Wiki » History » Version 23
Jason Bobe, 02/03/2010 12:56 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 | 23 | Jason Bobe | === Variant Quality Data === |
21 | 1 | Jason Bobe | 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 |
22 | 23 | Jason Bobe | a. ''In silico'': One star for each consistent prediction and one start subtracted for conflicting results from: |
23 | i. evolutionary conservation |
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24 | i. presence in active domain |
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25 | i. SIFT |
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26 | i. !PolyPhen |
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27 | i. NBLOSUM |
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28 | i. Other variants in this gene cause similar disease |
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29 | i. etc... |
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30 | a. ''In vitro'': One star for each experiment supporting the result, and penalize one star for conflicting results from: |
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31 | i. enzyme extracts |
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32 | i. cell lines |
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33 | i. animal models |
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34 | i. etc... |
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35 | 22 | Jason Bobe | a. Case/Control: Odds Ratio etc... 0 stars for OR<1, 1 star for 1<OR<1.5, 2 stars for 1.5<OR<2, 3 stars for 2<OR<3, 4 stars for 3<OR<5, 5 stars for OR>5. |
36 | 23 | Jason Bobe | a. Familial Disease Segregation: Zero stars for no segregation (LOD < -2), 1 star if segregation exists in one family pedigree, 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), 3 stars for more than one family no conflicting information, 4 stars for LOD > 2, 5 stars for LOD > 3. |
37 | 19 | Jason Bobe | 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 |
38 | |||
39 | === Impact === |
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40 | 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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42 | 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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43 | a. Putative Pathogenic: |
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44 | a. Putative Benign |
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45 | a. Benign |
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46 | a. Putative Protective |
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47 | 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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48 | a. Other |
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49 | a. Unknown |
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50 | |||
51 | === Inheritance Pattern === |
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52 | a. Dominant |
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53 | a. Recessive |
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54 | 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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55 | a. Undefined: Undefined in the literature. |
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56 | a. Unknown: The default value for all variants and all variants without literature. |
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58 | === Summary of published research, and additional commentary === |
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59 | 22 | Jason Bobe | * Free text providing a comprehensive review of the variant including youngest age of onset, oldest age of onset and oldest asymptomatic individual. |
60 | 1 | Jason Bobe | |
61 | 21 | Jason Bobe | === Allele Frequency === |
62 | 22 | Jason Bobe | * 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. |
63 | 21 | Jason Bobe | |
64 | === Publications === |
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66 | * 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). |
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67 | |||
68 | === Genomes === |
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70 | * 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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72 | === Other External References === |
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73 | These are automatically generated by web "robots": |
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74 | 13 | Jason Bobe | a. dbSNP: The link to the dbSNP entry for this nucleotide position (for this nucleotide change?) |
75 | 12 | 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. |
76 | a. Web Search Results: A web search for this exact variant using the Yahoo search engine |
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77 | 21 | Jason Bobe | |
78 | === Edit History === |
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79 | * Automatically generated history of all page edits with the contributor's name. |
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80 | 20 | Jason Bobe | |
81 | == To Do == |
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82 | * [wiki:GET-Evidence/23andWe] |
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83 | 3 | Jason Bobe | |
84 | 1 | Jason Bobe | == Suggestions == |
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86 | * your suggestion here. |