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Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting.

David K Crockett | Perry G Ridge | Andrew R Wilson | Elaine Lyon | Marc S Williams | Scott P Narus | Julio C Facelli | Joyce A Mitchell
Genome medicine | 2012

Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective manner. Here, complementary predictors for missense gene variants were incorporated into a weighted Consensus framework that includes calculated reference intervals from known disease outcomes. Data visualization for clinical reporting is also discussed.

Pubmed ID: 22640420

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This is a list of tools and resources that we have found mentioned in this publication.


HGVS Locus Specific Mutation Databases (tool)

RRID:SCR_006730

Database of Locus Specific Mutation Databases. Fields include HGNC Gene symbol / OMIM No., Database name / Internet address, and Curators. If you wish to add an LSDB please go to the LSDB Submission Page.

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HPRD - Human Protein Reference Database (tool)

RRID:SCR_007027

Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

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PMut (tool)

RRID:SCR_010783

A software aimed at the annotation and prediction of pathological mutations.

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PolyPhen: Polymorphism Phenotyping (tool)

RRID:SCR_013189

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

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