GET-Evidence

 = Genotype + Environment = Trait (GET) Evidence Database = 

The '''GET Evidence''' project was started by Abraham Rosenbaum, Joe Thakuria, Xiaodi Wu and Alexander Wait Zaranek to help the [http://personalgenomes.org Personal Genome Project], the clinical genetics community, and, the general public interpret individual genomes.  The database is closely integrated with [wiki:Trait-o-matic].

You can find the PGP production server at:

 * http://evidence.personalgenomes.org

A development sandbox can be found at: 

 * http://evidence-dev.personalgenomes.org

Many contributors helped make '''GET Evidence''' possible. You can find specific contributions at: 

 * http://evidence.personalgenomes.org/editors

Please help the project by editing the database or making suggestions on the wiki!  

 == Field Descriptions and Editing Guidelines ==

 === Short Summary === 

 * free text providing a one line summary of clinical action to be undertaken given this variant (possibly modified by known phenotypes). 

 === Variant Quality Data === 

Each of these fields is a sliding scale of 0-5 where 0 represents no evidence and 5 strong evidence that the Impact is correct. Where the data is not entered the default is N/A. When Genetests and/or the literature correlate this variant with a number of phenotypes the impact should be reported for the most extreme condition

 a. ''In silico'': One star for each consistent prediction and one start subtracted for conflicting results from:

  i. evolutionary conservation (minimum of three species)

  i. presence in active domain 

  i. SIFT 

  i. !PolyPhen 

  i. NBLOSUM 

  i. GVGD

  i. Other variants in this gene cause similar disease 

  i. etc... 

 a. ''In vitro'': One star for each experiment supporting the result, and penalize one star for conflicting results from: 

  i. enzyme extracts 

  i. cell lines  

  i. animal models

  i. etc... 

 a. Case/Control: Odds Ratio etc... 

  i. 0 stars for OR<1

  i. 1 star for 1<OR<1.5

  i. 2 stars for 1.5<OR<2

  i. 3 stars for 2<OR<3 

  i. 4 stars for 3<OR<5

  i. 5 stars for OR>5 

 a. Familial Disease Segregation

  i. 0 stars for no segregation (LOD < -2)

  i. 1 star if segregation exists in one family pedigree

  i. 2 stars for segregation in more than one family with some conflicting information (e.g. asymptomatic carrier of young age or possibility of second causative mutation)

  i. 3 stars for more than one family no conflicting information

  i. 4 stars for LOD > 2

  i. 5 stars for LOD > 3.

 a. Clinical Outcomes: The quality of studies investigating the effectiveness of action based on the described impact of this mutation given a specific phenotype/family history

  i. 0 stars for poor outcome for intervention (diagnostic and medical)

  i. 1 star no proven benefit for intervention

  i. 2 stars anecdotal evidence for intervention (unpublished results) 

  i. 3 stars weak evidence for intervention (less than 10 cases)

  i. 4 stars standard recommendations for further intervention in development (or more than 10 cases)

  i. 5 stars for further intervention in routine use  

 === Impact === 

 a. Pathogenic: Causative for disease. 

 a. Likely Pathogenic

 a. Likely Benign

 a. Benign: No clinically significant phenotype. 

 a. Likely Protective

 a. Protective: Protective from disease.

 a. Unknown Clinical Significance 

 a. Likely Pharmacogenetic 

 a. Pharmacogenetic: Clinically significant phenotype in the presence of a pharmacological agent.    

 a. None or not yet reviewed 

When Genetests and/or the literature give multiple phenotypes for a variant, the impact should be reported for the most extreme condition and annotated as such in the ''short summary''.  The evidence must have at least four stars in one of the clinical ''variant data quality'' categories and at least ten stars total for the: "pathogenic", "benign", "protective", "pharmacogenetic" categories.    The evidence must have three stars in one of the clinical ''variant data quality'' categories and at least six stars total for the: "likely pathogenic", "likely benign", "likely protective", "likely pharmacogenetic" categories.

 === Inheritance Pattern === 

 a. Dominant

 a. Recessive

 a. Other: A defined form of inheritance that is neither dominant or recessive (e.g. modifier, co-dominant, incomplete penetrance). These variants will get prioritized due to their potential phenotypic affect should the additional factors be present.

 a. Undefined: Undefined in the literature.

 a. Unknown: The default value for all variants and all variants without literature.

 === Summary of published research, and additional commentary === 

 * Free text providing a comprehensive review of the variant including youngest age of onset, oldest age of onset and oldest asymptomatic individual. 

 === Allele Frequency === 

 * Automatically generated frequencies for the !HapMap Project, 1000 Genomes Project and the weighted average of the two.  Sub-population frequencies and homozygous/heterozygous break-downs are currently not shown. 

 === Publications === 

 * User-entered publications and user entered synopses of the relevant details from the publication. A short summary is also entered for each paper (as above).

 === Genomes ===  

 * Automatically generated list of all genomes from Trait-o-matic in which this variant is seen. Additionally, specific actions taken by each individual harboring the variant can be reported.

 === Other External References === 

These are automatically generated by web "robots":  

   a. dbSNP: The link to the dbSNP entry for this nucleotide position (for this nucleotide change?)

   a. Genetests: Link to all clinical laboratories performing diagnostic tests on this gene and the list of diseases that the labs are looking for.

   a. Web Search Results: A web search for this exact variant using the Yahoo search engine

 === Edit History ===

 * Automatically generated history of all page edits with the contributor's name.

 == To Do ==

 * [wiki:GET-Evidence/23andWe]

 == Suggestions == 

 * your suggestion here.