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d ata b ase of G enotype a nd P henotype

d ata b ase of G enotype a nd P henotype. Kim Pruitt (for Matt Mailman) NCBI. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap. Overview. Phenotype Genotype Genotype X Phenotype Association. Overview. Phenotype Data tables Columns are phenotypes Rows are individuals

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d ata b ase of G enotype a nd P henotype

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  1. database of Genotype and Phenotype Kim Pruitt (for Matt Mailman) NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap

  2. Overview • Phenotype • Genotype • Genotype X Phenotype Association

  3. Overview • Phenotype • Data tables • Columns are phenotypes • Rows are individuals • Documents (ie: protocols, data collection forms) • Parts of documents linked to variables • Data dictionary • Genotype • Genotype X Phenotype Association

  4. Overview • Phenotype • Genotype • Genotype files directly from vendor • Intensity files (ie: .CEL) • Genotype X Phenotype Association

  5. Overview • Phenotype • Genotype • Genotype X Phenotype Association • Various statistical models and methods • P-value or LOD score for each marker • Filters by P-value, HWE, minor allele frequency • Map phenotypes onto genomic sequence

  6. Overview • Phenotype • Genotype • Genotype X Phenotype Association • Obvious expansion potential: • More species; different types of association data (QTL) • Critically important to archive all data: • Submit primary data to appropriate public archive! • Probe DB: primers, resequencing amplicons • dbSTS: STS markers • Maps: UniSTS; Map Viewer • GenBank: ESTs

  7. dbGaP Web Site • two levels of access - open and controlled • open access to non-sensitive data • study summaries and documents • measured variables and data elements • analysis reports • genome browser • controlled access provides oversight and accountability for use of sensitive datasets involving personal information • De-identified phenotypes and genotypes for individual subjects • Pedigrees

  8. Browse Studies http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap Link back to dbGaP homepage Description of dbGaP Instructions Link to study report List of variables in study List of documents in study Automated query to PubMed for genome-wide association study articles

  9. Link to study report Expand/collapse Link to Terms from MeSH vocabulary Browse Studies by Disease

  10. Advanced Search Fields to be searched Add any number of search criteria

  11. Study Report Citeable unique stable identifier Genotype x phenotype association or linkage analyses search this study Link to variable report History Publications Attribution Access Rules Links back to submitter website Criteria for inclusion/exclusion

  12. Variable Report Citeable unique stable identifier Documents containing a section that has been linked to this variable Statistical summary of values for this variable P-value is red if cases differ from controls

  13. Variable Report (continued) Document name Section of document that has been linked to this variable Link to document

  14. Analysis Report Link back to report for measured or derived variable that was analyzed Genome browser of analysis results

  15. Genome Browser of Analysis Results Slider filters results less significant than threshold 2MB bins colored to represent the most Significantly associated marker Click on bin of interest to zoom in and see association in context with other objects mapped to the same genomic region LINK

  16. Genome Browser – Higher Resolution Collapse table P-value of genotyped marker Scroll via boxes above Add maps CFH gene has been associated with AMD in several studies

  17. Studies Early 2007 Michael J. Fox Foundation Parkinson’s Disease Study (LEAPS) NINDS Stroke and ALS Spring 2007 GAIN (Genetic Association Information Network) Framingham SHARe – first two generations NIDDK GoKinD and EDIC Summer 2007 Framingham SHARe – third generation Late 2007- Early 2008 GEI (Genes and Environment Initiative) Features Search analysis results by: Gene SNP or microsatellite marker Genomic region Filter analysis results by: P-value HWE Minor allele frequency Call rate? Download Public summaries Authorized access for individual-level data Coming Soon…

  18. Phenotype Rinat Bagoutdinov Luning Hao Mas Kimura Jimmy Jin Natasha Popova Stephanie Pretels Karl Sirotkin Jack Wang Matt Mailman Genotype Mike Feolo Lon Phan David Shao Ming Ward Steve Sherry XML Kim Tryka Laura Kelly Jeff Beck Acknowledgements • Authorized Access • Steve Sherry • Eugene Yaschenko • Valdimir Soussov • Misha Kimmelman • Don Preuss • Al Graeff • Jim Ostell http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap

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