elements of wga
DESCRIPTION
Elements of WGA. Phenotype Model Genotype Association between Phenotype Model and Genotype. Elements of Phenotype. Protocols, Questionnaires, Documentation Best explanation of measured attributes Basically Text, often on paper or scanned PDF Often unavailable even to sponsoring IC Data - PowerPoint PPT PresentationTRANSCRIPT
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NCBIElements of WGAElements of WGAElements of WGAElements of WGA
Phenotype Model Genotype Association between Phenotype Model and
Genotype
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NCBIElements of PhenotypeElements of PhenotypeElements of PhenotypeElements of Phenotype
Protocols, Questionnaires, Documentation• Best explanation of measured attributes• Basically Text, often on paper or scanned PDF• Often unavailable even to sponsoring IC
Data
Data Dictionary
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NCBIElements of PhenotypeElements of PhenotypeElements of PhenotypeElements of Phenotype
Protocols, Questionnaires, Documentation
Data• Measured attributes in a square table
• Row is individual• Column is measure
• Column names often obscure (eg. “HO112”)• In many formats (Excel, SAS, RDB, text)
Data Dictionary
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NCBIElements of PhenotypeElements of PhenotypeElements of PhenotypeElements of Phenotype
Protocols, Questionnaires, Documentation
Data
Data Dictionary• Links Protocol element to Data column• Not generally available or widely usable
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NCBIOrganize Data FirstOrganize Data FirstOrganize Data FirstOrganize Data First
Take Data in whatever format available Automatically load columns and rows in Generic
Database Automatically analyze content of columns Review report with submitter
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NCBIOrganize Documents NextOrganize Documents NextOrganize Documents NextOrganize Documents Next
Manually link specific questions/measures to Data column names
Send out for tagging into XForms XML
View as HTML document Process for indexing Generate views of specific questions across forms
and studies
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NCBI
Identify Conflicts Identify Conflicts Between Data and Between Data and
MetadataMetadata
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NCBI
EnumeratedNOT HISPANIC 514CHINESE 359HISPANIC 27TURKISH 20SCOTTISH/IRISH 2ITALIAN 2AUSTRIAN/HUNGARIAN 1SOUTH WEST NETHERLANDS 1IRISH/CANADIAN INDIAN 1PUERTO RICAN 1SPANISH 1HUNGARIAN 1..(more)
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NCBINCBI WGA – What Can I Do?NCBI WGA – What Can I Do?NCBI WGA – What Can I Do?NCBI WGA – What Can I Do?
• [Unrestricted Public Use]
• Browse/Search Projects and Studies
• Browse/Search Protocols, Questionaires, Supporting Documents
• View Phenotype Measures Summary Data
• View Genotype Measures Summary Data
• Identify Studies of Interest and Authorization Authorities
• View Pre-computed and Published Associations
• [Authorized Users Only]
• Download Genotype/Phenotype Data for Individuals
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NCBIGenotype DataGenotype DataGenotype DataGenotype Data
NCBI is working with ICs on Genotype Data where possible
Both genotype calls and underlying intensity data directly from vendors to NCBI
NCBI is working with major vendors on appropriate data content and formats
Genotype summaries will be available to public as permitted
Individual genotypes available through the same authorization process as individual phenotypes
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NCBIdbGaP Current ActivitiesdbGaP Current ActivitiesdbGaP Current ActivitiesdbGaP Current Activities
Genetic Association Information Network (GAIN) Genetics and Environment Initiative (GEI) Framingham Genetic Study National Institute for Neurological Disease and
Stroke (NINDS) NHGRI Medical Resequencing NEI Macular Degeneration Control sets
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NCBI Finding dbGaPFinding dbGaPhttp://view.ncbi.nlm.nih.gov/dbGaPhttp://view.ncbi.nlm.nih.gov/dbGaP
Finding dbGaPFinding dbGaPhttp://view.ncbi.nlm.nih.gov/dbGaPhttp://view.ncbi.nlm.nih.gov/dbGaP
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NCBIdbGaP TourdbGaP TourdbGaP TourdbGaP Tour
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NCBI
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NCBI
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NCBI
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NCBI
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NCBI
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NCBI
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NCBI
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NCBIAssociations to the BasepairAssociations to the BasepairAssociations to the BasepairAssociations to the Basepair
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NCBI http://dbGaP.nih.govhttp://dbGaP.nih.govhttp://dbGaP.nih.govhttp://dbGaP.nih.gov
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NCBI
Data access requires request from PI and approval by institutional Signing Official (SD for NIH) – Requester must have PI role.
Uses NIH login for authentication Data Access Request uses SF424 R&R form with Co-PI form and Statement
of Intent Data is downloaded via Web with Commons account controlling access to
data.
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NCBIClosing the LoopClosing the LoopClosing the LoopClosing the Loop