NCBI Elements of WGA n Phenotype Model n Genotype n Association between Phenotype Model and Genotype

NCBI Elements of Phenotype n Protocols, Questionnaires, Documentation Best explanation of measured attributes Basically Text, often on paper or scanned PDF Often unavailable even to sponsoring IC n Data n Data Dictionary

NCBI Elements of Phenotype n Protocols, Questionnaires, Documentation n 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) n Data Dictionary

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

NCBI Organize Data First n Take Data in whatever format available n Automatically load columns and rows in Generic Database n Automatically analyze content of columns n Review report with submitter

NCBI Organize Documents Next n Manually link specific questions/measures to Data column names n Send out for tagging into XForms XML n View as HTML document n Process for indexing n Generate views of specific questions across forms and studies

NCBI Identify Conflicts Between Data and Metadata

NCBI Enumerated NOT HISPANIC514 CHINESE359 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)

NCBI 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

NCBI Genotype Data n NCBI is working with ICs on Genotype Data where possible n Both genotype calls and underlying intensity data directly from vendors to NCBI n NCBI is working with major vendors on appropriate data content and formats n Genotype summaries will be available to public as permitted n Individual genotypes available through the same authorization process as individual phenotypes

NCBI dbGaP Current Activities n Genetic Association Information Network (GAIN) n Genetics and Environment Initiative (GEI) n Framingham Genetic Study n National Institute for Neurological Disease and Stroke (NINDS) n NHGRI Medical Resequencing n NEI Macular Degeneration n Control sets

NCBI Finding dbGaP

NCBI dbGaP Tour

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NCBI Associations to the Basepair

NCBIhttp://dbGaP.nih.govhttp://dbGaP.nih.gov

NCBI n Data access requires request from PI and approval by institutional Signing Official (SD for NIH) – Requester must have PI role. n Uses NIH login for authentication n Data Access Request uses SF424 R&R form with Co-PI form and Statement of Intent n Data is downloaded via Web with Commons account controlling access to data.

NCBI Closing the Loop