d ata b ase of g enotype a nd p henotype
DESCRIPTION
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 - PowerPoint PPT PresentationTRANSCRIPT
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1National Center for Biotechnology Information
database of Genotype and Phenotype
Kim Pruitt(for Matt Mailman)
NCBI
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap
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2National Center for Biotechnology Information
Overview
• Phenotype• Genotype• Genotype X Phenotype Association
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3National Center for Biotechnology Information
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
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4National Center for Biotechnology Information
Overview
• Phenotype• Genotype
– Genotype files directly from vendor– Intensity files (ie: .CEL)
• Genotype X Phenotype Association
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5National Center for Biotechnology Information
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
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6National Center for Biotechnology Information
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
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7National Center for Biotechnology Information
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
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8National Center for Biotechnology Information
Browse Studies
Link to study reportList of variables in study
Instructions Description of dbGaP
List of documents in study
Link back to dbGaP homepage
Automated query to PubMed for genome-wide association study articles
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap
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9National Center for Biotechnology Information
Browse Studies by Disease
Expand/collapseLink to Terms from MeSH vocabulary
Link to study report
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10National Center for Biotechnology Information
Advanced Search
Fields to be searched
Add any number of search criteria
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Study Report
Links back to submitter websiteHistoryPublicationsAttributionAccess Rules
Link tovariablereport
search this studyGenotype x phenotypeassociation or linkageanalyses
Citeable unique stable identifier
Criteria for inclusion/exclusion
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12National Center for Biotechnology Information
Variable ReportCiteable unique stable identifier
Documents containing a section that has been linked to this variable
P-value is red if cases differ from controls
Statistical summary of values for this variable
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Variable Report (continued)
Document name Section of document that hasbeen linked to this variable
Link to document
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Analysis Report
Link back to report for measured or derived variable that was analyzed
Genome browser of analysis results
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15National Center for Biotechnology Information
Genome Browser of Analysis Results
Slider filters results less significant than threshold
2MB bins colored to represent the mostSignificantly associated marker
Click on bin of interest tozoom in and see associationin context with other objectsmapped to the same genomicregion
LINK
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16National Center for Biotechnology Information
Genome Browser – Higher Resolution
P-value of genotyped marker
Scroll viaboxesabove
Collapse table
CFH gene has beenassociated with AMDin several studies
Add maps
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Coming Soon…• 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
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Acknowledgements• 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
• 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