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Elements of WGA

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

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Elements of WGA

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  1. Elements of WGA • Phenotype Model • Genotype • Association between Phenotype Model and Genotype

  2. 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 • Data Dictionary

  3. Elements 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

  4. Elements of Phenotype • Protocols, Questionnaires, Documentation • Data • Data Dictionary • Links Protocol element to Data column • Not generally available or widely usable

  5. Organize 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

  6. Organize 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

  7. Identify Conflicts Between Data and Metadata

  8. Enumerated NOT HISPANIC 514 CHINESE 359 HISPANIC 27 TURKISH 20 SCOTTISH/IRISH 2 ITALIAN 2 AUSTRIAN/HUNGARIAN 1 SOUTH WEST NETHERLANDS 1 IRISH/CANADIAN INDIAN 1 PUERTO RICAN 1 SPANISH 1 HUNGARIAN 1 ..(more)

  9. 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

  10. Genotype 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

  11. dbGaP 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

  12. Finding dbGaPhttp://view.ncbi.nlm.nih.gov/dbGaP

  13. dbGaP Tour

  14. Associations to the Basepair

  15. http://dbGaP.nih.gov

  16. 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.

  17. Closing the Loop

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