Wiki » History » Version 20
Jason Bobe, 02/01/2010 03:31 PM
1 | 1 | Jason Bobe | = Genotype + Environment = Trait (GET) Evidence Database = |
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3 | 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]. |
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5 | You can find the PGP production server at: |
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6 | * http://evidence.personalgenomes.org |
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8 | A development sandbox can be found at: |
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9 | * http://evidence-dev.personalgenomes.org |
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11 | Many contributors helped make '''GET Evidence''' possible. You can find specific contributions at: |
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12 | * http://evidence.personalgenomes.org/editors |
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14 | Please help the project by editing the database or making suggestions on the wiki! |
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16 | 4 | Jason Bobe | == Field Descriptions and Definitions == |
17 | 19 | Jason Bobe | === Short Summary === |
18 | * free text providing a one line summary of clinical action to be undertaken given this variant (possibly modified by known phenotypes). |
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20 | === Variant Quality === |
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22 | 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 |
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23 | a. Computational: Average of predictions generated by SIFT, !PolyPhen and NBLOSUM. |
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24 | a. Molecular and Cellular: Results of experiments involving enzyme extracts, cell lines and animal models. |
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25 | a. Clinical Population: Odds Ratio |
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26 | a. Clinical Family: LOD score. |
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27 | 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 |
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28 | |||
29 | === Impact === |
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30 | When Genetests and/or the literature correlate this variant with a number of phenotypes the impact should be reported for the most extreme condition. |
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32 | 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. |
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33 | a. Putative Pathogenic: |
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34 | a. Putative Benign |
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35 | a. Benign |
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36 | a. Putative Protective |
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37 | 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. |
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38 | a. Other |
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39 | a. Unknown |
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41 | === Inheritance Pattern === |
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42 | a. Dominant |
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43 | a. Recessive |
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44 | 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. |
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45 | a. Undefined: Undefined in the literature. |
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46 | a. Unknown: The default value for all variants and all variants without literature. |
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48 | === Summary of published research, and additional commentary === |
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49 | * Free text providing a comprehensive review of the variant |
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51 | === Miscellaneous === |
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52 | 14 | Jason Bobe | * Allele Frequency: Automatically generated frequencies for the !HapMap Project, 1000 Genomes Project and the weighted average of the two. |
53 | 13 | Jason Bobe | * 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). |
54 | * 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. |
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55 | 12 | Jason Bobe | * Other External References: These are automatically generated |
56 | a. dbSNP: The link to the dbSNP entry for this nucleotide position (for this nucleotide change?) |
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57 | 1 | Jason Bobe | a. Genetests: Link to all clinical laboratories performing diagnostic tests on this gene and the list of diseases that the labs are looking for. |
58 | a. Web Search Results: A web search for this exact variant using the Yahoo search engine |
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59 | * Edit History: Automatically generated history of all page edits with the contributor's name. |
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60 | 20 | Jason Bobe | |
61 | == To Do == |
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62 | * [wiki:GET-Evidence/23andWe] |
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63 | 3 | Jason Bobe | |
64 | 1 | Jason Bobe | == Suggestions == |
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66 | * your suggestion here. |