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Revision 26 (Jason Bobe, 02/03/2010 01:19 PM) → Revision 27/88 (Jason Bobe, 02/03/2010 02:17 PM)
= 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 i. GVGD (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.