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!

To Do
[wiki:GET-Evidence/23andWe] 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 ===

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. 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. Computational: Average of predictions generated by SIFT, !PolyPhen and NBLOSUM.
a. Molecular and Cellular: Results of experiments involving enzyme extracts, cell lines and animal models.
a. Clinical Population: Odds Ratio
a. Clinical Family: LOD score.
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

=== Impact === 
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. 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

=== Miscellaneous ===

• Allele Frequency: Automatically generated frequencies for the !HapMap Project, 1000 Genomes Project and the weighted average of the two.
• 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
  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.

Suggestions

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