alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.

Open extrinsic genotype in VFB

VFB Term Json

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            "label": "extrinsic genotype"
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        "description": [
            "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state."
        ],
        "comment": [
            "An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state').  In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease.  It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations."
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