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 Definitions ==

 === 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 (score <= 0.05)

  i. !PolyPhen (possibly or probably damaging) 

  i. NBLOSUM (score => 3)

  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 === 

When Genetests and/or the literature this variant with a number of phenotypes the impact should be reported for the most extreme condition.

 a. Pathogenic: Causative for disease; the evidence must have four stars in one of the clinical categories and at least three stars in two other categories. 

 a. Putative Pathogenic:

 a. Putative Benign

 a. Benign

 a. Putative Protective

 a. Protective: Protective from disease; the evidence must have four stars in one of the clinical categories and at least three stars in two other categories.

 a. Other

 a. Unknown

 === 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.